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1
Method and kit for detecting a risk of essential arterial hypertension
BACKGROUND OF THE INVENTION
Field of the Invention
The present invention relates generally to the field of diagnosis of
cardiovascular diseases
(CVD) such as arterial hypertension (HT). More particularly, it provides a
method of
diagnosing or detecting a predisposition or propensity or susceptibility for
HT. Specifically,
the invention focuses on a method that comprises the steps of providing a
biological sample
from the subject to be tested and detecting the presence or absence of one or
several genomic
single nucleotide polymorphism (SNP) markers in the biological sample.
Furthermore, the
invention utilizes both genetic and phenotypic information as well as
information obtained by
questionnaires to construct a score that provides the probability of
developing HT. In addition,
the invention provides a kit to perform the method. The kit can be used to set
an etiology-
based diagnosis of HT for targeting of treatment and preventive interventions
such as dietary
advice, as well as stratification of the subject in clinical trials testing
drugs and other
interventions.
Description of Related Art
Public health significance of CVD and HT
Cardiovascular Diseases (CVD) (ICD/10 codes 100-199, Q20-Q28) include ischemic
(coronary) heart disease (IHD, CHD), hypertensive diseases, cerebrovascular
disease (stroke)
and rheumatic fever/rheumatic heart disease, among others (AHA, 2004). HT
(ICD/10 110-
115) is defined as systolic pressure of 140 mm Hg or higher, or diastolic
pressure of 90 mm
Hg or higher, or taking antihypertensive medicine (AHA, 2004). Apart from
being a CVD
itself, HT is a risk factor for other CVD, such as IHD, stroke and congestive
heart failure
(CHF). About half of those people who have a first heart attack and two thirds
of those who
have a first stroke, have blood pressure (BP) higher than 160/95 mm Hg. HT
precedes the
development of CHF in 91% of cases (AHA, 2004).
Of patients with HT, 90-95% have essential HT in which the underlying cause
remains
unknown. Essential HT refers to a lasting increase in BP with heterogeneous
genetic and
environmental causes. Its prevalence rises with age irrespective of the type
of BP
measurement and the operational thresholds used for diagnosis. HT aggregates
with other
cardiovascular risk factors such as abdominal obesity, dyslipidaemia, glucose
intolerance,
hyperinsulinaemia and hyperuricaemia, possibly because of a common underlying
cause
(Salonen JT et al, 1981, 1998, Staessen JA et al, 2003).
In 2001 an estimated 16.6 million - or one-third of total global deaths -
resulted from the
various forms of CVD (7.2 million due to HT, 5.5 million to cerebrovascular
disease, and an
additiona13.9 million to hypertensive and other heart conditions). At least 20
million people
survive heart attacks and strokes every year, a significant proportion of them
requiring costly
clinical care, putting a huge burden on long-term care resources. It is
necessary to recognize
that CVDs are devastating to men, women and children (AHA, 2004).
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Around 80% of all CVD deaths worldwide took place in developing, low and
middle-income
countries. It is estimated that by 2010, CVD will be the leading cause of
death in both
developed and developing countries. The rise in CVDs reflects a significant
change in dietary
habits, physical activity levels, and tobacco consumption worldwide as a
result of
industrialization, urbanization, economic development and food market
globalization (WHO,
2004). This emphasizes the role of relatively modem environmental or
behavioral risk factors.
However, ethnic differences in the incidence and prevalence of CVD and the
enrichment of
CVD in families suggest that heritable risk factors play a major role.
In terms of disability measured in disability-adjusted life years (DALYs) CVD
caused 9.7%
of global DALYs, 20.4% of DALYs in developed countries and 8.3% of DALYs in
the
developing countries. HT caused 1.4% of global DALYs, 4.7% of DALYs in
developed
countries and 0.9% of DALYs in the developing countries (Murray CJL and Lopez
AD,
1997).
On the basis of data from the NHANES III study (1988-1994), it is estimated
that in 2001,
64.4 million Americans were affected by some form of CVD, which corresponds to
a
prevalence of 22.6% (21.5% for males, 22.4% for females). Of these, 50 million
had HT (20%
prevalence). Of those with HT, 30% do not know they have HT; 34% are on
medication and
have HT controlled; 25% are on medication but do not have their HT under
control; and 11%
are not on medication (AHA, 2004). HT is also a public health problem in
developing
countries where prevalences of 10% or higher are common and it is frequently
associated with
low levels of awareness, treatment and control (Fuentes RM et al, 2000).
The cost of CVD in the United States in 2004 was estimated at $368.4 billion
($133.2 billion
for HT, $53.6 billion for stroke, $55.5 billion for hypertensive disease).
This figure includes
health expenditures (direct costs) and lost productivity resulting from
morbidity and mortality
(indirect costs) (AHA, 2004).
Pathophysiology of essential HT
The pressure required to move blood through the circulatory bed is provided by
the pumping
action of the heart [cardiac output (CO)] and the tone of the arteries
[peripheral resistance
(PR)]. Each of these primary determinants of BP is, in turn, determined by the
interaction of a
complex series of factors.
Factors affecting cardiac output
An increased CO has been found in some young, borderline hypertensives who may
display a
hyperkinetic circulation. If it is responsible for HT, the increase in CO
could logically arise in
two ways: either from an increase in fluid volume (preload) or from an
increase in
contractility from neural stimulation of the heart. However, even if it is
involved in the
initiation of HT, the increased CO probably does not persist. The typical
hemodynamic
finding in established HT is an elevated PR and normal CO (Cowley AW, 1992).
Although an increased heart rate may not simply be a reflection of a
hyperdynamic circulation
or an indicator of increased sympathetic activity, multiple epidemiologic
surveys have shown
that an elevated heart rate is an independent predictor of the development of
HT (Palatini P
and Julius S, 1999).
Left ventricular hypertrophy has generally been considered a compensatory
mechanism to an
increased vascular resistance. However, it could also reflect a primary
response to repeated
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neural stimulation and, thereby, could be an initiating mechanism for HT
(Julius S et al.,
1991 c) as well as an amplifier of CO that reinforces the elevation of BP from
arterial
stiffening (Segers P et al., 2000).
Another mechanism that could induce HT by increasing CO would be an increased
circulating
fluid volume (preload). However, in most studies, subjects with high BP have a
lower blood
volume and total exchangeable sodium than normal subjects (Harrap SB et al.,
2000). Even
without an expanded total volume, blood may be redistributed so that more is
in the central or
cardiopulmonary section because of greater peripheral vasoconstriction
(Schobel HP et al.,
1993). Venous return to the heart would thereby be increased and could mediate
an increased
CO.
Excess sodium intake induces HT by increasing fluid volume and preload,
thereby increasing
CO (Chobanian AV and Hill M, 2000). Both experimental data (Tobian L, 1991)
and
epidemiologic evidence (Stamler J et al., 1997) support a close association
between HT and a
high sodium-potassium ratio in humans. Because almost everyone in
industrialized societies
ingests a high-sodium diet, the fact that only about half will develop HT
suggests a variable
degree of BP sensitivity to sodium (Weinberger MH, 1996).
In healthy people, when BP increases, renal excretion of sodium and water
increases,
shrinking fluid volume and returning the BP to normal - this phenomenon is
pressure-
natriuresis. On the basis of animal experiments and computer models, the
regulation of body
fluid volume by the kidneys is considered to be the dominant mechanism for the
long-term
control of BP (Guyton AC 1961, 1992). Therefore, if HT develops, something
must be wrong
with the pressure-natriuresis control mechanism; otherwise the BP would return
to normal
(Cowley AW and Roman RJ, 1996). In patients with primary HT a resetting of the
pressure-
sodium excretion curve prevents the return of BP to normal (Palmer BF, 2001).
The shift in
pressure-natriuresis requires increased BP to maintain fluid balance. The
pressure-natriuresis
relationship can be modified by neural and humoral factors including the renin-
angiotensin
system (RAS), sympathetic nervous activity, atrial natriuretic factor,
metabolites of
arachidonic acid, and intrarenal nitric oxide (Moreno C et al., 2001; Majid DS
et al., 2001).
The major modifier is likely to be theRAS (Hall JE et al., 1999; van Paassen P
et al., 2000),
with an increase in renal sodium reabsorption occurring at concentrations of
Angiotensin II
much below those needed for peripheral vasoconstriction. Angiotensin II acts
not only on
vascular smooth muscle and the adrenal cortex but also within the heart,
kidneys, and central
and autonomic nervous systems. These actions amplify its volume-retaining and
vasoconstrictive effects on the peripheral vascular system, thus affecting
both CO and PR.
Furthermore, Angiotensin II induces cell growth and hypertrophy independent of
its effect on
BP (Su EJ et al., 1998). Moreover, Angiotensin II appears to induce an
inflammatory response
in vascular smooth muscle cells (Kranzhofer R et al., 1999), with activation
of nuclear factor
k-B (Luft FC, 2001) and adhesion molecule-1 expression (Tummala PE et al.,
1999), which
may serve as direct links to atherosclerosis.
Stress may activate the sympathetic nervous system (SNS) directly; and SNS
overactivity, in
turn, may interact with high sodium intake, the RAS, and insulin resistance,
among other
possible mechanisms. Considerable evidence supports increased SNS activity in
early HT
(Esler M et al., 2001) and, even more impressively, in the still-normotensive
offspring of
hypertensive parents, of whom a large number are likely to develop HT.
Whatever the
specific role of SNS activity in the pathogenesis of HT, it appears to be
involved in the
increased cardiovascular morbidity and mortality that afflicts hypertensive
patients during the
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early morning hours. Epinephrine levels begin to increase after awakening and
norepinephrine
rises sharply on standing (Dodt C et al., 1997). As a consequence of the
increased SNS
activity, BP rises suddenly and markedly, and this rise is at least partly
responsible for the
increase in sudden death, heart attack, and stroke during the early morning
hours. Increased
sympathetic activity is probably also responsible for the increased heart rate
present in many
hypertensives that was previously noted to be associated with increased
cardiovascular
mortality.
Factors affecting peripheral resistance
HT is maintained by increased PR, largely due to decreased arterial lumen size
or radius.
According to Poiseuille's law, vascular resistance is positively related to
both the viscosity of
blood and the length of the arterial system, and negatively related to the
third power of the
luminal radius. Because neither viscosity nor length is altered much if at
all, and because
small changes in the luminal radius can have a major effect, it is apparent
that the increased
vascular resistance seen in established HT must reflect changes in the calibre
of the small
resistance arteries and arterioles (Folkow B et al., 1970). Because of the
increased wall
thickness-lumen diameter ratio, higher wall stress and intraluminal pressure
develop when
resistance vessels are stimulated.
In HT, small arteries undergo functional, structural and mechanical changes,
resulting in
reduced lumen size and increased peripheral resistance (Mulvany MJ, 2002;
Intengan HD and
Schiffrin EL. 2001). Functional alterations include enhanced reactivity or
impaired relaxation,
and reflect changes in excitation-contraction coupling, altered electrical
properties of vascular
smooth muscle cells, or endothelial dysfunction (Johns DG et al, 2000; Feldman
RD and Gros
R, 1998). Major structural changes include remodelling due to increased cell
growth,
extracellular matrix deposition and inflammation (Mulvany MJ, 2002; Intengan
HD and
Schiffrin EL, 2001; Brasier AR, 2002). Vascular smooth muscle cells are
central to these
events and play a fundamental role in the dynamic processes underlying the
alterations that
occur in HT.
Vascular changes in HT are associated with humoral and mechanical factors that
modulate
signalling events, resulting in abnormal function and growth of cellular
components of the
media (Touyz RM, 2000; Koller A, 2002). The humoral factors that regulate
arteries in HT
include vasoconstrictor agents such as angiotensin II, endothelin-1,
catecholamines and
vasopressin; vasodilator agents such as nitric oxide, endothelium-derived
hyperpolarizing
factor and natriuretic peptides; growth factors such as insulin-like growth
factor-1, platelet-
derived growth factor (PDGF), epidermal growth factor (EGF) and basic
fibroblast growth
factor; and cytokines such as transforming growth factor-[beta], tumour
necrosis factor and
interleukins (Touyz RM, 2000). Mechanical factors that influence the
vasculature in HT
include shear stress, wall stress and the direct actions of pressure itself
(Touyz RM, 2000;
Koller A, 2002). In addition to these factors, there is growing evidence that
reactive oxygen
species (ROS) that act as intercellular and intracellular signalling
molecules, regulate vascular
tone and structure (Wilcox CS, 2002; Berry C et al, 2001).
A recent advance in the field of angiotensin II signalling was the
demonstration that, in
addition to its vasoconstrictor properties, angiotensin II has potent
mitogenic-like and
proinflammatory-like characteristics. These actions are mediated through
phosphorylation of
both nonreceptor tyrosine kinases and receptor tyrosine kinases (Touyz RM,
2003). It is also
becoming increasingly apparent that many signalling events that underlie
abnormal vascular
function in HT are influenced by changes in intracellular redox status. In
particular, increased
bioavailability of ROS stimulates growth-signalling pathways, induces
expression of
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proinflammatory genes, alters contraction-excitation coupling and impairs
endothelial
function (Touyz RM, 2003).
In concert with the various functional and structural changes that are
responsible for HT, the
arteries become stiffer or less elastic. Vascular stiffness progressively
increases with age
5 (Slotwiner DJ et al., 2001) and is responsible for the progressive increase
in systolic as
compared to diastolic pressure, leading to the typical increase of pulse
pressure that is now
recognized to be the major determinant of cardiovascular risk (Beltran A et
al., 2001).
Measures of stiffness and elasticity have been shown to be an independent
predictor of the
development of HT (Liao D et al., 1999) and a marker of cardiovascular risk in
those with HT
(Blacher J et al., 1999). Changes in the physical characteristics of the large
arteries reflected
in the BP pulse contour alter not only BP and pulse pressure, but also cardiac
work and
performance.
The complexity of pathophysiologic mechanisms that lead to BP elevation is
such that
selective, mechanistically based antihypertensive treatment is rarely possible
in any
hypertensive patient. HT is highly prevalent among middle-aged and elderly
persons, and the
success rate in controlling BP in these individuals is poor. Current treatment
guidelines
generally recommend a generic approach to treating HT, with little emphasis on
selecting
therapy on the basis of the underlying pathophysiology of the elevated BP
(Chobanian AV et
al, 2003; ESH/ESC, 2003). With increased recognition of specific causes, it
may be possible
to develop therapies selective for distinct pathophysiologic mechanisms with
fewer adverse
effects, resulting in more effective BP reduction. The use of powerful new
techniques of
genetics, genomics, and proteomics, integrated with systems physiology and
population
studies, will make more selective and effective approaches to treating and
even preventing HT
possible in the coming decades (Oparil S et al, 2003).
Essential HT: a polygenic disease
Nuclear family studies show greater similarity in BP within families than
between families,
with heritability estimates ranging between 0.20 and 0.46 (Fuentes RM, 2003).
Twin studies
document greater concordance of BP in monozygotic than dizygotic twins, giving
the highest
heritability estimates between 0.48 and 0.64 (Fuentes RM, 2003). Adoption
studies
demonstrate greater concordance of BP among biological siblings than adoptive
siblings
living in the same household, estimating heritability between 0.45 and 0.61
(Fuentes RM,
2003).
Single genes can have major effects on BP, accounting for the rare Mendelian
forms of high
and low BP (Lifton RP et al, 2001). Although identifiable single-gene
mutations account for
only a small percentage of HT cases, studying these rare disorders may
elucidate
pathophysiologic mechanisms that predispose to more common forms of HT and may
suggest
novel therapeutic approaches (Lifton RP et al, 2001). Mutations in 10 genes
that cause
Mendelian forms of human HT and 9 genes that cause hypotension have been
described to
date (Lifton RP et al, 2001; Wilson FH et al, 2001). These mutations affect BP
by altering
renal salt handling, reinforcing the hypothesis that the development of HT
depends on
genetically determined renal dysfunction with resultant salt and water
retention (Guyton AC,
1991). Importantly, all the monogenic HT syndromes identified to date are
caused by defects
resulting in renal salt retention, whereas all the low BP syndromes share a
common
mechanism of excess renal sodium loss (Hopkins PN and Hunt SC, 2003).
The best studied monogenic cause of HT is the Liddle syndrome, a rare but
clinically
important disorder in which constitutive activation of the epithelial sodium
channel
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predisposes to severe, treatment-resistant HT (Shimkets RA et al, 1994).
Epithelial sodium
channel activation has been traced to mutations in the beta or gamma subunits
of the channel,
resulting in inappropriate sodium retention at the renal collecting duct
level. Patients with the
Liddle syndrome typically display volume-dependent, low-renin, and low-
aldosterone HT.
In most cases, HT results from a complex interaction of genetic,
environmental, and
demographic factors. Improved techniques of genetic analysis, especially
candidate gene
association studies and genome wide linkage analysis (genome wide scan, GWS),
have
enabled a search for genes that contribute to the development of primary HT in
the
population.
Thus far, the candidate gene approach has provided more examples than the
linkage approach
of gene variants that appear to affect BP. Reasonable candidate genes to
consider include
genes related to physiological systems known to be involved in the control of
BP and genes
known to affect BP in mouse models. To date more than 80 candidate genes have
been
evaluated for HT (Fuentes RM, 2004, unpublished review). However, the
association with HT
of only three genes have been widely replicated: angiotensinogen precursor
(AGT), adducin 1
(ADD1) and guanine nucleotide-binding protein, beta-3 subunit (GNB3) (Hopkins
PN and
Hunt SC, 2003). Gene-environment interactions affecting HT treatment have been
shown
between AGT, ADD1 and salt intake reduction (Hunt SC et al, 1998; Hunt SC et
al, 1999;
Cusi D et al, 1997), and between ADD1, GNB3 and diuretic treatment (Cusi D et
al, 1997;
Turner ST et al, 2001). Gene-gene interactions affecting HT risk development
have been
shown between ADD1 and the ACE gene I/D polymorphisms (Staessen JA et al,
2001).
Lessons learned from the studies of candidate genes to date include the
shortcomings that
result from the limited statistical power of many studies, expected variation
from one
population to another, the need for better phenotyping of study subjects, the
relatively small
effect of the genes studied on population prevalence of HT, and the lack of
sufficient certainty
of consequences of any genes studied thus far to make treatment
recommendations based on
genotype (Hopkins PN and Hunt SC, 2003).
To date more than 30 GWS studies have been reported to identify loci for BP/HT
(Fuentes
RM, 2004, unpublished review).Some studies utilized families, others affected
or dissimilar
sibling pairs. Linked loci with at least indicative LOD scores to BP/HT have
been observed
on every chromosome. Perhaps most striking is the lack of consistently linked
loci.
Koivukoski L et al, 2004 found evidence of susceptibility regions for BP/HT on
chromosomes
2p12-q22.1 and 3p14.1-q12.3 that had modest or non-significant linkage in each
individual
study when applying the genome-search meta-analysis method (GSMA) to nine
published
genome-wide scans of BP (n = 5) and HT (n = 4) from Caucasian populations.
This may serve
to illustrate the heterogeneity of human HT as well as the potential
shortcomings of
attempting to compare studies using different methodologies.
Opportunity for population genetics
Previous medical research concerning the genetic etiology of HT has been based
to a large
extent on retrospective case-control and family studies in humans and studies
in genetically
modified animals. As recognized only recently, retrospective case-control
studies are prone to
survival and selection biases, and they have produced a myriad of biased
findings concerning
a large number of candidate genes. A commonly used approach is to compare gene
expression
between affected and unaffected persons. Gene expression studies, which are
mostly cross-
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sectional, cannot however separate cause and consequence. Findings from animal
models
concerning HT cannot be generalised to humans, as the pathophysiology in
humans is unique.
The unsuitability of the animal studies is the main reason why genetic
epidemiologic studies
are the most important means in the clarification of genetic etiologies of
human diseases.
Prospective cohort studies in humans overcome these problems. Developments in
GWS and
sequencing technology and methods of data analysis render possible the attempt
to identify
liability genes in complex, multifactorial traits, and to dissect the role of
genetic
predisposition and environment/life style factors in these disorders with new
precision.
Genetic and environmental effects vary over the life span, and only
longitudinal studies in
genetically informative data sets permit the study of such effects. A major
advantage of
population genetics approaches in disease gene discovery over other
methodologies is that it
will yield diagnostic markers that are valid in humans.
The identification of genes causing major public health problems such as HT is
now enabled
by the following recent advances in molecular biology, population genetics and
bioinformatics: 1. the availability of new genotyping platforms that will
dramatically lower
operating costs and increase throughputs; 2. the application of genome scans
using dense
marker maps; 3. data analysis using new powerful statistical methods testing
for linkage
disequilibrium using haplotype sharing analysis, and 4. the recognition that a
smaller number
of genetic markers than previously thought is sufficient for genome scans in
genetically
homogeneous populations.
Traditional GWS using microsatellite markers with linkage analyses have not
been successful
in finding genes causing common diseases. The failure has in part been due to
too small a
number of genetic markers used in GWS, and in part due to too heterogeneous
study
populations. With the advancements of the human genome project and genotyping
technology, the first dense marker maps have recently become available for
mapping the
entire human genome. The microarrays used by Jurilab include probes for over
100,000 single
nucleotide polymorphism (SNP) markers. These SNPs form a marker map covering,
for the
first time, the entire genome tightly enough for the discovery of most disease
genes causing
HT.
Genetic homogeneity of the East Finland founder population
Finns descend from two human immigration waves occurring about 4,000 and 2,000
years
ago. Both Y-chromosomal haplotypes and mitochondrial sequences show low
genetic
diversity among Finns compared with other European populations and confirm the
long-
standing isolation of Finland (Sajantila A et al, 1996). During King Gustavus
of Vasa (1523-
1560) over 400 years ago, internal migrations created regional subisolates,
the late settlements
(Peltonen L et al, 1999). The most isolated of these are the East Finns.
The East Finnish population is the most genetically-homogenous population
isolate known
that is large enough for effective gene discovery program. The reasons for
homogeneity are:
the young age of the population (fewer generations); the small number of
founders; long-term
geographical isolation; and population bottlenecks because of wars, famine and
fatal disease
epidemics.
Owing to the genetic homogeneity of the East Finland population, there are
fewer mutations
in important disease predisposing genes and the affected individuals share a
similar genetic
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background. Because of the stronger linkage disequilibrium (LD), fewer SNPs
and fewer
subjects are needed for GWS than in other populations.
SUMMARY OF THE INVENTION
The present invention relates to single nucleotide polymorphism (SNP) markers,
combinations of such markers and haplotypes associated with altered risk of
HT, and genes
associated with HT within or close to which said markers or haplotypes are
located. Said SNP
markers may be associated either with increased HT risk or reduced HT risk
i.e. protective of
HT. The "prediction" or risk implies here that the risk is either increased or
reduced.
Thus, the present invention provides individual SNP markers associated with HT
and
combinations of SNP markers and haplotypes in genetic regions associated with
HT, genes
previously known in the art, but not known to be associated with HT, methods
of estimating
susceptibility or predisposition of an individual to HT, as well as methods
for prediction of
clinical course and efficacy of treatments for HT using polymorphisms in the
HT risk genes.
Accordingly, the present invention provides novel methods and compositions
based on the
disclosed HT associated SNP markers, combinations of SNP markers, haplotypes
and genes.
The invention further relates to a method for estimating susceptibility or
predisposition of an
individual to HT comprising the detection of the presence of SNP markers and
haplotypes, or
an alteration in expression of an HT risk gene set forth in tables 2 through
8, as well as
alterations in the polypeptides encoded by the said HT risk genes. The
alterations may be
quantitative, qualitative, or both.
The invention yet further relates to a method for estimating susceptibility or
predisposition of
an individual to HT. The method for estimating susceptibility or
predisposition of an
individual to HT is comprised of detecting the presence of at-risk haplotypes
in an
individual's nucleic acid.
The invention further relates to a kit for estimating susceptibility to HT in
an individual
comprising wholly or in part: amplification reagents for amplifying nucleic
acid fragments
containing SNP markers, detection reagents for genotyping SNP markers and
interpretation
software for data analysis and risk assessment.
In one aspect, the invention relates to methods of diagnosing a predisposition
to HT. The
methods of diagnosing a predisposition to HT in an individual include
detecting the presence
of SNP markers predicting HT, as well as detecting alterations in expression
of genes which
are associated with said markers. The alterations in expression can be
quantitative, qualitative,
or both.
A further object of the present invention is a method of identifying the risk
of HT by detecting
SNP markers in a biological sample of the subject. The information obtained
from this
method can be combined with other information concerning an individual, e.g.
results from
blood measurements, clinical examination and questionnaires. The blood
measurements
include but are not restricted to the determination of plasma or serum
cholesterol and high-
density lipoprotein cholesterol. The information to be collected by
questionnaire includes
information concerning gender, age, family and medical history such as the
family history of
HT and diabetes. Clinical information collected by examination includes e.g.
information
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9
concerning height, weight, hip and waist circumference, systolic and diastolic
BP, and heart
rate.
The methods of the invention allow the accurate diagnosis of HT at or before
disease onset,
thus reducing or minimizing the debilitating effects of HT. The method can be
applied in
persons who are free of clinical symptoms and signs of HT, in those who
already have clinical
HT, in those who have a family history of HT, or in those who have an elevated
level or levels
of risk factors of HT.
The invention further provides a method of diagnosing susceptibility to HT in
an individual.
This method comprises screening for at-risk haplotypes that predict HT that
are more
frequently present in an individual susceptible to HT, compared to the
frequency of its
presence in the general population, wherein the presence of an at-risk
haplotype is indicative
of a susceptibility to HT. The "at-risk haplotype" may also be associated with
a reduced rather
than increased risk of HT. An "at-risk haplotype" is intended to embrace one
or a combination
of haplotypes described herein over the markers that show high correlation to
HT. Kits for
diagnosing susceptibility to HT in an individual are also disclosed.
Those skilled in the art will readily recognize that the analysis of the
nucleotides present in
one or several of the SNP markers of this invention in an individual's nucleic
acid can be
done by any method or technique capable of determining nucleotides present in
a
polymorphic site. As it is obvious in the art the nucleotides present in SNP
markers can be
determined from either nucleic acid strand or from both strands.
The major application of the current invention involves prediction of those at
higher risk of
developing HT. Diagnostic tests that define genetic factors contributing to HT
might be used
together with or independent of the known clinical risk factors to define an
individual's risk
relative to the general population. Better means for identifying those
individuals at risk of HT
should lead to better preventive and treatment regimens, including more
aggressive
management of the current clinical risk factors for sequelae of HT such as
cigarette smoking,
hypercholesterolemia, elevated LDL cholesterol, low HDL cholesterol, HT and
elevated BP,
diabetes mellitus, glucose intolerance, insulin resistance and the metabolic
syndrome, obesity,
lack of physical activity, and inflammatory components as reflected by
increased C-reactive
protein levels or other inflammatory markers. Information on genetic risk may
be used by
physicians to help convince particular patients to adjust life style (e.g. to
stop smoking, reduce
caloric intake, to increase exercise). Finally, preventive measures aimed at
lowering blood
pressure such as reduction of weight, intake of salt and alcohol, can be both
better motivated
to the patients and selected on the basis of the molecular subdiagnosis of HT.
A further object of the invention is to provide a method for the selection of
human subjects for
studies testing antihypertensive effects of drugs.
Another object of the invention is a method for the selection of subjects for
clinical trials
testing antihypertensive drugs.
Still another object of the invention is to provide a method for prediction of
clinical course
and efficacy of treatments for HT using polymorphisms in the HT risk genes.
The genes, gene
products and agents of the invention are also useful for treating HT, for
monitoring the
effectiveness of the treatment, and for drug development. Kits are also
provided for the
diagnosis, treatment and prognosis of HT.
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DETAILED DESCRIPTION OF THE INVENTION
Representative Target Population
5
An individual at risk of HT is an individual who has at least one risk factor
of HT, such as
family history of HT, central or other type of obesity, lack of physical
activity, high sodium
intake, high intake of saturated fats, low intake of potassium and/or
magnesium, low HDL
cholesterol, diabetes mellitus, glucose intolerance, insulin resistance and
the metabolic
10 syndrome, elevated inflammatory marker, and an at-risk allele or haplotype
with one or
several HT risk SNP markers.
In another embodiment of the invention, an individual who is at risk of HT is
an individual
who has a risk-increasing allele in an HT risk gene, in which the presence of
the
polymorphism is indicative of a susceptibility to HT. The term "gene," as used
herein, refers
to an entirety containing all regulatory elements located both upstream and
downstream as
well as within of a polypeptide encoding sequence, 5' and 3' untranslated
regions of mRNA
and the entire polypeptide encoding sequence including all exon and intron
sequences (also
alternatively spliced exons and introns) of a gene.
Assessment for At-Risk Alleles and At-Risk Haplotypes
The genetic markers are particular "alleles" at "polymorphic sites" associated
with HT. A
nucleotide position at which more than one sequence is possible in a
population, is referred to
herein as a "polymorphic site". Where a polymorphic site is a single
nucleotide in length, the
site is referred to as a SNP. For example, if at a particular chromosomal
location, one member
of a population has an adenine and another member of the population has a
thymine at the
same position, then this position is a polymorphic site, and, more
specifically, the
polymorphic site is a SNP. Polymorphic sites may be several nucleotides in
length due to
insertions, deletions, conversions or translocations. Each version of the
sequence with respect
to the polymorphic site is referred to herein as an "allele" of the
polymorphic site. Thus, in the
previous example, the SNP allows for both an adenine allele and a thymine
allele.
Typically, a reference nucleotide sequence is referred to for a particular
gene. Alleles that
differ from the reference are referred to as "variant" alleles. The
polypeptide encoded by the
reference nucleotide sequence is the "reference" polypeptide with a particular
reference amino
acid sequence, and polypeptides encoded by variant alleles are referred to as
"variant"
polypeptides with variant amino acid sequences.
Nucleotide sequence variants can result in changes affecting the properties of
a polypeptide.
These sequence differences, when compared to a reference nucleotide sequence,
include
insertions, deletions, conversions and substitutions: e.g. an insertion, a
deletion or a
conversion may result in a frame shift generating an altered polypeptide; a
substitution of at
least one nucleotide may result in a premature stop codon, aminoacid change or
abnormal
mRNA splicing; the deletion of several nucleotides, resulting in a deletion of
one or more
amino acids encoded by the nucleotides; the insertion of several nucleotides,
such as by
unequal recombination or gene conversion, resulting in an interruption of the
coding sequence
of a reading frame; duplication of all or a part of a sequence; transposition;
or a rearrangement
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11
of a nucleotide sequence, as described in detail above. Such sequence changes
alter the
polypeptide encoded by an HT susceptibility gene. For example, a nucleotide
change in a
gene resulting in a change in corresponding polypeptide aminoacid sequence can
alter the
physiological properties of a polypeptide resulting in a polypeptide having
altered biological
activity/function, distribution or stability.
Alternatively, nucleotide sequence variants can result in changes affecting
transcription of a
gene or translation of it's mRNA. A polymorphic site located in a regulatory
region of a gene
may result in altered transcription of a gene e.g. due to altered tissue
specifity, altered
transcription rate or altered response to transcription factors. A polymorphic
site located in a
region corresponding to the mRNA of a gene may result in altered translation
of the mRNA
e.g. by inducing stable secondary structures to the mRNA and affecting the
stability of the
mRNA. Such sequence changes may alter the expression of an HT susceptibility
gene.
A "haplotype," as described herein, refers to any combination of genetic
markers ("alleles"),
such as those set forth in tables 3, 4, 5, 7 and 8. A haplotype can comprise
two or more alleles.
As it is recognized by those skilled in the art, the same haplotype can be
described differently
by determining the haplotype defining alleles from different strands e.g. the
haplotype
rs222151 1, rs4940595, rs1522723, rs1395266 (A T C C) described in this
invention is the
same as haplotype rs222151 1, rs4940595, rs1522723, rs1395266 (T A G G) in
which the
alleles are determined from the other strand or haplotype rs222151 1,
rs4940595, rs1522723,
rs1395266 (T T C C), in which the first allele is determined from the other
strand.
The haplotypes described herein, e.g. having markers such as those shown in
tables 3, 4, 5, 7
and 8, are found more frequently in individuals with HT than in individuals
without HT.
Therefore, these haplotypes have predictive value for detecting HT or a
susceptibility to HT in
an individual. Therefore, detecting haplotypes can be accomplished by methods
known in the
art for detecting sequences at polymorphic sites.
It is understood that the HT associated at-risk alleles and at-risk haplotypes
described in this
invention may be associated with other "polymorphic sites" located in HT
associated genes of
this invention. These other HT associated polymorphic sites may be either
equally useful as
genetic markers or even more useful as causative variations explaining the
observed
association of the at-risk alleles and at-risk haplotypes of this invention to
HT.
In certain methods described herein, an individual who is at risk of HT is an
individual in
whom an at-risk allele or an at-risk haplotype is identified. In one
embodiment, the at-risk
allele or the at-risk haplotype is one that confers a significant risk of HT.
In one embodiment,
significance associated with an allele or a haplotype is measured by an odds
ratio. In a further
embodiment, the significance is measured by a percentage. In one embodiment, a
significant
risk is measured as an odds ratio of at least about 1.2, including but not
limited to: 0.1, 0.2,
0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9,
2.0, 2.5, 3.0, 4.0, 5.0, 10.0,
15.0, 20.0, 25.0, 30.0 and 40Ø In a further embodiment, a significant
increase or reduction in
risk is at least about 20%, including but not limited to about 25%, 30%, 35%,
40%, 45%,
50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% and 98%. In a further
embodiment, a
significant increase in risk is at least about 50%. It is understood however,
that identifying
whether a risk is medically significant may also depend on a variety of
factors, including the
specific disease, the allele or the haplotype, and often, environmental
factors.
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An at-risk haplotype in, or comprising portions of, the HT risk gene, is one
where the
haplotype is more frequently present in an individual at risk of HT
(affected), compared to the
frequency of its presence in a healthy individual (control), and wherein the
presence of the
haplotype is indicative of HT or susceptibility to HT.
In a preferred embodiment, the method comprises assessing in an individual the
presence or
frequency of SNPs in, comprising portions of, an HT risk gene, wherein an
excess or higher
frequency of the SNPs compared to healthy control individuals is indicative
that the
individual has HT, or is susceptible to HT. See, for example, tables 3, 4, 5,
7 and 8 for SNPs
that can form haplotypes that can be used as screening tools. These SNP
markers can be
identified in at-risk haploptypes. For example, an at-risk haplotype can
include microsatellite
markers and/or SNPs such as those set forth in tables 3, 4, 5, 7 and 8. The
presence of the
haplotype is indicative of HT, or a susceptibility to HT, and therefore is
indicative of an
individual who falls within a target population for the treatment methods
described herein.
Consequently, the method of the invention is particularly directed to the
detection of one or
several of the SNP markers defining the following at-risk haplotypes
indicative of HT:
1) rs4845303 (A/T) (SEQ ID NO: 980), rs6428195 (C/G) (SEQ ID NO: 1030) and
rs1935659
(A/G) (SEQ ID NO: 637) defining the haplotype ACG;
2) rs1997454 (A/G) (SEQ ID NO: 656), rs2139502 (A/G) (SEQ ID NO: 709) and
rs1519991
(A/C) (SEQ ID NO: 542) defining the haplotype AGC;
3) rs1521409 (A/G) (SEQ ID NO: 544), rs10511365 (C/T) (SEQ ID NO: 316) and
rs10511366 (C/T) (SEQ ID NO: 317) defming the haplotype ACT;
4) rs7679959 (C/G) (SEQ ID NO: 1178), rs10517338 (C/G) (SEQ ID NO: 381) and
rs959297
(A/T) (SEQ ID NO: 1338) defining the haplotype CGA;
5) rs2278677 (A/G) (SEQ ID NO: 749), rs3886091 (C/G) (SEQ ID NO: 899),
rs1998167
(A/G) (SEQ ID NO: 657), rs1998168 (A/G) (SEQ ID NO: 658) and rs2235280 (A/G)
(SEQ
ID NO: 740) defining the haplotype GCAGG;
6) rs 10521062 (A/C) (SEQ ID NO: 404), rs 10512296 (A/G) (SEQ ID NO: 331), rs
1924001
(C/G) (SEQ ID NO: 633) and rs2417359 (A/G) (SEQ ID NO: 784) defining the
haplotype
AACG;
7) rs10508933 (C/G) (SEQ ID NO: 289), rs10509071 (A/G) (SEQ ID NO: 295) and
rs10490967 (A/G) (SEQ ID NO: 94) defining the haplotype GGA;
8) rs10508771 (A/T) (SEQ ID NO: 286), rs3006608 (C/T) (SEQ ID NO: 854),
rs10508773
(C/T) (SEQ ID NO: 287) and rs950132 (C/T) (SEQ ID NO: 1325) defining the
haplotype
TCCC;
9) rs1386486 (C/T) (SEQ ID NO: 472), rs1386485 (A/C) (SEQ ID NO: 471),
rs1386483
(A/G) (SEQ ID NO: 470) and rs7977245 (C/T) (SEQ ID NO: 1212) defining the
haplotype
CAGT;
10) rs276002 (A/G) (SEQ ID NO: 814) and rs274460 (A/G) (SEQ ID NO: 810)
defining the
haplotype AA;
11) rs1245383 (A/G) (SEQ ID NO: 430), rs2133829 (C/T) (SEQ ID NO: 707),
rs2173738
(C/T) (SEQ ID NO: 722), rs2050528 (C/T) (SEQ ID NO: 677) and rs202970 (C/T)
(SEQ ID
NO: 671) defining the haplotype GCTTC;
12) rs1395266 (C/T) (SEQ ID NO: 476), rs931850 (A/G) (SEQ ID NO: 1303) and
rs1522722
(C/T) (SEQ ID NO: 547) defining the haplotype TAC;
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13
13) rs2221511 (A/G) (SEQ ID NO: 733), rs4940595 (G/T) (SEQ ID NO: 986),
rs1522723
(C/T) (SEQ ID NO: 548) and rs1395266 (C/T) (SEQ ID NO: 476) defining the
haplotype
ATCC;
14) rs2825555 (A/G) (SEQ ID NO: 819), rs2825583 (C/T) (SEQ ID NO: 820),
rs2825601
(A/G) (SEQ ID NO: 821), rs2825610 (G/T) (SEQ ID NO: 822) and rs1489734 (A/G)
(SEQ
ID NO: 532) defining the haplotype ATGGA
Monitoring Progress of Treatment
The current invention also pertains to methods of monitoring the effectiveness
of a treatment
of HT on the expression (e.g. relative or absolute expression) of one or more
HT risk genes.
The HT susceptibility gene mRNA, the polypeptide it is encoding, or the
biological activity of
the encoded polypeptide can be measured in a sample of peripheral blood or
cells derived
therefrom. An assessment of the levels of expression or biological activity of
the polypeptide
can be made before and during treatment with HT therapeutic agents.
Alternatively the effectiveness of a treatment of HT can be followed by
monitoring biological
networks and/or metabolic pathways related to one or several polypeptides
encoded by HT
risk genes listed in table 6. Monitoring biological networks and/or metabolic
pathways can be
done e.g. by measuring one or several polypeptides from plasma proteome and/or
by
measuring one or several metabolites from plasma metabolome before and during
treatment.
Effectiveness of a treatment is evaluated by comparing observed changes in
biological
networks and or metabolic pathways following treatment with HT therapeutic
agents to the
data available from healthy subjects.
For example, in one embodiment of the invention, an individual who is a member
of the target
population can be assessed for response to treatment with an HT inhibitor, by
examining the
HT risk gene encoding polypeptide biological activity or absolute and/or
relative levels of HT
risk gene encoding polypeptide or mRNA in peripheral blood in general or
specific cell
subfractions or combination of cell subfractions.
In addition, variations such as haplotypes or mutations within or near (within
one to hundreds
of kb) the HT risk gene may be used to identify individuals who are at higher
risk for HT to
increase the power and efficiency of clinical trials for pharmaceutical agents
to prevent or
treat HT or its complications. The haplotypes and other variations may be used
to exclude or
fractionate patients in a clinical trial who are likely to have involvement of
another pathway in
their HT in order to enrich patients who have pathways involved that are
relevant regarding to
the treatment tested and boost the power and sensitivity of the clinical
trial. Such variations
may be used as a pharmacogenetic test to guide selection of pharmaceutical
agents for
individuals.
Primers, probes and nucleic acid molecules
"Probes" or "primers" are oligonucleotides that hybridize in a base-specific
manner to a
complementary strand of nucleic acid molecules. "Base specific manner" means
that the two
sequences must have a degree of nucleotide complementarity sufficient for the
primer or
probe to hybridize. Accordingly, the primer or probe sequence is not required
to be perfectly
complementary to the sequence of the template. Non-complementary bases or
modified bases
can be interspersed into the primer or probe, provided that base substitutions
do not inhibit
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14
hybridization. The nucleic acid template may also include "nonspecific priming
sequences" or
"nonspecific sequences" to which the primer or probe has varying degrees of
complementarity. Such probes and primers include polypeptide nucleic acids
(Nielsen PE et
al, 1991).
A probe or primer comprises a region of nucleic acid that hybridizes to at
least about 15, for
example about 20-25, and in certain embodiments about 40, 50, or 75
consecutive nucleotides
of a nucleic acid of the invention, such as a nucleic acid comprising a
contiguous nucleic acid
sequence.
In preferred embodiments, a probe or primer comprises 100 or fewer
nucleotides, in certain
embodiments, from 6 to 50 nucleotides, for example, from 12 to 30 nucleotides.
In other
embodiments, the probe or primer is at least 70% identical to the contiguous
nucleic acid
sequence or to the complement of the contiguous nucleotide sequence, for
example, at least
80% identical, in certain embodiments at least 90% identical, and in other
embodiments at
least 95% identical, or even capable of selectively hybridizing to the
contiguous nucleic acid
sequence or to the complement of the contiguous nucleotide sequence. Often,
the probe or
primer further comprises a label, e.g. radioisotope, fluorescent compound,
enzyme, or enzyme
co-factor.
Antisense nucleic acid molecules of the invention can be designed using the
nucleotide
sequences available e.g. in GenBank database for HT associated genes of table
6 as well as
nucleotide sequences containing polymorphic sites listed in tables 2 to 5 and
7 to 11.
Antisense oligonucleotides can be constructed using chemical synthesis and
enzymatic
ligation reactions using procedures known in the art. For example, an
antisense nucleic acid
molecule (e.g. an antisense oligonucleotide) can be chemically synthesized
using naturally
occurring nucleotides or variously modified nucleotides designed to increase
the biological
stability of the molecules or to increase the physical stability of the duplex
formed between
the antisense and sense nucleic acids, e.g. phosphorothioate derivatives and
acridine
substituted nucleotides can be used. Alternatively, the antisense nucleic acid
molecule can be
produced biologically using an expression vector into which a nucleic acid
molecule has been
subcloned in an antisense orientation (i.e. RNA transcribed from the inserted
nucleic acid
molecule will be of an antisense orientation to a target nucleic acid of
interest).
The nucleic acid sequences of the HT associated genes of table 6 described in
this invention
can also be used to compare with endogenous DNA sequences in patients to
identify genetic
disorders (e.g. a predisposition for, or susceptibility to HT), and as probes,
such as to
hybridize and discover related DNA sequences or to extract known sequences
from a sample.
The nucleic acid sequences can further be used to derive primers for genetic
fmgerprinting, to
raise anti-polypeptide antibodies using DNA immunization techniques, and as an
antigen to
raise anti-DNA antibodies or elicit immune responses. Portions or fragments of
the nucleotide
sequences identified herein (and the corresponding complete gene sequences)
can be used in
numerous ways as polynucleotide reagents. For example, these sequences can be
used to: (i)
map their respective genes on a chromosome; and thus locate gene regions
associated with
genetic disease; (ii) identify an individual from a minute biological sample
(tissue typing);
and (iii) aid in forensic identification of a biological sample. Additionally,
the nucleotide
sequences of the invention can be used to identify and express recombinant
polypeptides for
analysis, characterization or therapeutic use, or as markers for tissues in
which the
corresponding polypeptide is expressed, either constitutively, during tissue
differentiation, or
in diseased states. The nucleic acid sequences can additionally be used as
reagents in the
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screening and/or diagnostic assays described herein, and can also be included
as components
of kits (e.g. reagent kits) for use in the screening and/or diagnostic assays
described herein.
5 Polyclonal and monoclonal antibodies
Polyclonal and/or monoclonal antibodies that specifically bind one form of the
gene product
but not to the other form of the gene product are also provided. Antibodies
are also provided
that bind a portion of either the variant or the reference gene product that
contains the
10 polymorphic site or sites. The term "antibody" as used herein refers to
immunoglobulin
molecules and immunologically active portions of immunoglobulin molecules,
i.e. molecules
that contain an antigen binding site that specifically binds an antigen. A
molecule that
specifically binds to a polypeptide of the invention is a molecule that binds
to that polypeptide
or a fragment thereof, but does not substantially bind other molecules in a
sample, e.g. a
15 biological sample, which naturally contains the polypeptide. Examples of
immunologically
active portions of immunoglobulin molecules include F(ab) and F(ab') fragments
which can
be generated by treating the antibody with an enzyme such as pepsin. The
invention provides
polyclonal and monoclonal antibodies that bind to a polypeptide of the
invention. The term
"monoclonal antibody" or "monoclonal antibody composition" as used herein,
refers to a
population of antibody molecules that contain only one species of an antigen
binding site
capable of immunoreacting with a particular epitope of a polypeptide of the
invention. A
monoclonal antibody composition thus typically displays a single binding
affinity for a
particular polypeptide of the invention with which it immunoreacts.
Polyclonal antibodies can be prepared as known by those skilled in the art by
immunizing a
suitable subject with a desired immunogen, e.g. a polypeptide of the invention
or fragment
thereof. The antibody titer in the immunized subject can be monitored over
time by standard
techniques such as with an enzyme linked immunosorbent assay (ELISA) using
immobilized
polypeptide. If desired, the antibody molecules directed against the
polypeptide can be
isolated from the mammal (e.g. from blood) and further purified by well-known
techniques,
such as protein A chromatography to obtain the IgG fraction. At an appropriate
time after
immunization, e.g. when the antibody titers are highest, antibody-producing
cells can be
obtained from the subject and used to prepare monoclonal antibodies by
standard techniques,
such as the hybridoma technique (Kohler G and Milstein C, 1975), the human B
cell
hybridoma technique (Kozbor D et al, 1982), the EBV-hybridoma technique (Cole
SP et al,
1994), or trioma techniques (Hering S et al, 1988). To produce a hybridoma an
immortal cell
line (typically a myeloma) is fused to lymphocytes (typically splenocytes)
from a mammal
immunized with an immunogen as described above, and the culture supernatants
of the
resulting hybridoma cells are screened to identify a hybridoma producing a
monoclonal
antibody that binds a polypeptide of the invention.
Any of the many well known protocols used for fusing lymphocytes and
immortalized cell
lines can be applied for the purpose of generating a monoclonal antibody to a
polypeptide of
the invention (Bierer B et al, 2002). Moreover, the ordinarily skilled worker
will appreciate
that there are many variations of such methods that would also be useful.
As an alternative to preparing monoclonal antibody-secreting hybridomas, a
monoclonal
antibody to a polypeptide of the invention can be identified and isolated by
screening a
recombinant combinatorial immunoglobulin library (e.g. an antibody phage
display library)
with the polypeptide to thereby isolate immunoglobulin library members that
bind the
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16
polypeptide (Hayashi N et al, 1995; Hay BN et al, 1992; Huse WD et al, 1989;
Griffiths AD
et al, 1993). Kits for generating and screening phage display libraries are
commercially
available.
Additionally, recombinant antibodies, such as chimeric and humanized
monoclonal antibodies
comprising both human and nonhuman portions, which can be made using standard
recombinant DNA techniques, are within the scope of the invention. Such
chimeric and
humanized monoclonal antibodies can be produced by recombinant DNA techniques
known
in the art.
In general, antibodies of the invention (e.g. a monoclonal antibody) can be
used to isolate a
polypeptide of the invention by standard techniques such as affmity
chromatography or
immunoprecipitation. A polypeptide-specific antibody can facilitate the
purification of natural
polypeptide from cells and of recombinantly produced polypeptide expressed in
host cells.
Moreover, an antibody specific for a polypeptide of the invention can be used
to detect the
polypeptide (e.g. in a cellular lysate, cell supernatant, or tissue sample) in
order to evaluate
the abundance and pattern of expression of the polypeptide. Antibodies can be
used
diagnostically to monitor protein levels in tissue such as blood as part of a
test predicting the
susceptibility to HT or as part of a clinical testing procedure, e.g. to
determine the efficacy of
a given treatment regimen. Detection can be facilitated by coupling the
antibody to a
detectable substance. Examples of detectable substances include various
enzymes, prosthetic
groups, fluorescent materials, luminescent materials, bioluminescent
materials, and
radioactive materials. Examples of suitable enzymes include horseradish
peroxidase, alkaline
phosphatase, beta-galactosidase, and acetylcholinesterase; examples of
suitable prosthetic
group complexes include streptavidin/biotin and avidin/biotin; examples of
suitable
fluorescent materials include umbelliferone, fluorescein, fluorescein
isothiocyanate,
rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or
phycoerythrin; an example
of a luminescent material includes luminol; examples of bioluminescent
materials include
luciferase, luciferin, and aequorin, and examples of suitable radioactive
material include 125I330 131I33sS and 3H.
Diagnostic Assays
The probes, primers and antibodies described herein can be used in methods of
diagnosis of
HT or diagnosis of a susceptibility to HT, as well as in kits useful for the
diagnosis of HT or
susceptibility to HT, or to a disease or condition associated with HT.
In one embodiment of the invention, diagnosis of HT or susceptibility to HT
(or diagnosis of
or susceptibility to a disease or condition associated with HT), is made by
detecting one or
several of at-risk alleles or at-risk haplotypes or a combination of at-risk
alleles and at-risk
haplotypes described in this invention in the subject's nucleic acid as
described herein.
In one embodiment of the invention, diagnosis of HT or susceptibility to HT
(or diagnosis of
or susceptibility to a disease or condition associated with HT) is made by
detecting one or
several polymorphic sites that are associated with at-risk alleles and/or at-
risk haplotypes
described in this invention, in the subject's nucleic acid. Diagnostically,
the most useful
polymorphic sites are those altering the polypeptide structure of an HT
associated gene due to
a frame shift; due to a premature stop codon, due to an aminoacid change or
due to abnormal
mRNA splicing. Nucleotide changes in a gene resulting in a change in
corresponding
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17
polypeptide aminoacid sequence in many case alter the physiological properties
of a
polypeptide by resulting in a polypeptide having altered biological
activity/function,
distribution or stability. Other diagnostically useful polymorphic sites are
those affecting
transcription of an HT associated gene or translation of it's mRNA due to
altered tissue
specifity, altered transcription rate, altered response to physiological
status, altered translation
efficiency of the mRNA and altered stability of the mRNA. The presence of
nucleotide
sequence variants altering the polypeptide structure of HT associated genes or
altering the
expression of HT associated genes is diagnostic for susceptibility to HT.
For diagnostic applications, there may be informative polymorphisms for
prediction of
disease risk that are in linkage disequilibrium with the functional
polymorphism. Such a
functional polymorphism may alter splicing sites, affect the stability or
transport of mRNA, or
otherwise affect the transcription or translation of the nucleic acid. The
presence of nucleotide
sequence variants associated with functional polymorphism is diagnostic for
susceptibility to
HT.
While we have genotyped and included a limited number of example SNP markers
in the
experimental section, any functional, regulatory or other mutation or
alteration described
above in any of the HT risk genes identified herein is expected to predict the
risk of HT.
In diagnostic assays determination of the nucleotides present in one or
several of the HT
associated SNP markers of this invention, as well as polymorphic sites
associated with HT
associated SNP markers of this invention, in an individual's nucleic acid can
be done by any
method or technique which can accurately determine nucleotides present in a
polymorphic
site. Numerous suitable methods have been described in the art (Kwok P-Y,
2001; Syvanen
A-C, 2001). These methods include, but are not limited to, hybridization
assays, ligation
assays, primer extension assays, enzymatic cleavage assays, chemical cleavage
assays and
any combinations of these assays. The assays may or may not include PCR, solid
phase step,
modified oligonucleotides, labeled probes or labeled nucleotides, and the
assay may be
multiplex or singleplex. As it is obvious in the art the nucleotides present
in polymorphic site
can be determined from one nucleic acid strand or from both strands.
In another embodiment of the invention, diagnosis of a susceptibility to HT
can also be made
by examining transcription of one or several HT associated genes. Alterations
in transcription
can be analyzed by a variety of methods as described in the art, including
e.g. hybridization
methods, enzymatic cleavage assays, RT-PCR assays and microarrays. A test
sample from an
individual is collected and the alterations in the transcription of HT
associated genes are
assessed from the RNA present in the sample. Altered transcription is
diagnostic for a
susceptibility to HT.
In another embodiment of the invention, diagnosis of a susceptibility to HT
can also be made
by examining expression and/or structure and/or function of an HT
susceptibility polypeptide.
A test sample from an individual is assessed for the presence of an alteration
in the expression
and/or an alteration in structure and/or function of the polypeptide encoded
by an HT risk
gene, or for the presence of a particular polypeptide variant (e.g. an
isoform) encoded by an
HT risk gene. An alteration in expression of a polypeptide encoded by an HT
risk gene can be
for example, an alteration in the quantitative polypeptide expression (i.e.
the amount of
polypeptide produced); an alteration in the structure and/or function of a
polypeptide encoded
by an HT risk gene is an alteration in the qualitative polypeptide expression
(e.g. expression
of a mutant HT susceptibility polypeptide or of a different splicing variant
or isoform). In a
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preferred embodiment, detection of a particular splicing variant encoded by an
HT risk gene,
or a particular pattern of splicing variants makes diagnosis of the disease or
condition
associated with HT or a susceptibility to a disease or condition associated
with HT possible.
Alterations in expression and/or structure and/or function of an HT
susceptibility polypeptide
can be determined by various methods known in the art e.g. by assays based on
chromatography, spectroscopy, colorimetry, electrophoresis, isoelectric
focusing, specific
cleavage, immunologic techniques and measurement of biological activity as
well as
combinations of different assays. An "alteration" in the polypeptide
expression or
composition, as used herein, refers to an alteration in expression or
composition in a test
sample, as compared with the expression or composition of polypeptide by an HT
risk gene in
a control sample. A control sample is a sample that corresponds to the test
sample (i.e. is from
the same type of cells), and is from an individual who is not affected by HT.
An alteration in
the expression or composition of the polypeptide in the test sample, as
compared with the
control sample, is indicative of a susceptibility to HT.
Western blotting analysis using an antibody as described above that
specifically binds to a
polypeptide encoded by a mutant HT risk gene, or an antibody that specifically
binds to a
polypeptide encoded by a nonmutant gene, or an antibody that specifically
binds to a
particular splicing variant encoded by an HT risk gene, can be used to
identify the presence in
a test sample of a particular splicing variant or isoform, or of a polypeptide
encoded by a
polymorphic or mutant HT risk gene, or the absence in a test sample of a
particular splicing
variant or isoform, or of a polypeptide encoded by a nonpolymorphic or
nonmutant gene. The
presence of a polypeptide encoded by a polymorphic or mutant gene, or the
absence of a
polypeptide encoded by a nonpolymorphic or nonmutant gene, is diagnostic for
susceptibility
to HT, as is the presence (or absence) of particular splicing variants encoded
by an HT risk
gene.
In one embodiment of this method, the level or amount of polypeptide encoded
by an HT risk
gene in a test sample is compared with the level or amount of the polypeptide
encoded by an
HT risk gene in a control sample. A level or amount of the polypeptide in the
test sample that
is higher or lower than the level or amount of the polypeptide in the control
sample, such that
the difference is statistically significant, is indicative of an alteration in
the expression of the
polypeptide encoded by an HT risk gene, and is diagnostic for susceptibility
to HT.
Alternatively, the composition of the polypeptide encoded by an HT risk gene
in a test sample
is compared with the composition of the polypeptide encoded by an HT risk gene
in a control
sample (e.g. the presence of different splicing variants). A difference in the
composition of the
polypeptide in the test sample, as compared with the composition of the
polypeptide in the
control sample, is diagnostic for susceptibility to HT. In another embodiment,
both the level
or amount, and the composition of the polypeptide can be assessed in the test
sample and in
the control sample. A difference in the amount or level of the polypeptide in
the test sample
compared to the control sample; a difference in composition in the test sample
compared to
the control sample; or both a difference in the amount or level, and a
difference in the
composition, is indicative of susceptibility to HT.
In another embodiment, assessment of the splicing variant or isoform(s) of a
polypeptide
encoded by a polymorphic or mutant HT risk gene can be performed. The
assessment can be
performed directly (e.g. by examining the polypeptide itself), or indirectly
(e.g. by examining
the mRNA encoding the polypeptide, e.g. by mRNA profiling). For example,
probes or
primers as described herein can be used to determine which splicing variants
or isoforms are
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19
encoded by an HT risk gene mRNA, using standard methods.
The presence in a test sample of a particular splicing variant(s) or
isoform(s) associated with
HT or risk of HT, or the absence in a test sample of a particular splicing
variant(s) or
isoform(s) not associated with HT or risk of HT, is diagnostic for a disease
or condition
associated with an HT risk gene or susceptibility to a disease or condition
associated with an
HT risk gene. Similarly, the absence in a test sample of a particular splicing
variant(s) or
isoform(s) associated with HT or risk of HT, or the presence in a test sample
of a particular
splicing variant(s) or isoform(s) not associated with HT or risk of HT, is
diagnostic for the
absence of disease or condition associated with an HT risk gene or
susceptibility to a disease
or condition associated with an HT risk gene.
The invention further pertains to a method for the diagnosis and
identification of susceptibility
to HT in an individual by identifying an at-risk allele or an at-risk
haplotype in an HT risk
gene. In one embodiment, the at-risk allele or the at-risk haplotype is an
allele or haplotype
for which the presence of the haplotype increases the risk of HT
significantly. Although it is
to be understood that identifying whether a risk is significant may depend on
a variety of
factors, including the specific disease, the haplotype, and often,
environmental factors, the
significance may be measured by an odds ratio or a percentage. In a further
embodiment, the
significance is measured by a percentage. In one embodiment, a significant
risk is measured
as an odds ratio of 0.8 or less or at least about 1.2, including but not
limited to: 0.1, 0.2, 0.3,
0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0,
2.5, 3.0, 4.0, 5.0, 10.0, 15.0,
20.0, 25.0, 30.0 and 40Ø In a further embodiment an odds ratio of at least
1.2 is significant.
In a further embodiment, an odds ratio of at least about 1.5 is significant.
In a further
embodiment a significant increase or decrease in risk is at least about 1.7.
In a further
embodiment, a significant increase in risk is at least about 20%, including
but not limited to
about 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,
95%
and 98%. In a further embodiment a significant increase or reduction in risk
is at least about
50%. It is understood, however, that identifying whether a risk is medically
significant may
also depend on a variety of factors, including the specific disease, the
allele or the haplotype,
and often, environmental factors.
The invention also pertains to methods of diagnosing HT or susceptibility to
HT in an
individual, comprising screening for an at-risk haplotype in the HT risk gene
that is more
frequently present in an individual susceptible to HT (affected), compared to
the frequency of
its presence in a healthy individual (control), wherein the presence of the
haplotype is
indicative of HT or susceptibility to HT. See tables 3, 4, 6, 7 and 8 for SNP
markers that
comprise haplotypes that can be used as screening tools. SNP markers from
these lists
represent at-risk haplotypes and can be used to design diagnostic tests for
determining
susceptibility to HT.
Kits (e.g. reagent kits) useful in the methods of diagnosis comprise
components useful in any
of the methods described herein, including for example, PCR primers,
hybridization probes or
primers as described herein (e.g. labeled probes or primers), reagents for
genotyping SNP
markers, reagents for detection of labeled molecules, restriction enzymes
(e.g. for RFLP
analysis), allele-specific oligonucleotides, DNA polymerases, RNA polymerases,
marker
enzymes, antibodies which bind to altered or to nonaltered (native) HT
susceptibility
polypeptide, means for amplification of nucleic acids comprising one or
several HT risk
genes, or means for analyzing the nucleic acid sequence of one or several HT
risk genes or for
analyzing the amino acid sequence of one or several HT susceptibility
polypeptides, etc. In
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one embodiment, a kit for diagnosing susceptibility to HT can comprise primers
for nucleic
acid amplification of a region in an HT risk gene comprising an at-risk
haplotype that is more
frequently present in an individual susceptible to HT. The primers can be
designed using
portions of the nucleic acids flanking SNPs that are indicative of HT.
5
This invention is based on the principle that one or a small number of
genotypings are
performed and the sequence variations to be typed are selected on the basis of
their ability to
predict HT. For this reason any method to genotype sequence variations in a
genomic DNA
sample can be used.
Thus, the detection method of the invention may further comprise a step of
combining
information concerning age, gender, the family history of HT, diabetes and
hypercholesterolemia, and the medical history concerning CVD or diabetes of
the subject with
the results obtained from step b) of the method (see claim 1) for confirming
the indication
obtained from the detection step. Said information may also concern
hypercholesterolemia in
the family, smoking status, HT in the family, history of CVD, obesity in the
family, and
waist-to-hip circumference ratio (cm/cm)
The detection method of the invention may also further comprise a step
determining blood,
serum or plasma cholesterol, HDL cholesterol, LDL cholesterol, triglyceride,
apolipoprotein
B and Al, fibrinogen, ferritin, transferrin receptor, C-reactive protein,
serum or plasma insulin
concentration.
The score that predicts the probability of HT may be calculated using a
multivariate failure
time model or a logistic regression equation. The results from the further
steps of the method
as described above render possible a step of calculating the probability of
developing HT
using a logistic regression equation as follows.
Probability of HT = 1/[1 + e(-(-a + E(bi*Xi))], where e is Napier's constant,
Xi are variables
related to HT, bi are coefficients of these variables in the logistic
function, and a is the
constant term in the logistic function, and wherein a and bi are preferably
determined in the
population in which the method is to be used, and Xi are prefereably selected
among the
variables that have been measured in the population in which the method is to
be used.
Preferable values for b; are between -20 and 20; and for i between 0 (zero)
and 100,000. A
negative coefficient b; implies that the marker is risk-reducing and a
positive coefficient
implies that the marker is risk-increasing.
Xi are binary variables that can have values or are coded as 0 (zero) or
1(one) such as SNP
markers. The model may additionally include any interaction (product) or terms
of any
variables Xi, e.g. biXi. An algorithm is developed for combining the
information to yield a
simple prediction of HT as percentage of risk in one year, two years, five
years, 10 years or 20
years.
Alternative statistical models are failure-time models such as the Cox's
proportional hazards'
model, other iterative models and neural networking models.
The test can be applied to test the risk of developing HT in both healthy
persons, as a
screening or predisposition test, and high-risk persons (who have e.g. family
history of HT,
central or other type of obesity, lack of physical activity, high sodium
intake, high intake of
saturated fats, low intake of potassium and/or magnesium, low HDL cholesterol,
diabetes
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mellitus, glucose intolerance, insulin resistance and the metabolic syndrome,
elevated
inflammatory marker, or any combination of these or an elevated level of any
other risk factor
for HT).
The method can be used in the prediction and early diagnosis of HT in adult
persons,
stratification and selection of subjects in clinical trials, and/or
stratiflcation and selection of
persons for intensified preventive and curative interventions. The aim is to
reduce the cost of
clinical drug trials and health care.
Pharmaceutical Compositions
The present invention also pertains to pharmaceutical compositions comprising
agents
described herein, particularly nucleotides in HT risk genes, and/or comprising
other splicing
variants encoded by HT risk genes; and/or an agent that alters (e.g. enhances
or inhibits) HT
risk gene expression or HT susceptibility gene polypeptide activity as
described herein. For
instance, a polypeptide, protein (e.g. a receptor), an agent that alters an HT
risk gene
expression, or an HT susceptibility polypeptide binding agent or binding
partner, fragment,
fusion protein or prodrug thereof, or a nucleotide or nucleic acid construct
(vector)
comprising a nucleotide of the present invention, or an agent that alters HT
susceptibility gene
polypeptide activity, can be formulated with a physiologically acceptable
carrier or excipient
to prepare a pharmaceutical composition. The carrier and composition can be
sterile. The
formulation should suit the mode of administration.
In a preferred embodiment pharmaceutical compositions comprise an agent or
agents
reversing, at least partially, HT associated changes in biological networks
and/or metabolic
pathways related to the HT associated genes of this invention (Table 6).
Suitable pharmaceutically acceptable carriers include but are not limited to
water, salt
solutions (e.g. NaC1), saline, buffered saline, alcohols, glycerol, ethanol,
gum arabic,
vegetable oils, benzyl alcohols, polyethylene glycols, gelatin, carbohydrates
such as lactose,
amylose or starch, dextrose, magnesium stearate, talc, silicic acid, viscous
paraffin, perfume
oil, fatty acid esters, hydroxymethylcellulose, polyvinyl pyrolidone, etc., as
well as
combinations thereof. The pharmaceutical preparations can, if desired, be
mixed with
auxiliary agents, e.g. lubricants, preservatives, stabilizers, wetting agents,
emulsifiers, salts for
influencing osmotic pressure, buffers, coloring, flavoring and/or aromatic
substances and the
like that do not deleteriously react with the active agents.
The composition, if desired, can also contain minor amounts of wetting or
emulsifying agents,
or pH buffering agents. The composition can be a liquid solution, suspension,
emulsion,
tablet, pill, capsule, sustained release formulation, or powder. The
composition can be
formulated as a suppository, with traditional binders and carriers such as
triglycerides. Oral
formulation can include standard carriers such as pharmaceutical grades of
mannitol, lactose,
starch, magnesium stearate, polyvinyl pyrolidone, sodium saccharine,
cellulose, magnesium
carbonate, etc.
Methods of introduction of these compositions include, but are not limited to,
intradermal,
intramuscular, intraperitoneal, intraocular, intravenous, subcutaneous,
topical, oral and
intranasal. Other suitable methods of introduction can also include gene
therapy (as described
below), rechargeable or biodegradable devices, particle acceleration devices
("gene guns")
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and slow release polymeric devices. The pharmaceutical compositions of this
invention can
also be administered as part of a combinatorial therapy with other agents.
The composition can be formulated in accordance with the routine procedures as
a
pharmaceutical composition adapted for administration to human beings. For
example,
compositions for intravenous administration are typically solutions in sterile
isotonic aqueous
buffer. Where necessary, the composition may also include a solubilizing agent
and a local
anesthetic to ease pain at the site of the injection. Generally, the
ingredients are supplied
either separately or mixed together in unit dosage form, for example, as a dry
lyophilized
powder or water free concentrate in a hermetically sealed container such as an
ampule or
sachette indicating the quantity of active agent. Where the composition is to
be administered
by infusion, it can be dispensed with an infusion bottle containing sterile
pharmaceutical
grade water, saline or dextrose/water. Where the composition is administered
by injection, an
ampule of sterile water for injection or saline can be provided so that the
ingredients may be
mixed prior to administration.
For topical application, nonsprayable forms, viscous to semi-solid or solid
forms comprising a
carrier compatible with topical application and having a dynamic viscosity
preferably greater
than water, can be employed. Suitable formulations include but are not limited
to solutions,
suspensions, emulsions, creams, ointments, powders, enemas, lotions, sols,
liniments, salves,
aerosols, etc., which are, if desired, sterilized or mixed with auxiliary
agents, e.g.
preservatives, stabilizers, wetting agents, buffers or salts for influencing
osmotic pressure, etc.
The agent may be incorporated into a cosmetic formulation. For topical
application, sprayable
aerosol preparations wherein the active ingredient, preferably in combination
with a solid or
liquid inert carrier material, is packaged in a squeeze bottle or in admixture
with a pressurized
volatile, normally gaseous propellant, e.g. pressurized air, are also
suitable.
Agents described herein can be formulated as neutral or salt forms.
Pharmaceutically
acceptable salts include those formed with free amino groups such as those
derived from
hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those
formed with free
carboxyl groups such as those derived from sodium, potassium, ammonium,
calcium, ferric
hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine,
procaine, etc.
The agents are administered in a therapeutically effective amount. The amount
of agents
which will be therapeutically effective in the treatment of a particular
disorder or condition
will depend on the nature of the disorder or condition, and can be determined
by standard
clinical techniques. In addition, in vitro or in vivo assays may optionally be
employed to help
identify optimal dosage ranges. The precise dose to be employed in the
formulation will also
depend on the route of administration, and the severity of the symptoms of HT,
and should be
decided according to the judgment of a practitioner and each patient's
circumstances.
Effective doses may be extrapolated from dose-response curves derived from in
vitro or
animal model test systems.
Methods of Therapy
The present invention encompasses methods of treatment (prophylactic and/or
therapeutic) for
HT or a susceptibility to HT, such as individuals in the target populations
described herein,
using an HT therapeutic agent. An "HT therapeutic agent" is an agent that
alters (e.g.
enhances or inhibits) HT risk affecting polypeptide (enzymatic activity or
quantity) and/or an
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23
HT risk gene expression, as described herein (e.g. an agonist or antagonist).
HT therapeutic
agents can alter an HT susceptibility polypeptide activity or nucleic acid
expression by a
variety of means, for example, by providing additional HT susceptibility
polypeptide or by
upregulating the transcription or translation of the HT risk gene; by altering
posttranslational
processing of the HT susceptibility polypeptide; by altering transcription of
an HT risk gene
splicing variants; or by interfering with an HT susceptibility polypeptide
activity (e.g. by
binding to an HT susceptibility polypeptide); or by downregulating the
transcription or
translation of the HT risk gene, or by inhibiting or enhancing the elimination
of an HT
susceptibility polypeptide.
In particular, the invention relates to methods of treatment for HT or
susceptibility to HT (for
example, for individuals in an at-risk population such as those described
herein); as well as to
methods of treatment for manifestations and subtypes of HT.
Representative HT therapeutic agents include the following:
nucleic acids or fragments or derivatives thereof described herein,
particularly nucleotides
encoding the polypeptides described herein and vectors comprising such nucleic
acids (e.g. a
gene, cDNA, and/or mRNA, double-stranded interfering RNA, a nucleic acid
encoding an HT
susceptibility polypeptide or active fragment or derivative thereof, or an
oligonucleotide; for
examples see tables 2 through 8;
other polypeptides (e.g. HT susceptibility receptors); HT susceptibility
polypeptide binding
agents; peptidomimetics; fusion proteins or prodrugs thereof, antibodies (e.g.
an antibody to a
mutant HT susceptibility polypeptide, or an antibody to a non-mutant HT
susceptibility
polypeptide, or an antibody to a particular splicing variant encoded by an HT
risk gene, as
described above); ribozymes; other small molecules;
and other agents that alter (e.g. inhibit or antagonize) an HT risk gene
expression or
polypeptide activity or that regulate transcription of an HT risk gene
splicing variants (e.g.
agents that affect which splicing variants are expressed, or that affect the
amount of each
splicing variant that is expressed);
and other reagents that alter (e.g. induce or agonize) an HT risk gene
expression or
polypeptide activity or that regulate transcription of an HT risk gene
splicing variants (e.g.
agents that affect which splicing variants are expressed or that affect the
amount of each
splicing variant that is expressed).
More than one HT therapeutic agent can be used concurrently, if desired.
The HT therapeutic agent that is a nucleic acid is used in the treatment of
HT. The term,
"treatment" as used herein, refers not only to ameliorating symptoms
associated with the
disease, but also preventing or delaying the onset of the disease and also
lessening the severity
or frequency of symptoms of the disease, preventing or delaying the occurrence
of a second
episode of the disease or condition; and/or also lessening the severity or
frequency of
symptoms of the disease or condition. In the case of atherosclerosis,
"treatment" also refers to
a minimization or reversal of the development of plaques. The therapy is
designed to alter
(e.g. inhibit or enhance), replace or supplement activity of an HT polypeptide
in an individual.
For example, an HT therapeutic agent can be administered in order to
upregulate or increase
the expression or availability of an HT risk gene or of specific splicing
variants of an HT
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24
susceptibility, gene or, conversely, to downregulate or decrease the
expression or availability
of an HT risk gene or specific splicing variants of an HT risk gene.
Upregulation or increasing
expression or availability of a native HT risk gene or of a particular
splicing variant could
interfere with or compensate for the expression or activity of a defective
gene or another
splicing variant; downregulation or decreasing expression or availability of a
native HT risk
gene or of a particular splicing variant could minimize the expression or
activity of a defective
gene or the particular splicing variant and thereby minimize the impact of the
defective gene
or the particular splicing variant.
The HT therapeutic agent(s) are administered in a therapeutically effective
amount (i.e. an
amount that is sufficient to treat the disease, e.g. by ameliorating symptoms
associated with
the disease, preventing or delaying the onset of the disease, and/or also
lessening the severity
or frequency of symptoms of the disease). The amount which will be
therapeutically effective
in the treatment of a particular individual's disorder or condition will
depend on the symptoms
and severity of the disease and can be determined by standard clinical
techniques. In addition,
in vitro or in vivo assays may optionally be employed to help identify optimal
dosage ranges.
The precise dose to be employed in the formulation will also depend on the
route of
administration and the severity of the disease or disorder, and should be
decided according to
the judgment of a practitioner and each patient's circumstances. Effective
doses may be
extrapolated from dose-response curves derived from in vitro or animal model
test systems.
In one embodiment, a nucleic acid of the invention (e.g. a nucleic acid
encoding an HT
susceptibility polypeptide set forth in table 6 optionally comprising at least
one polymorphism
shown in tables 2 through 11; or another nucleic acid that encodes an HT
susceptibility
polypeptide or a splicing variant, derivative or fragment thereof, can be
used, either alone or
in a pharmaceutical composition as described above. For example, an HT risk
gene or a
cDNA encoding an HT susceptibility polypeptide, either by itself or included
within a vector,
can be introduced into cells (either in vitro or in vivo) such that the cells
produce native HT
susceptibility polypeptide. If necessary, cells that have been transformed
with the gene or
cDNA or a vector comprising the gene or cDNA can be introduced (or re-
introduced) into an
individual affected with the disease. Thus, cells that in nature lack a native
HT risk gene
expression and activity, or have mutant HT risk gene expression and activity,
or have
expression of a disease-associated HT risk gene splicing variant, can be
engineered to express
an HT susceptibility polypeptide or an active fragment of an HT susceptibility
polypeptide (or
a different variant of an HT susceptibility polypeptide). In a preferred
embodiment, nucleic
acid encoding an HT susceptibility polypeptide, or an active fragment or
derivative thereof,
can be introduced into an expression vector, such as a viral vector, and the
vector can be
introduced into appropriate cells in an animal. Other gene transfer systems
including viral and
nonviral transfer systems can be used. Alternatively, nonviral gene transfer
methods such as
calcium phosphate coprecipitation, mechanical techniques (e.g.
microinjection); membrane
fusion-mediated transfer via liposomes; or direct DNA uptake, can also be
used.
Alternatively, in another embodiment of the invention, a nucleic acid of the
invention; a
nucleic acid complementary to a nucleic acid of the invention; or a portion of
such a nucleic
acid (e.g. an oligonucleotide as described below) can be used in "antisense"
therapy in which
a nucleic acid (e.g. an oligonucleotide) that specifically hybridizes to the
mRNA and/or
genomic DNA of an HT risk gene is administered or generated in situ. The
antisense nucleic
acid that specifically hybridizes to the mRNA and/or DNA inhibits expression
of the HT
susceptibility polypeptide, e.g. by inhibiting translation and/or
transcription. Binding of the
antisense nucleic acid can be by conventional base pair complementarity, or
for example in
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the case of binding to DNA duplexes, through specific interaction in the major
groove of the
double helix.
An antisense construct of the present invention can be delivered, for example,
as an
5 expression plasmid as described above. When the plasmid is transcribed in
the cell it produces
RNA that is complementary to a portion of the mRNA and/or DNA which encodes an
HT
susceptibility polypeptide. Alternatively, the antisense construct can be an
oligonucleotide
probe that is generated ex vivo and introduced into cells; it then inhibits
expression by
hybridizing with the mRNA and/or genomic DNA of an HT risk gene. In one
embodiment,
10 the oligonucleotide probes are modified oligonucleotides that are resistant
to endogenous
nucleases, e.g. exonucleases and/or endonucleases, thereby rendering them
stable in vivo.
Exemplary nucleic acid molecules for use as antisense oligonucleotides are
phosphoramidate,
phosphothioate and methylphosphonate analogs of DNA. Additionally, general
approaches to
constructing oligomers useful in antisense therapy are also described by van
der Krol AR et
15 al, 1988 and Stein CA and Cohen JS, 1988. With respect to antisense DNA,
oligodeoxyribonucleotides derived from the translation initiation site, e.g.
between the -10
and +10 regions of an HT risk gene sequence, are preferred.
To perform antisense therapy, oligonucleotides (mRNA, cDNA or DNA) are
designed that are
20 complementary to the mRNA encoding an HT susceptibility polypeptide. The
antisense
oligonucleotides bind to HT susceptibility mRNA transcripts and prevent
translation.
Absolute complementarity, although preferred, is not required. A sequence
"complementary"
to a portion of an RNA, as referred to herein, indicates that a sequence has
sufficient
complementarity to be able to hybridize with the RNA forming a stable duplex;
in the case of
25 double-stranded antisense nucleic acids, a single strand of the duplex DNA
may thus be
tested, or triplex formation may be assayed. The ability to hybridize will
depend on both the
degree of complementarity and the length of the antisense nucleic acid, as
described in detail
above. Generally, the longer the hybridizing nucleic acid, the more base
mismatches with an
RNA it may contain and still form a stable duplex (or triplex, as the case may
be). One skilled
in the art can ascertain a tolerable degree of mismatch by use of standard
procedures.
The oligonucleotides used in antisense therapy can be DNA, RNA, or chimeric
mixtures or
derivatives or modified versions thereof, single-stranded or double-stranded.
The
oligonucleotides can be modified at the base moiety, sugar moiety, or
phosphate backbone,
for example, to improve stability of the molecule, hybridization, etc. The
oligonucleotides can
include other appended groups such as peptides (e.g. for targeting host cell
receptors in vivo),
or agents facilitating transport across the cell membrane (Letsinger RL et al,
1989; Lemaitre
M et al, 1987) or the blood-brain barrier (Jaeger LB and Banks WA, 2004), or
hybridization-
triggered cleavage agents (van der Krol AR et al, 1988) or intercalating
agents. (Zon G,
1988). To this end, the oligonucleotide may be conjugated to another molecule
(e.g. a peptide,
hybridization triggered cross-linking agent, transport agent, hybridization-
triggered cleavage
agent).
The antisense molecules are delivered to cells that express an HT risk gene in
vivo. A number
of methods can be used for delivering antisense DNA or RNA to cells; e.g.
antisense
molecules can be injected directly into the tissue site, or modified antisense
molecules,
designed to target the desired cells (e.g. antisense linked to peptides or
antibodies that
specifically bind receptors or antigens expressed on the target cell surface)
can be
administered systematically. Alternatively, in a preferred embodiment, a
recombinant DNA
construct is utilized in which the antisense oligonucleotide is placed under
the control of a
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26
strong promoter (e.g. pol III or pol II). The use of such a construct to
transfect target cells in
the patient results in the transcription of sufficient amounts of single
stranded RNAs that will
form complementary base pairs with the endogenous HT risk gene transcripts and
thereby
prevent translation of the HT susceptibility mRNA. For example, a vector can
be introduced
in vivo such that it is taken up by a cell and directs the transcription of an
antisense RNA.
Such a vector can remain episomal or become chromosomally integrated, as long
as it can be
transcribed to produce the desired antisense RNA. Such vectors can be
constructed by
recombinant DNA technology methods standard in the art and described above.
For example,
a plasmid, cosmid, YAC or viral vector can be used to prepare the recombinant
DNA
construct that can be introduced directly into the tissue site. Alternatively,
viral vectors can be
used which selectively infect the desired tissue, in which case administration
may be
accomplished by another route (e.g. systemically).
An endogenous HT risk gene expression can be also reduced by inactivating or
"knocking
out" an HT risk gene or its promoter using targeted homologous recombination
(Smithies 0 et
al, 1985; Thomas KR and Capecchi MR, 1987; Thompson S et al, 1989). For
example, a
mutant, non-functional HT risk gene (or a completely unrelated DNA sequence)
flanked by
DNA homologous to the endogenous HT risk gene (either the coding regions or
regulatory
regions of an HT risk gene) can be used, with or without a selectable marker
and/or a negative
selectable marker, to transfect cells that express an HT risk gene in vivo.
Insertion of the
DNA construct, via targeted homologous recombination, results in inactivation
of the HT risk
gene. The recombinant DNA constructs can be directly administered or targeted
to the
required site in vivo using appropriate vectors, as described above.
Alternatively, expression
of nonmutant HT risk gene can be increased using a similar method: targeted
homologous
recombination can be used to insert a DNA construct comprising a nonmutant,
functional HT
risk gene (e.g. any gene shown in table 6 that may optionally comprise at
least one
polymorphism shown in tables 2 through 11), or a portion thereof, in place of
a mutant HT
risk gene in the cell as described above. In another embodiment, targeted
homologous
recombination can be used to insert a DNA construct comprising a nucleic acid
that encodes
an HT susceptibility polypeptide variant that differs from that present in the
cell.
Alternatively, an endogenous HT risk gene expression can be reduced by
targeting
deoxyribonucleotide sequences complementary to the regulatory region of an HT
risk gene
(i.e. the HT risk gene promoter and/or enhancers) to form triple helical
structures that prevent
transcription of an HT risk gene in target cells in the body (Helene C, 1991;
Helene C et al,
1992; Maher LJ, 1992). Likewise, the antisense constructs described herein can
be used in the
manipulation of tissue, by antagonizing the normal biological activity of one
of the HT
proteins, e.g. tissue differentiation both in vivo and for ex vivo tissue
cultures. Furthermore,
the anti-sense techniques (e.g. microinjection of antisense molecules, or
transfection with
plasmids whose transcripts are anti-sense with regard to an HT mRNA or gene
sequence) can
be used to investigate the role of an HT risk gene in developmental events, as
well as the
normal cellular function of an HT risk gene in adult tissue. Such techniques
can be utilized in
cell culture, but can also be used in the creation of transgenic animals.
In yet another embodiment of the invention, other HT therapeutic agents as
described herein
can also be used in the treatment or prevention of HT. The therapeutic agents
can be delivered
in a composition, as described above, or by themshelves. They can be
administered
systemically, or can be targeted to a particular tissue. The therapeutic
agents can be produced
by a variety of means including chemical synthesis; recombinant production; in
vivo
production, e.g. a transgenic animal (Meade H et al, 1990) and can be isolated
using standard
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27
means such as those described herein.
A combination of any of the above methods of treatment (e.g. administration of
non-mutant
HT susceptibility polypeptide in conjunction with antisense therapy targeting
mutant HT
susceptibility mRNA; administration of a first splicing variant encoded by an
HT risk gene in
conjunction with antisense therapy targeting a second splicing encoded by an
HT risk gene),
can also be used.
The invention will be further described by the following nonlimiting examples.
The teachings
of all publications cited herein are incorporated herein by reference in their
entirety.
EXPERIMENTAL SECTION
East Finnish HT Patients and Phenotype Characterization
The subjects were participants of the Kuopio Ischaemic Heart Disease Risk
Factor Study
(KIHD), which is an ongoing prospective population-based study designed to
investigate risk
factors for chronic diseases, including HT and CVD, in middle-aged men
(Salonen JT 1988,
Salonen JT et al 1998, 1999, Tuomainen T-P et al 1999). The study population
was a random
age-stratified sample of men living in Eastern Finland who were 42, 48, 54 or
60 years old at
baseline examinations in 1984-1989. A total of 2682 men were examined during
1984-89.
The male cohort was complemented by a random population sample of 920 women
first
examined during 1998-2001, at the time of the 11-year follow up of the male
cohort. The
recruitment and examination of the subjects has been described previously in
detail (Salonen
JT, 1988). The University of Kuopio Research Ethics Committee approved the
study. All
participants gave their written informed consent.
The analyses are based on logistic modeling in a case-control set of 81 cases
with HT (SBP
140 mmHg or more or DBP 90 mmHg or more or antihypertensive medication) and HT
in
either sibling or parent, and 82 controls who had neither HT nor family
history of HT, both
from the KIHD cohort. Three of the subjects (two cases, one control) were
women, 160 were
men. Thirty-eight of the 81 cases had antihypertensive medication at the time
of BP
measurements in the KIHD baseline examination.
HT was defined as either systolic BP (SBP) _140 mmHg or diastolic BP (DBP) _90
mmHg or
antihypertensive medication. Both BPs were measured in the morning by a nurse
with a
random-zero mercury sphygmomanometer. The measuring protocol included three
measurements in supine, one in standing and two in sitting position with 5-
minutes intervals.
The mean of all six measurements were used as SBP and DBP (Salonen JT et al,
1998). The
family history of HT was defined positive, if either father, the mother or a
sibling of the study
subject had reported a history or prevalent hypertension.
50
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28
Table 1. Selected characteristics of the cases and controls
Hypertensive cases (n=81) Normotensive controls (n=82)
Mean Min Max Mean Min Max
Age (years) 54.6 42.1 71.9 54.6 42.2 61.1
Cigarettes/day 5.3 0 40 7.4 0 40
S-Cholesterol (-vi,) 6.2 3.8 9.1 6.0 3.2 8.7
S-HIDL-Chol (mmovp 1.21 0.82 2.15 1.34 0.76 2.77
B-Glucose (mmovi,> 5.13 3.3 12.6 4.55 3.5 5.9
S-Insulin (U/L) 14.7 4.7 59.6 9.33 1.7 22.5
Mean SBP (mmHg) 140.0 110.0 182.33 124.5 99.0 148.33
Mean DBP (mmHg) 92.1 63.3 122.3 81.3 66.0 94.3
In table 1 selected characteristics of the cases and controls are summarized.
Age and tobacco
smoking were recorded on a self-administered questionnaire checked by an
interviewer.
Fasting blood glucose was measured using a glucose dehydrogenase method after
precipitation of proteins by trichloroacetic acid. Serum insulin was
determined with a Novo
Biolabs radioimmunoassay kit (Novo Nordisk). HDL fractions were separated from
fresh
serum by combined ultracentrifugation and precipitation. The cholesterol
contents of
lipoprotein fractions and serum triglycerides were measured enzymatically.
Fibrinogen was
measured based on the clotting of diluted plasma with excess thrombin.
Adulthood socioeconomical status (SES) is an index comprised of measures of
education,
occupation, income and material living conditions. The scale is inverse, low
score
corresponding to high SES. These data have been collected by a self
administered
questionnaire.
Serum ferritin was assessed with a commercial double antibody radioimmunoassay
(Amersham International, Amersham, UK). Lipoproteins, including high density
lipoprotein
(HDL) and low density lipoprotein (LDL), were separated from fresh serum
samples by
ultracentrifugation followed by direct very low density lipoprotein (VLDL)
removal and LDL
precipitation (Salonen et al 1991). Cholesterol concentration was then
determined
enzymically. Serum C-reactive protein was measured by a commercial high-
sensitive
immunometric assay (Immulite High Sensitivity CR Assay, DPC, Los Angeles).
Genomic DNA isolation and quality testing
High molecular weight genomic DNA samples were extracted from frozen venous
whole
blood using standard methods, and dissolved in standard TE buffer. The
quantity and purity of
each DNA sample was evaluated by measuring the absorbance at 260 and 280 nm
and
integrity of isolated DNA samples was evaluated with 0.9% agarose gel
electrophoresis and
Ethidiumbromide staining. A sample was qualified for genome wide scan (GWS)
analysis if
the A260/A280 ratio was _1.7 and the average size of isolated DNA was over 20
kb in
agarose gel electrophoresis. Before GWS, analysis samples were diluted to a
concentration of
50 ng/ l in reduced EDTA TE buffer (TEKnova).
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29
Genome-Wide Scan
Genotyping of SNP markers was performed using the technology access version of
Affymetrix GeneChip human mapping 100k system. The assay consisted of two
arrays, Xba
and Hind, which were used to genotype over 126,000 SNP markers from each DNA
sample.
The assays were performed according to the instructions provided by the
manufacturer. A
total of 250 ng of genomic DNA was used for each individual assay. The DNA
sample was
digested with either Xba I or Hind III enzyme (New England Biolabs, NEB) in
the mixture of
NE Buffer 2 (1 x; NEB), bovine serum albumin (1 x; NEB), and either Xba I or
Hind III (0,5
U/ l; NEB) for 2h at +37 C followed by enzyme inactivation for 20 min at +70
C. Xba I or
Hind III adapters were then ligated to the digested DNA samples by adding Xba
or Hind III
adapter (0,25 M, Affymetrix), T4 DNA ligase buffer (1 x; NEB), and T4 DNA
ligase (250
U; NEB). Ligation reactions were allowed to proceed for 2h at +16 C followed
by 20 min
incubation at +70 C. Each ligated DNA sample was diluted with 75 l of
molecular biology-
grade water (BioWhittaker Molecular Applications/Cambrex).
Diluted ligated DNA samples were subjected to four identical 100 l volume
polymerase
chain reactions (PCR) by implementing a 10 l aliquot of DNA sample with Pfx
Amplification Buffer (1 x; Invitrogen), PCR Enhancer (1 x; Invitrogen), MgSO4
(1 mM;
Invitrogen), dNTP (300 M each; Takara), PCR primer (1 M; Affymetrix), and
Pfx
Polymerase (0,05 U/ l; Invitrogen). The PCR was allowed to proceed for 3 min
at +94 C,
followed by 30 cycles of 15 sec at +94 C, 30 sec at +60 C, 60 sec at +68 C,
and finally for
the final extension for 7 min at +68 C. The performance of the PCR was checked
by standard
2% agarose gel electrophoresis in 1 x TBE buffer for lh at 120V.
PCR products were purified according to the Affymetrix manual using MinElute
96 UF PCR
Purification kit (Qiagen) by combining all four PCR products of an individual
sample into the
same purification reaction. The purified PCR products were eluted with 40 l
of EB buffer
(Qiagen), and the yields of the products were measured at the absorbance 260
nm. A total of
40 g of each PCR product was then subjected to fragmentation reaction
consisting of 0.2
U/ l fragmentation reagent (Affymetrix) in lx Fragmentation Buffer. The
fragmentation
reaction was allowed to proceed for 35 min at +37 C followed by 15 min
incubation at +95 C
for enzyme inactivation. Completeness of fragmentation was checked by running
an aliquot of
each fragmented PCR product in 4% agarose 1 x TBE (BMA Reliant precast) for 30-
45 min
at 120V.
Fragmented PCR products were then labeled using 1 x Terminal Deoxinucleotidyl
Transferase (TdT) buffer (Affymetrix), GeneChip DNA Labeling Reagent (0.214
mM;
Affymetrix), and TdT (1,5 U/ l; Affymetrix) for 2h at +37 C followed by 15 min
at +95 C.
Labeled DNA samples were combined with hybridization buffer consisting of
0.056 M MES
solution (Sigma), 5% DMSO (Sigma), 2.5 x Denhardt's solution (Sigma), 5.77 mM
EDTA
(Ambion), 0.115 mg/ml Herring Sperm DNA (Promega), 1 x Oligonucleotide Control
reagent
(Affymetrix), 11.5 g/ml Human Cot-1 (Invitrogen), 0.0115% Tween-20 (Pierce),
and 2.69 M
Tetramethyl Ammonium Chloride (Sigma). DNA-hybridization buffer mix was
denatured for
10 min at +95 C, cooled on ice for 10 sec and incubated for 2 min at +48 C
prior to
hybridization onto corresponding Xba or Hind GeneChip array. Hybridization
was
completed at +48 C for 16-18 h at 60 rpm in an Affymetrix GeneChip
Hybridization Oven.
Following hybridization, the arrays were stained and washed in GeneChip
Fluidics Station
450 according to fluidics station protocol Mapping10Kv1_450 as recommended by
the
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manufacturer. Arrays were scanned with GeneChip 3000 Scanner and the genotype
calls for
each of the SNP markers on the array were generated using Affymetrix
Genotyping Tools
(GTT) software. The confidence score in SNP calling algorithm was adjusted to
0.20.
5
Initial SNP selection for statistical analysis
Prior to the statistical analysis, SNP quality was assessed on the basis of
three values: the call
rate (CR), minor allele frequency (MAF), and Hardy-Weinberg equilibrium (H-W).
The CR is
10 the proportion of samples genotyped successfully. It does not take into
account whether the
genotypes are correct or not. The call rate was calculated as: CR = number of
samples with
successful genotype call / total number of samples. The MAF is the frequency
of the allele
that is less frequent in the study sample. MAF was calculated as: MAF = min(p,
q), where p
is frequency of the SNP allele 'A' and q is frequency of the SNP allele 'B';
p=(number of
15 samples with "AA"-genotype + 0.5*number of samples with "AB"-genotype) /
total number
of samples with successful genotype call; q = 1- p. SNPs that are homozygous
(MAF=O)
cannot be used in genetic analysis and were thus discarded. H-W equilibrium is
tested for
controls. The test is based on the standard Chi-square test of goodness of
fit. The observed
genotype distribution is compared with the expected genotype distribution
under H-W
20 equilibrium. For two alleles this distribution is p2, 2pq, and q2 for
genotypes 'AA', 'AB' and
'BB', respectively. If the SNP is not in H-W equilibrium it can be due to
genotyping error or
some unknown population dynamics (e.g. random drift, selection).
Only the SNPs that had CR > 50%, MAF > 1%, and were in H-W equilibrium (Chi-
square
25 test statistic < 23.93) were used in the statistical analysis. A total of
107,895 SNPs fulfilled
the above criteria and were included in the statistical analysis.
Statistical Methods
30 Single SNP analysis
Differences in allele distributions between cases and controls were screened
for all 107,895
SNPs. The screening was carried out using the standard Chi-square independence
test with 1
df (allele distribution, 2x2 table). SNPs that gave a P-value less than 0.005
(Chi-square
distribution with 1 df of 7.88 or more) were considered as statistically
significant and selected
for further analysis. There were 529 SNPs that fulfilled this criterium.
Haplotype analysis
The data set was analyzed with a haplotype pattern mining algorithm either
with HPM-G
software (Sevon P et al, 2004) or with HPM software (Toivonen HT et al, 2000).
For HPM
software, genotypes must be phase known to determine which alleles come from
the mother
and which from the father. Without family data, phases must be estimated based
on
population data. We used HaploRec-program (Eronen L et al, 2004) to estimate
the phases.
HPM-G and HPM are very fast and can handle a large number of SNPs in a single
run
The difference between HPM and HPM-G is that HPM-G can use phase unknown
genotypic
data and HPM uses phase known (or estimated by HaploRec or similar program)
data. HPM-
G fmds all haplotype patterns that fit the genotype configuration. For phase-
known data HPM
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finds all haplotype patterns that are in concordance with the phase
configuration. The length
of the haplotype patterns can vary. As an example, if there are four SNPs and
an individual
has alleles A T for SNP1, C C for SNP2, C G for SNP3, and A C for SNP4, then
HPM-G
considers haplotype patterns (of length 4 SNPs): ACCA, TCGC, TCCA, ACGC, ACGA,
TCCC, TCGA, ACCC. HPM considers only haplotype patterns that are in
concordance with
the estimated phase (done by HaploRec). If the estimated phase is ACGA (from
the
mother/father) and TCCC (from the father/mother) then HPM considers only two
patterns (of
length 4 SNPs): ACGA and TCCC.
A SNP is scored based on the number of times it is included in a haplotype
pattern that differs
between cases and controls (a threshold Chi-square value can be selected by
the user).
Significance of the score values is tested based on permutation tests.
Several parameters can be modified in the HPM-G and HPM programs including the
Chi-
square threshold value (-x), the maximum haplotype pattern length (-1), the
maximum number
of wildcards that can be included in a haplotype pattern (-w), and the number
of permutation
tests in order to estimate the P-value (-p). Wildcards allow gaps in
haplotypes. The HPM-G
program was run with the following parameter settings: haplotype analysis with
5 SNPs (-x9
-15 -wl p10000). HaploRec+ HPM was run with the following parameter settings:
haplotype analysis with 5 SNPs (-x9 -15 -wl p10000). HPM-G analysis was based
on the
order of the SNP given in dbSNP122 and HaploRec+HPM was based on the order of
the SNP
given in dbSNP123. Based on 10,000 replicates (-p10000) in the HPM-G analyses
570 SNPs
were significant at P-value less than 0.005 and 642 SNPs were significant in
the HPM
analysis.
Definition of terms used in the haplotype analysis results
The term "haplotype genomic region" or "haplotype region" refers to a genomic
region that
has been found significant in the haplotype analysis (HPM, HPMG or similar
statistical
method/program). The haplotype region is defined as 100Kbp up/downstream from
the
physical position of the first/last SNP that was included in the statistical
analysis (haplotype
analysis) and was found statistically significant. This region is given in
base pairs based on
the given genome build e.g. SNP physical position (base pair position)
according to NCBI
Human Genome Build 35.
The term "haplotype" as described herein, refers to any combination of alleles
e.g. A T C C
that is found in the given genetic markers e.g rs222151 1, rs4940595,
rs1522723, rs1395266.
A defined haplotype gives the name of the genetic markers (dbSNP rs-id for the
SNPs) and
the alleles. As it is recognized by those skilled in the art, the same
haplotype can be described
differently by determining alleles from different strands e.g. the haplotype
rs222151 1,
rs4940595, rs1522723, rs1395266 (A T C C) is the same as haplotype rs222151 1,
rs4940595,
rs1522723, rs1395266 (T A G G) in which the alleles are determined from the
other strand, or
haplotype rs222151 1, rs4940595, rs1522723, rs1395266 (T T C C), in which the
first allele is
determined from the other strand.
The haplotypes described herein, e.g. having markers such as those shown in
tables 3, 4, 5, 7
and 8, are found more frequently in individuals with HT than in individuals
without HT.
Therefore, these haplotypes have predictive value for detecting HT or a
susceptibility to HT in
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32
an individual. Therefore, detecting haplotypes can be accomplished by methods
known in the
art for detecting sequences at polymorphic sites.
It is understood that the HT associated at-risk alleles and at-risk haplotypes
described in this
invention may be associated with other "polymorphic sites" located in HT
associated genes of
this invention. These other HT associated polymorphic sites may be either
equally useful as
genetic markers or even more useful as causative variations explaining the
observed
association of at-risk alleles and at-risk haplotypes of this invention to HT.
Multivariate modeling
For modeling for hypertension as a binary outcome, the 734 strongest
predicting SNP markers
from the individual SNP analysis and 14 strongest haplotypes from the HPM
analysis were
tested for entry to the model. These were recoded as 0, if homozygote of the
major allele, 1, if
heterozygote and 2, if homozygote of the minor allele. A multivariate binary
logistic function
regression analysis was used to: a) Find the SNPs that were most predictive of
HT and b)
Construct a multivariate model that predicted HT the strongest. A forward step-
up model
construction was used with p-value to enter of 0.01 and p-value to exclude
from the model of
0.02. The predictivity of the models was estimated by two methods: the
Nagelkerke R square
and the reclassification of the subjects to cases and controls on the basis of
the logistic model
contructed. The predicted probability used as cut-off was 0.5. A data
reduction analysis was
carried out by step-down and step-up logistic modeling.
Multivariate least-squares linear regression modeling was used to identify the
SNP markers
that were most strongly associated with the mean systolic and diastolic blood
pressure as
quantitative traits. A forward step-up model construction was used with p-
value to enter of
0.001 and p-value to exclude from the model of 0.005.
The statistical software used was SPSS for Windows, version 11.5.
Results
In table 2 are summarized the characteristics of the SNP markers with the
strongest
association with HT in the individual marker analysis (n = 529). SNP
identification numbers
are according to NCBI dbSNP database build 124. Physical positions of SNP
markers are
according to NCBI Human Genome Build 35. Gene locus as reported by NCBI dbSNP
database build 124. SNP flanking sequence provided by Affymetrix "csv"
commercial access
Human Mapping 100K array annotation files.
In table 3 are summarized the characteristics of the haplotype genomic regions
with the
strongest association with HT in the HPM-G analysis with 5 SNPs. SNP
identification
numbers are according to NCBI dbSNP database build 124. Physical positions of
SNP
markers are according to NCBI Human Genome Build 35. Associated genes are
those genes
positioned within 100Kbp up/downstream from the physical position of the SNPs
bordering
the haplotype genomic region found using NCBI MapViewer, based on NCBI Human
Genome Build 35. SNP flanking sequence provided by Affymetrix "csv" commercial
access
Human Mapping 100K array annotation files.
In table 4 are summarized the characteristics of the haplotype genomic regions
with the
strongest association with HT in the HaploRec + HPM analysis with 5 SNPs. SNP
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33
identification numbers are according to NCBI dbSNP database build 124.
Physical positions
of SNP markers are according to NCBI Human Genome Build 35. Associated genes
are those
genes positioned within 100Kbp up/downstream from the physical position of the
SNPs
bordering the haplotype genomic region found using NCBI MapViewer, based on
NCBI
Human Genome Build 35. SNP flanking sequence provided by Affymetrix "csv"
commercial
access Human Mapping 100K array annotation files.
In table 5 are listed haplotype blocks with the strongest association with HT
based on
HaploRec + HPM analysis (n = 14). SNP identification numbers are according to
NCBI
dbSNP database build 124.
In table 6 are listed all genes found associated with HT according to point
wise and haplotype
analyses (n = 722). Names of genes are according to HUGO Gene Nomenclature
Committee
(HGNC).
In table 7 are listed the SNP-markers and haplotypes that best predicted risk
of familial HT in
a multivariate logistic model. SNP identification numbers are according to
NCBI dbSNP
database build 124. The 8-variable model predicts 91.4% of familial HT
correctly. The
statistics are based on 81 KIHD participants who were hypertensive in the KIHD
baseline
examination (SBP 140 mmHg or more or DBP 90 mmHg or more or antihypertensive
medication) and either sibling or parent had HT and 82 KIHD participants who
neither had
HT at KIHD baseline nor had family history of HT. The controls were matched
according to
age.
In table 8 are listed the SNP-markers, haplotypes and phenotypic data that
best predicted risk
of familial HT in a multivariate logistic model. SNP identification numbers
are according to
NCBI dbSNP database build 124. The 12-variable model, including two
haplotypes, five SNP
markers and two phenotypic variables, predicted 87.1% of familial HT
correctly. The
strongest loci pinpointed by the multivariate logistic models were SERPINs B3,
B4, B7 and
B11 and EPC1, OR1J4 and LOC401406, 439953, 441550 and 441551.
Table 9 presents a multivariate linear regression model of the strongest SNPs
predicting the
mean systolic and diastolic BP. Tables 10 and 11 show the means and standard
deviations of
the mean systolic (Table 10) and diastolic (Table 11) BP in the genotypes of
the strongest
SNP markers, which predicted BP the strongest in both the univariate single-
SNP, haplotype
and multivariate analyses. The rank order of markers is according to the
strength of
association with the diastolic BP. The strongest pinpointed genes concerning
BP as
quantitative trait were SERPINS B3, B7 and B11, A100A7, S100A6, FARS1, SPOCK3,
and
TLL 1.
Implications and Conclusions
We have found 1365 SNP markers associated with the risk of HT and/or blood
pressure in a
population-based set of familial cases and healthy controls without family
history. Of these,
529 were identified in the analysis of individual SNPs and 1080 in haplotype
pattern mining
or haplotype analysis. Of the 1365 markers, 244 predicted HT in both types of
statistical
analysis. We further identified SNP markers, which predict in a multivariate
logistic model
virtually fully the development of HT.
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34
The results of the point wise and haplotype analyses identified a total of 722
genes associated
with HT, of which 330 genes had at least one of the 1365 SNP markers
physically linked to
the gene.
Thus, we have discovered a total of 722 HT genes, in which any genetic markers
can be used
to predict HT, and thus these markers can be used as part of molecular
diagnostic tests of HT
predisposition. In addition, we have disclosed a set of 1365 SNP markers which
are predictive
of HT. The markers can also be used as part of pharmacogenetic tests
predicting the efficacy
and adverse reactions of antihypertensive agents and compounds. The genes
discovered are
also targets to new therapies of HT, such as drugs. Other therapies are
molecular, including
gene transfer. The new genes can also be used to develop and produce new
transgenic animals
for studies of antihypertensive agents and compounds.
While this invention has been particularly shown and described with reference
to preferred
embodiments thereof, it will be understood by those skilled in the art that
various changes in
form and details may be made therein without departing from the spirit and
scope of the
invention as defined by the appended claims.
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Table 2. SNP markers with the strongest association with HT
in the individual marker analysis (n = 529).
d I G I S I C IA IA I M I A I 0
b l e I e I h 11 11 I i I 1 I d
S n I q I r Il Il I n I 1 I d
N I e I u I o le le I o I e I s
P I I e I m Il Il I r 1 1 I
1 1 I n I o le le I I e I r
r I o I c I s I I I A I I a
s I c I e I o IA IB I 1 I X I t
I u I I m I I I 1 1 2 I i
1 I s I 1 I e I I I e I I o
D I I D I I I 1 1 1 I
I I I I I 1 e I I
------------------------------------------------------------------
rs1395266 SERPINBII 476 18 C T C 20.29 0.23
rs931850 None 1303 18 A G G 18.10 0.27
rs1386483 TPH2 470 12 A G A 17.88 2.61
rs1386485 TPH2 471 12 A C C 17.80 2.84
rs10506395 None 246 12 C T T 17.04 0.29
rs1410425 None 491 13 C T T 16.89 0.11
rs10500913 None 186 11 A G A 16.68 3.02
rs1935659 None 637 1 A G G 16.53 0.36
rs1318392 OR1J4 438 9 A G G 15.69 2.50
rs6428195 None 1030 1 C G C 15.39 0.39
rs7112382 None 1105 11 A G A 15.28 2.64
rs2469828 None 792 17 C T T 14.97 4.59
rs1386486 TPH2 472 12 C T T 14.87 2.46
rs10513404 NT008470 343 9 C T C 14.74 0.32
rs10515283 None 356 5 C T C 14.55 5.73
rs1884389 None 618 20 C T T 14.21 2.66
rs10494019 None 124 1 A T T 14.03 0.33
rs4756190 None 965 11 A G G 14.03 2.38
rs10517655 PDGFC 387 4 A G G 13.88 10.16
rs1157122 GABRAI 417 5 C T C 13.83 0.22
rs668498 FBX018 1058 10 C T T 13.74 2.60
rs473232 COL24A1 959 1 C T C 13.72 0.34
rs1986902 None 653 1 A G A 13.72 2.83
rs627777 L0C388458 1026 18 C T T 13.70 0.41
rs9315991 None 1294 13 G T T 13.68 4.55
rs9299552 PCDH15 1267 10 C T T 13.66 0.39
rs868299 None 1233 15 C T C 13.65 2.37
rs4845303 None 980 1 A T T 13.59 2.64
rs6935462 None 1082 6 A T A 13.51 6.29
rs7536312 None 1161 1 A G A 13.26 0.30
rs7521497 None 1159 1 C T T 13.25 2.86
rs270454 None 805 4 A G A 13.20 0.36
rs1374038 None 465 5 A C C 13.03 3.56
rs3213829 ANK3 869 10 G T G 12.94 2.30
rs10494628 None 128 1 C T C 12.86 0.43
rs2885625 L0C145497 839 14 A G G 12.82 0.29
rs2476847 SEC5L1 793 6 C T T 12.77 2.26
rs1521409 None 544 3 A G G 12.77 9.50
rs274460 None 810 12 A G G 12.72 0.35
rs10483354 STRN3 21 14 A C A 12.62 0.00
rs5957594 None 1010 X G T G 12.61 0.00
rs1394380 None 475 12 A G G 12.59 0.37
rs1391130 None 473 12 A G G 12.58 0.36
rs1842328 None 609 12 C T C 12.56 0.34
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rs387619 None 898 11 A G A 12.56 2.22
rs9291304 GABRB1 1259 4 A G A 12.53 0.06
rs10514437 WWOX 349 16 C T T 12.53 5.88
rs2209672 None 730 10 A G A 12.49 2.26
rs1912914 None 628 1 A G G 12.45 0.41
rs2416472 None 781 5 A G G 12.44 0.42
rs1837426 None 607 2 A G G 12.44 0.43
rs301748 USH2A 855 1 A G A 12.31 0.00
rs1335311 None 447 10 C G C 12.31 2.29
rs10499961 None 175 7 C T C 12.27 3.24
rs1866565 None 616 2 C T T 12.25 0.40
rs2060688 None 682 8 C T T 12.23 0.35
rs951573 UTRN 1328 6 A G G 12.20 2.22
rs572166 None 1008 18 A G G 12.17 2.32
rs10493787 COL24A1 122 1 C G C 12.17 0.32
rs10514689 None 352 3 A G G 12.15 2.86
rs10494663 None 134 1 A G A 12.14 0.29
rs1997454 None 656 2 A G G 12.12 0.31
rs10499538 DNAH11 171 7 A G A 12.00 0.06
rs474106 COL24A1 961 1 A G A 11.96 0.35
rs916853 None 1240 7 C T T 11.93 0.29
rs10492479 None 112 13 A G G 11.91 0.24
rs4680266 KCNAB1 955 3 C T C 11.83 2.18
rs4691246 None 956 4 C T C 11.82 2.36
rs9289965 KCNAB1 1257 3 C G C 11.82 2.17
rs10519989 MGC14798 397 15 A C A 11.82 0.07
rs10485822 SNPH 49 20 C G C 11.82 3.90
rs9298688 None 1266 9 C T T 11.81 0.39
rs892271 None 1236 12 A G G 11.81 0.11
rs29800 None 849 5 A C C 11.71 0.38
rs1598978 None 575 12 A G A 11.70 2.22
rs10494659 None 130 1 C T C 11.69 0.27
rs10515461 None 362 5 A G A 11.68 0.28
rs9283795 CMYA5 1248 5 C T T 11.67 3.39
rs503208 None 989 11 C G G 11.66 2.32
rs1578704 None 568 1 A G A 11.63 0.43
rs715732 None 1114 8 C G G 11.60 0.24
rs6469061 None 1038 8 C T T 11.53 0.00
rs1578705 None 569 1 A G G 11.51 0.45
rs716193 NPAS3 1117 14 G T T 11.49 2.28
rs9328130 None 1314 6 C T C 11.46 3.37
rs1487275 TPH2 531 12 A C C 11.45 2.20
rs10488914 None 76 4 A G A 11.42 0.11
rs1521770 None 545 8 C T C 11.42 0.44
rs6976996 CNTNAP2 1089 7 A G A 11.42 2.34
rs1173476 None 424 5 G T G 11.40 2.16
rs10486619 None 58 7 C T C 11.31 2.55
rs2105233 None 696 1 A G G 11.31 2.89
rs921382 None 1243 8 C G C 11.28 0.35
rs1452356 FLJ31810 513 9 C T C 11.25 2.16
rs956316 None 1336 7 C T C 11.25 0.43
rs7524749 SSBP3 1160 1 C T T 11.22 3.11
rs1913157 None 630 3 C G G 11.22 0.44
rs10499668 PKD1L1 172 7 A G G 11.21 2.13
rs1614336 None 582 5 A C A 11.18 2.17
rs477862 COL24A1 972 1 C T T 11.14 0.39
rs1912941 None 629 1 C T C 11.13 0.44
rs2198044 None 729 8 A G A 11.09 0.38
rs7156058 None 1113 14 A C A 11.09 2.90
rs10511192 L0C152225 314 3 C T T 11.09 2.57
rs10507107 EB-1 257 12 C G C 11.07 0.40
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rs10505140 None 238 8 A G A 11.04 0.35
rs6601146 None 1054 5 G T G 11.04 2.33
rs2861215 None 832 2 C T C 11.03 2.19
rs10482862 None 19 21 A G G 11.03 3.19
rs175741 None 592 X G T T 11.02 0.00
rs964888 None 1344 6 C T C 11.02 2.16
rs1649882 SP100 586 2 G T T 10.89 0.34
rs8047401 CDYL2 1221 16 C T T 10.84 0.41
rs2048506 None 674 4 C T T 10.84 2.12
rs1409367 None 490 1 C T C 10.79 0.00
rs8010717 L0C388001 1217 14 C T C 10.76 2.14
rs792762 None 1206 17 A C A 10.74 2.11
rs2175550 None 724 1 A G G 10.70 0.46
rs1391533 None 474 11 C T C 10.70 2.11
rs3856852 None 897 3 A G A 10.70 0.12
rs1160054 None 419 8 A G G 10.66 0.46
rs1882233 None 617 2 A T T 10.63 2.10
rs536617 FAT3 1001 11 C T C 10.63 2.09
rs10488849 None 73 4 C T C 10.62 2.49
rs666899 None 1055 11 A G G 10.61 0.39
rs1376089 None 468 4 A G A 10.60 13.87
rs475553 None 964 3 C T T 10.59 0.07
rs1408356 None 486 10 A G G 10.58 3.43
rs1113983 MTHFS 413 15 G T T 10.57 2.09
rs1512828 None 538 3 A C C 10.57 0.46
rs6746500 None 1062 2 C T T 10.56 2.33
rs1430692 None 506 2 A C C 10.55 3.09
rs10270433 None 11 7 A T A 10.51 0.24
rs10489134 None 81 1 C G C 10.47 6.23
rs1580964 None 570 12 C T T 10.47 2.08
rs2849597 PARK2 828 6 A G G 10.45 0.00
rs2279120 MATN2 751 8 C T T 10.44 5.27
rs9300909 None 1269 13 A G G 10.41 2.39
rs1281590 None 434 1 A G A 10.40 2.61
rs2417359 None 784 9 A G G 10.37 2.06
rs10484614 STX11 35 6 C T T 10.37 3.44
rs10491030 None 95 10 C T C 10.34 2.06
rs605627 None 1015 7 C T T 10.33 2.28
rs2222186 None 735 2 C T T 10.28 2.74
rs2121956 None 705 1 C T T 10.25 2.11
rs10495082 None 137 1 C T C 10.25 0.47
rs9288697 ACVR1 1256 2 A C A 10.25 0.29
rs9304252 None 1277 18 A T A 10.25 4.15
rs438418 None 936 5 A G G 10.24 0.29
rs1865290 None 615 18 A T T 10.23 4.18
rs1944404 RIT2 639 18 C T C 10.21 0.35
rs10504127 None 226 8 A G A 10.20 0.00
rs10504596 None 228 8 C T T 10.19 0.00
rs2372643 EB-1 768 12 A G A 10.19 2.07
rs10502283 L0C338661 202 11 C T T 10.18 0.32
rs9308066 None 1281 4 A G G 10.17 7.97
rs9321214 None 1306 6 C T C 10.15 0.40
rs10501504 None 199 11 C T C 10.15 2.61
rs10513802 DGKG 346 3 A T T 10.14 0.20
rs9290835 None 1258 3 A T A 10.13 2.21
rs9287120 None 1251 1 C G C 10.13 0.26
rs10515406 None 360 5 A G G 10.12 3.40
rs2429555 None 785 17 C G C 10.11 3.81
rs10494664 None 135 1 A C C 10.09 0.34
rs6961386 HIC 1085 7 C T T 10.07 0.26
rs1978503 None 649 18 A G G 10.06 2.85
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rs3847653 None 894 12 C G C 10.03 2.41
rs10502667 KIAA1328 209 18 C G G 10.02 0.38
rs10502582 None 206 18 A T T 10.01 2.05
rs730694 L0C401406 1149 7 C T C 10.00 2.18
rs10486935 None 59 7 A G A 10.00 0.31
rs9323707 L0C400234 1312 14 A G A 10.00 0.31
rs723107 None 1138 8 A G A 9.98 13.22
rs1281611 None 435 1 C T T 9.98 2.52
rs956274 None 1335 5 A C A 9.97 0.41
rs7777049 None 1190 7 A G A 9.96 2.13
rs10517654 PDGFC 386 4 G T T 9.96 5.09
rs10515622 L0C255187 364 5 G T G 9.96 2.65
rs10510664 L0C389105 311 3 C G G 9.95 3.44
rs2173802 NPAS3 723 14 A G A 9.95 0.34
rs1423485 ADAMTS12 503 5 A G A 9.95 5.08
rs4131804 RGS7 923 1 G T T 9.91 2.45
rs10508220 None 272 10 A G G 9.90 2.04
rs2192947 None 728 2 A G G 9.90 2.05
rs10492232 None 109 12 C T C 9.88 3.77
rs383096 None 892 5 A G A 9.86 13.08
rs701665 None 1098 6 C T C 9.85 2.30
rs256825 SGCD 799 5 C T T 9.83 2.18
rs6879659 None 1074 5 C T T 9.80 2.81
rs10496096 COMMD1 140 2 C G G 9.80 0.44
rs10508229 None 274 10 A G G 9.79 0.31
rs8089921 NET01 1223 18 C T C 9.79 2.05
rs7081811 CACNB2 1101 10 A G G 9.78 0.43
rs420350 None 929 6 A C A 9.77 2.05
rs8007568 NPAS3 1214 14 C G C 9.75 0.28
rs2381194 None 773 9 C T T 9.74 0.34
rs9741 PSD3 1350 8 C T C 9.72 0.43
rs1514471 L0C152225 540 3 A G G 9.71 2.40
rs10512853 None 339 5 C T C 9.71 0.08
rs895800 None 1237 1 A T A 9.70 0.48
rs542873 DAB1 1002 1 A G A 9.69 0.49
rs10515314 None 357 5 C T C 9.66 0.13
rs10508223 None 273 10 C T C 9.66 2.05
rs6990997 ZFPM2 1091 8 C T C 9.64 0.30
rs6832042 None 1071 4 A G G 9.63 0.45
rs2089918 None 694 1 A G A 9.60 2.87
rs2113030 None 700 5 A G G 9.59 0.13
rs10515942 AOX2 371 2 A G A 9.59 2.68
rs1827309 None 600 21 A G G 9.58 2.14
rs741283 MY03B 1154 2 G T T 9.58 0.29
rs10499728 None 174 7 A G A 9.58 0.46
rs1041778 None 18 21 A G G 9.57 2.18
rs1446255 None 510 9 C T T 9.57 0.23
rs10485601 TMC2 44 20 A G A 9.57 0.35
rs2077833 None 689 12 A G A 9.56 0.45
rs129752 FBLN1 437 22 A G A 9.56 0.08
rs293443 None 847 4 C T C 9.56 0.36
rs285790 None 829 8 C T C 9.55 0.08
rs10270360 L0C401406 10 7 A G G 9.55 2.04
rs10513702 None 345 3 A G G 9.50 2.03
rs10497952 ERBB4 159 2 C T T 9.49 2.29
rs10516740 None 378 4 A G G 9.49 0.00
rs1529647 None 550 7 A G G 9.48 2.95
rs1362828 None 458 3 C G C 9.48 2.06
rs6981960 None 1090 8 C T T 9.48 2.33
rs1992906 None 655 5 A G G 9.46 7.64
rs1928326 None 635 1 C T C 9.42 2.06
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rs607872 None 1017 7 C G C 9.42 2.19
rs953160 None 1330 7 A G G 9.42 0.46
rs360559 CRISP2 877 6 G T T 9.40 2.09
rs10488631 None 68 7 C T C 9.39 0.25
rs4719652 None 958 7 C T T 9.39 0.49
rs10520170 None 398 2 C T C 9.39 2.54
rs10511824 FLJ31810 323 9 A G A 9.38 2.92
rs10501243 None 190 11 A G A 9.38 0.21
rs8092610 None 1225 18 C T T 9.38 0.21
rs1513120 L0C152225 539 3 C T C 9.38 2.20
rs9316871 None 1298 13 C T C 9.37 2.36
rs10501242 None 189 11 A G A 9.37 0.21
rs10516731 None 377 4 A G A 9.37 0.00
rs3906713 None 904 7 A T A 9.36 4.31
rs997661 KIAA1328 1362 18 C T T 9.36 0.39
rs2089273 None 693 4 A T A 9.34 0.39
rs960791 L0C389938 1339 10 A T T 9.34 2.11
rs7176436 ADAM10 1122 15 A G G 9.34 0.38
rs10512731 L0C389285 338 5 C G C 9.33 2.55
rs4775086 ADAM10 970 15 C T T 9.31 0.48
rs4086865 None 913 11 C T T 9.29 0.17
rs10506726 None 253 12 A G A 9.29 0.29
rs10490758 None 93 2 C G G 9.29 0.43
rs10488777 None 71 11 C T C 9.29 3.92
rs4884068 None 984 13 C G G 9.28 2.15
rs802296 TCBA1 1220 6 A G A 9.28 2.17
rs572241 FAT3 1009 11 C T C 9.27 2.00
rs2168792 None 721 19 C G C 9.26 0.00
rs344924 L0C391046 872 1 A G G 9.25 2.74
rs1438048 PDE11A 508 2 A C A 9.25 2.78
rs716376 None 1118 5 A G G 9.24 2.53
rs10488747 L0C260340 69 11 C G C 9.22 0.45
rs10490757 None 92 2 C T C 9.21 0.44
rs3897770 None 901 12 A C A 9.21 2.29
rs1544774 None 554 5 G T T 9.20 0.21
rs10509035 None 293 10 G T G 9.19 0.49
rs6586445 None 1052 1 A C C 9.18 2.01
rs2091169 None 695 2 A G G 9.17 1.98
rs2164857 PDE11A 719 2 A C C 9.16 2.47
rs9308440 XM372814 1282 1 G T T 9.16 3.12
rs1550740 None 557 12 C T C 9.14 0.08
rs237112 None 767 6 C T T 9.14 2.46
rs2416863 NT008470 782 9 C T T 9.13 0.26
rs1331772 None 445 13 A G G 9.13 0.35
rs1363522 L0C255187 460 5 C T T 9.12 2.81
rs422621 None 930 21 C T C 9.12 0.48
rs6972578 OSBPL3 1087 7 C T C 9.09 2.19
rs10503506 None 220 8 C T C 9.09 0.36
rs747334 None 1156 10 A G G 9.08 1.97
rs342818 None 871 1 C T C 9.08 2.12
rs824848 None 1230 5 A G A 9.08 2.06
rs10483100 DGCR2 20 22 C T C 9.07 3.38
rs1548348 NUMA1 555 11 C T T 9.07 12.23
rs10502666 KIAA1328 208 18 C T C 9.07 0.40
rs10502671 KIAA1328 210 18 C T T 9.07 0.40
rs2514288 None 796 11 C T C 9.07 0.46
rs9320728 None 1305 6 C T C 9.06 0.45
rs10512709 None 337 5 A G A 9.06 2.02
rs10498935 C6orf157 167 6 A T T 9.06 2.96
rs10484484 None 33 6 A G G 9.05 2.73
rs1411270 L0C138882 492 9 C G G 9.05 0.45
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rs8010105 L0C388001 1216 14 A G A 9.04 1.99
rs9379628 None 1319 6 C T C 9.04 5.75
rs10505797 None 240 12 A G A 9.03 0.00
rs2152634 None 714 9 C T T 9.03 0.00
rs4766492 VPS29 968 12 A G A 9.03 1.96
rs7085103 MY03A 1102 10 C T C 9.03 2.02
rs2373717 None 771 11 A T T 9.01 2.12
rs997418 None 1361 10 A G A 9.01 0.50
rs951232 None 1327 4 C T T 9.01 0.48
rs927348 SLC35F1 1246 6 A G G 9.00 1.96
rs1497763 SCHIP1 533 3 C G G 8.99 4.83
rs10507130 DRIM 258 12 A G A 8.98 0.34
rs2871869 None 838 1 A G A 8.97 0.37
rs1370656 PDE11A 463 2 A C A 8.97 2.59
rs10512117 None 326 9 A T A 8.97 0.50
rs1346671 None 454 11 A T T 8.96 2.32
rs970604 DNAH11 1348 7 A G A 8.95 2.12
rs1959429 None 644 14 C T T 8.92 3.07
rs4814909 None 975 20 C T T 8.92 0.08
rs1405589 L0C402640 484 7 A G A 8.92 0.00
rs7069564 None 1100 10 C T T 8.92 0.31
rs891255 None 1235 2 C T T 8.91 2.04
rs4519041 NY-BR-1 943 10 A C A 8.91 12.03
rs10512241 None 329 9 C T T 8.90 2.00
rs987312 None 1354 10 A G A 8.89 2.12
rs2000112 None 660 9 C T T 8.87 0.43
rs721599 None 1136 1 C G G 8.86 2.03
rs948159 L0C390263 1322 11 C T C 8.86 0.39
rs10502774 None 213 18 G T G 8.86 3.19
rs717293 None 1120 16 C T T 8.85 0.50
rs2070513 None 686 21 G T T 8.83 2.34
rs10508731 MPP7 285 10 C T C 8.82 2.10
rs3169160 ARRDC4 864 15 A G A 8.81 3.38
rs3934674 None 906 4 A G A 8.79 0.36
rs2750452 None 811 6 C G C 8.79 2.11
rs10521300 None 406 16 C T T 8.78 11.87
rs10521301 None 407 16 G T T 8.78 11.87
rs305218 PRKCL2 858 1 C T T 8.78 11.87
rs724417 None 1141 12 G T G 8.78 3.85
rs9283603 None 1247 3 A G A 8.77 2.18
rs1181875 FLJ32825 427 1 A G G 8.77 0.28
rs4600228 None 950 11 A G A 8.77 2.10
rs1928322 None 634 1 A G A 8.76 2.01
rs3846211 None 893 3 A G A 8.76 2.01
rs9332453 None 1317 9 A G A 8.76 0.49
rs10511366 None 317 3 C T C 8.75 7.16
rs2177520 DNAH11 725 7 C G C 8.74 2.10
rs2319248 None 759 4 C T T 8.74 0.50
rs1893814 None 622 11 C T T 8.73 2.17
rs2892734 FARP1 841 13 A G G 8.72 1.96
rs6799641 None 1067 3 A T A 8.72 2.56
rs2017712 None 665 21 A G G 8.71 2.05
rs1489734 None 532 21 A G A 8.71 0.51
rs12654 L0C401255 432 6 C T C 8.70 0.30
rs1969025 L0C391858 645 5 A G G 8.70 0.47
rs382190 None 889 5 A G A 8.68 0.08
rs10511049 None 313 3 A G G 8.67 0.30
rs1581413 FLJ12604 571 3 A G G 8.67 1.96
rs10497893 CRYGEP1 156 2 A C A 8.66 0.51
rs2217110 C18orf10 732 18 A G G 8.64 0.41
rs7667905 L0C339979 1176 4 A G A 8.63 2.24
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rs10502700 None 211 18 A G A 8.63 0.24
rs4627439 None 951 18 G T T 8.63 0.24
rs251470 FLJ10904 797 5 G T T 8.63 1.96
rs10507224 L0C390359 262 12 C T T 8.63 0.46
rs543224 None 1003 18 C T T 8.63 0.46
rs2241748 ARL4 742 7 A G A 8.62 5.48
rs2263356 None 746 9 C T T 8.62 2.33
rs935661 PRKCE 1318 2 G T T 8.61 1.97
rs2183024 None 727 9 C G C 8.61 0.38
rs10495321 SIPA1L2 138 1 A G G 8.61 4.64
rs994214 None 1357 2 C T C 8.61 1.95
rs10507505 None 265 13 C T C 8.61 2.29
rs10490387 L0C130576 90 2 C T T 8.61 3.30
rs361161 None 878 4 A G G 8.60 2.35
rs2394081 None 776 10 A G A 8.60 7.07
rs719639 C6orf157 1128 6 G T G 8.59 2.18
rs1744510 None 591 6 A T A 8.59 0.45
rs1860752 None 612 7 C G C 8.58 0.48
rs2357761 None 763 6 C G G 8.58 0.48
rs10516708 None 376 4 C T T 8.57 1.96
rs10499381 PHF14 169 7 C T T 8.57 0.39
rs10511318 None 315 3 C G C 8.56 2.71
rs3964705 L0C390561 907 15 A G G 8.56 0.43
rs10487921 None 62 7 A G A 8.56 0.38
rs10512097 None 325 9 C T T 8.56 2.80
rs10485602 TMC2 45 20 C T C 8.54 0.37
rs3751877 RRN3 882 16 A G G 8.54 2.72
rs10485608 None 47 20 A G G 8.54 2.94
rs2060850 FLJ31810 683 9 A G G 8.54 1.94
rs1120712 None 416 7 C T C 8.53 1.95
rs6864370 None 1072 5 C T T 8.53 0.42
rs10508410 L0C389938 276 10 C G G 8.53 0.09
rs10509281 CTNNA3 298 10 C T C 8.53 0.09
rs1904641 CTNNA3 626 10 A C C 8.53 0.09
rs4102401 RRM2B 914 8 C T C 8.53 0.09
rs4404874 None 937 8 A G A 8.52 0.48
rs10496213 REGL 145 2 A C C 8.52 3.48
rs10500296 GRLF1 180 19 C G G 8.52 0.00
rs1403105 FLJ12604 482 3 A G G 8.51 1.95
rs4129499 None 919 8 A C A 8.50 0.18
rs2252646 None 745 12 A G G 8.49 0.50
rs161912 None 583 3 A G G 8.49 2.03
rs10484683 None 39 6 A G G 8.49 11.67
rs802279 TCBA1 1219 6 C G C 8.48 2.40
rs6592456 NUMA1 1053 11 C T C 8.47 5.41
rs9301083 None 1273 13 A G A 8.47 1.94
rs2241443 DGKI 741 7 C T C 8.46 2.05
rs10512918 None 340 5 A G G 8.46 2.64
rs1402319 None 481 12 C T C 8.45 2.02
rs10520415 FLJ13110 400 2 C T C 8.44 0.49
rs10503122 None 217 18 C T T 8.44 0.22
rs966118 ASAH1 1345 8 C T T 8.43 2.02
rs10491771 None 99 9 A G A 8.43 0.51
rs1037124 ARNT2 15 15 C T T 8.43 0.32
rs10513473 None 344 9 C T T 8.42 2.39
rs10508171 None 271 13 A G A 8.42 1.96
rs10518928 MEIS2 394 15 C T C 8.42 0.45
rs10508412 L0C389938 278 10 C T T 8.42 1.93
rs2439538 TBC1D7 787 6 A G G 8.42 1.93
rs950171 pp9099 1326 15 C G G 8.41 1.95
rs10512629 TRAD 334 3 A T A 8.41 2.35
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rs3731572 LTBP1 880 2 C T C 8.41 0.00
rs10516839 None 379 4 A C C 8.40 0.42
rs2888378 EB-1 840 12 A G A 8.40 1.92
rs4762559 EB-1 967 12 C T T 8.39 1.92
rs10491747 None 97 9 A G G 8.39 2.01
rs1561365 None 560 5 A T A 8.38 2.64
rs10485603 TMC2 46 20 A G G 8.38 0.36
rs10519536 KIAA0882 396 4 C T T 8.36 0.42
rs4336940 None 934 10 A G G 8.36 0.51
rs964664 BA13 1343 6 A G A 8.36 2.06
rs7908118 None 1202 10 C T T 8.35 0.50
rs10515457 KIAA1061 361 5 C T C 8.35 2.27
rs10484858 BPAG1 40 6 C T C 8.35 0.46
rs1998570 None 659 13 A G A 8.35 2.00
rs6969674 HDAC9 1086 7 A C A 8.35 0.32
rs7763613 None 1187 6 A G G 8.35 1.91
rs10498789 None 165 6 A G A 8.34 1.99
rs10503493 SGCZ 219 8 G T T 8.34 3.44
rs10503869 RBPMS 225 8 C T C 8.33 5.36
rs10507223 L0C390359 261 12 C G G 8.32 0.46
rs9295562 L0C389370 1261 6 C T T 8.32 2.14
rs10504702 None 230 8 A G A 8.32 0.19
rs10484126 None 31 14 C T T 8.32 5.34
rs10487982 None 64 1 A C C 8.32 2.27
rs1498767 None 535 16 C T C 8.31 2.10
rs923312 None 1245 11 A G A 8.31 0.19
rs10515934 GORASP2 370 2 A G A 8.31 2.18
rs4073846 MAST2 911 1 C T C 8.31 1.92
rs10485760 None 48 20 C T C 8.31 0.00
rs1407508 None 485 9 A G G 8.30 0.00
rs1455780 SIAT8B 517 15 A G A 8.30 1.91
rs4669134 None 953 2 A G A 8.30 0.49
rs2369942 None 765 12 A G A 8.30 1.96
rs2274154 None 748 6 C T T 8.29 2.78
rs6808403 None 1068 3 A G A 8.28 2.51
rs438405 RCL1 935 9 A C C 8.27 0.22
rs10515512 NDFIP1 363 5 C T C 8.25 3.69
rs1116163 L0C400019 414 12 A G G 8.24 0.35
rs340978 None 870 11 A C C 8.24 2.32
rs10509071 None 295 10 A G A 8.23 2.18
rs719548 TLK1 1127 2 A G A 8.21 2.28
rs6490721 None 1042 13 G T G 8.21 0.00
rs10498018 None 161 2 A G A 8.21 2.60
rs10503837 None 224 8 C G G 8.21 3.67
rs1335310 None 446 10 C T C 8.20 2.02
rs10489505 None 84 1 C G C 8.20 11.33
rs2008927 None 662 5 C T T 8.20 1.97
rs2160836 None 716 3 A C C 8.20 2.00
rs2298457 NUMA1 757 11 C T T 8.19 4.52
rs10508230 None 275 10 A G A 8.18 0.40
rs10496800 None 147 2 A G A 8.18 2.40
rs10520676 NTRK3 402 15 A G A 8.18 2.40
rs2901383 None 846 4 C T C 8.17 0.51
rs731693 GORASP2 1151 2 C T T 8.17 2.09
rs4976621 None 988 5 C T C 8.16 0.41
rs1398868 FAF1 478 1 C T C 8.16 2.44
rs159347 None 574 20 C T C 8.14 2.04
rs10500474 None 181 16 A G A 8.14 0.37
rs4131886 LHCGR 924 2 A C C 8.13 2.46
rs770163 NAV3 1179 12 C T C 8.13 1.99
rs1947032 CTNNA2 640 2 A G A 8.12 2.21
CA 02587979 2007-05-18
WO 2006/053955 PCT/F12005/050429
43
rs2297139 L0C400758 754 1 A G G 8.12 0.37
rs1573219 NTRK2 563 9 C T T 8.12 2.32
rs10508139 None 270 13 C T T 8.10 0.00
rs3774258 MRPL47 886 3 C T C 8.10 0.00
rs9312054 None 1284 4 C T C 8.10 0.00
rs10486445 OSBPL3 55 7 C T C 8.10 2.33
rs974059 None 1349 3 A G A 8.09 0.52
rs10484595 None 34 6 C T C 8.09 0.43
rs10491806 ECM2 100 9 C T C 8.09 2.85
rs2861427 None 834 1 G T G 8.09 0.50
rs508544 None 991 2 C T C 8.08 2.10
rs10493731 None 121 1 A G A 8.08 3.98
rs2900362 None 844 12 A C C 8.07 0.35
rs7905537 None 1201 10 G T G 8.07 0.47
rs2270861 DRIM 747 12 C T C 8.07 0.37
rs1857706 FSHR 610 2 C T T 8.07 0.40
rs6461373 None 1035 7 G T T 8.07 2.02
rs6534623 None 1045 4 G T T 8.06 0.49
rs2414768 None 780 15 A T T 8.06 0.40
rs8092873 None 1226 18 A G G 8.05 2.92
rs2981196 None 850 8 A C C 8.05 2.34
rs9312682 L0C255130 1285 4 C T T 8.04 0.47
rs1173085 None 423 9 A G G 8.04 0.43
rs1834476 UNQ739 606 7 A T T 8.03 0.32
rs7007471 None 1094 8 A G A 8.03 0.38
rs9301082 None 1272 13 C T T 8.02 1.90
rs362492 ANK2 879 4 A G G 8.02 0.38
rs2248815 ITSN1 744 21 C T C 8.02 2.82
rs2725653 None 808 8 A C C 8.01 0.09
rs3770688 LANCLI 885 2 C T T 8.01 0.38
rs7720796 None 1182 5 A G A 8.01 0.28
rs10500943 GAS2 187 11 A C A 8.00 1.99
rs7975812 None 1211 12 C G G 8.00 2.27
rs10502526 None 204 18 A G A 7.98 2.13
rs7763189 None 1186 6 A G A 7.98 2.64
rs10498017 None 160 2 A T A 7.98 2.58
rs10517087 None 380 4 C T T 7.97 0.39
rs4125962 None 915 2 C T C 7.96 2.52
rs1519956 None 541 12 C T T 7.96 0.48
rs10508904 ClOorf64 288 10 G T G 7.96 1.98
rs445607 CTNND2 940 5 A G A 7.95 0.45
rs627069 MGC29875 1024 1 C G G 7.94 2.12
rs10493583 SIAT7C 120 1 C T C 7.94 1.91
rs720884 C6orf65 1134 6 C T C 7.94 2.22
rs6972736 OSBPL3 1088 7 C T T 7.93 2.11
rs1357194 None 457 6 C T C 7.93 0.43
rs1906923 None 627 5 C G G 7.92 0.40
rs633198 PROCR 1027 20 A G G 7.92 1.89
rs997285 RASGRFI 1360 15 A C A 7.91 2.30
rs10497919 None 158 2 C T C 7.91 0.45
rs1430242 None 505 2 A G G 7.90 1.95
rs10275635 None 12 7 A G A 7.90 0.00
rs10492406 None 110 13 C T C 7.90 0.00
rs10503636 EFA6R 221 8 C T T 7.90 1.88
rs1354348 None 456 3 A C C 7.89 0.15
rs3212220 IL12B 868 5 A C A 7.89 2.34
rs9315132 None 1290 13 C T T 7.89 0.37
rs1458088 None 519 11 C G G 7.88 1.99
-------------------------------------------------------------------------------
-
dbSNPrsID: SNP identification number in NCBI dbSNP database
Gene locus: Gene locus as reported by NCBI dbSNP database build 124
CA 02587979 2007-05-18
WO 2006/053955 PCT/F12005/050429
44
SequenceID: Sequence identification number
Allele A: Alternate SNP allele or its complementary nucleotide in
the position indicated by dbSNP RS ID and basepair position
Allele B: Alternate SNP allele or its complementary nucleotide in
the position indicated by dbSNP RS ID and basepair position
Minor Allele: SNP allele or its complementary nucleotide that is less common
in the control population
Allele X2: Chi-squared test based on allele frequencies
Table 3. Haplotype genomic regions with the strongest association with HT in
the
haplotype sharing analysis (HPM-G) with 5 SNPs.
O
d I G I S IAIAI P I C I P I S I E I E I G
b I e I e 11111 I h I o I t I n I X I e
S I n I q Illll v I r I s I a I d I t I n
N I e I u lelel a I o I i I r I I e I e
P I I e 11111 1 I m I t I t I I n I
I 1 I n lelel u I o I i I I I s I c
r I o I c I I I e I s I o I I I i I o
s I c I e IAIBI I o I n I I I o I n
I u I I I I I m I I I I n I t
1 I s I 1 I I I I e I I I I I e
D I I D I I I I I I I I I n
I I I I I I I I I I I t
-------------------------------------------------------------------------------
-------------
rs10489134 None 81 C G 0.0033 1 4322203 4222203 4444135 221932 None n0,
rs10489133 None 80 C T 0.0043 1 4344135 aL'o
tD
rs10493327 APG4C 119 C T 0.0041 1 62673762 62573762 62828733 254971 APG4C tD
rs1413242 None 498 C T 0.0034 1 62701781 0
rs998096 None 1364 A C 0.0029 1 62701822 0
rs7512480 None 1158 C T 0.0038 1 62728733 0
Ln
rs787493 L0C391046 1199 C G 0.002 1 67455635 67355635 67627512 271877 GADD45A
ao
rs344924 L0C391046 872 A G 0.0002 1 67475369 GNG12
rs1408956 None 489 C T 0.0001 1 67506979 L0C391046
rs344935 None 873 C T 0.0006 1 67507779
rs647008 None 1039 C T 0.0008 1 67514855
rs675327 None 1064 G T 0.0023 1 67527512
rs2596268 LOC399701 802 A T 0.0046 1 142748636 142648636 142853825 205189
MGC8902
rs10494238 None 125 C T 0.0028 1 142751002 L0C399701
rs3124683 None 862 A G 0.0021 1 142753825
SEC22L1
rs1858232 CAPON 611 A G 0.0038 1 159491215 159391215 159591215 200000 CAPON
L0C284680
EAT2
rs1577567 None 566 A G 0.0047 1 163876348 163776348 164007533 231185 L0C116123
rs1577566 None 565 A G 0.0032 1 163876551 POGK
rs484666 None 981 A T 0.0026 1 163907533
rs1415678 None 501 A G 0.0039 1 165841708 165741708 165946218 204510 DPT
rs10489358 None 82 A G 0.003 1 165842250 O
rs726055 None 1146 C T 0.003 1 165845239
rs10489359 None 83 A G 0.0029 1 165845921
rs1412336 None 496 A C 0.0046 1 165846218
rs1578704 None 568 A G 0.0049 1 186525471 186425471 186648423 222952 None
rs1578705 None 569 A G 0.0049 1 186525536
rs10494628 None 128 C T 0.0036 1 186548423
rs10494627 None 127 C T 0.0021 1 186790071 186690071 186931835 241764 None
rs9287136 None 1252 C T 0.0018 1 186831672
rs10494626 None 126 C T 0.0047 1 186831835
rs10494659 None 130 C T 0.0023 1 189007732 188907732 189165779 258047 None
rs2785762 None 816 C G 0.0029 1 189010208
rs10494660 None 131 C T 0.0033 1 189015552
rs7536312 None 1161 A G 0.0021 1 189015619 tD
rs10494661 None 132 A T 0.0038 1 189016441
tD
rs10494662 None 133 C T 0.0027 1 189063888 N
rs10494663 None 134 A G 0.002 1 189064337 0
rs6683269 None 1057 C T 0.0037 1 189064497 0
rs10494664 None 135 A C 0.0036 1 189065779 L n
CD
rs2154329 None 715 C T 0.0046 1 196232097 196132097 196332097 200000 None
rs301748 USH2A 855 A G 0.0041 1 213418522 213318522 213518522 200000 USH2A
rs10495082 None 137 C T 0.004 1 215101968 215001968 215201968 200000 L0C128153
rs2089918 None 694 A G 0.0035 1 231717337 231617337 231817337 200000 TARBP1
rs10508223 None 273 C T 0.0025 10 2154068 2054068 2254068 200000 None
rs10508416 L0C389938 279 A G 0.0031 10 10727688 10627688 11016891 389203
L0C389938
rs4749978 L0C389938 963 C G 0.0005 10 10744535
rs2224673 L0C389938 738 C G 0.0001 10 10758538
rs10508417 L0C389938 280 A T 0 10 10797859
rs10508419 None 281 A G 0.0004 10 10910370
rs1473737 None 527 C T 0.0041 10 10916891
rs1537611 MCM10 551 A G 0.0023 10 13213838 13113838 13314331 200493 OPTN
rs10508454 MCM10 282 G T 0.0034 10 13214331 MCM10 0
ClOorf49 rs950132 EPC1 1325 C T 0.0046 10 32628642 32528642 32728642 200000
EPC1
rs7905537 None 1201 G T 0.0043 10 34235281 34135281 34416715 281434 PARD3
rs161411 None 581 A G 0.005 10 34316715
rs9299552 PCDH15 1267 C T 0.0034 10 55585793 55485793 55685793 200000 PCDH15
rs7908118 None 1202 C T 0.0038 10 56557629 56457629 56709343 251714 None
rs2050318 None 676 G T 0.0041 10 56609343
~
rs10509301 RUFY2 299 C T 0.0042 10 69489280 69389280 69791343 402063 MAWBP
rs10509302 DNA2L 300 C G 0.0011 10 69575078 HNRPH3 n0,
rs10509303 DNA2L 301 A C 0.0021 10 69575202 RUFY2 a"'o
rs2298117 CXXC6 756 A G 0.0042 10 69691343 CXXC6 tD
DNA2L tD
N
0
rs10509319 None 305 A G 0.0033 10 70747505 70647505 70876882 229377 NEUROG3 0
rs10509318 None 304 A G 0.0028 10 70748147 C10orf35 0
rs10509317 None 303 C G 0.0029 10 70776662 'i'
rs10509316 None 302 A G 0.0024 10 70776882 ao
rs7898235 None 1200 A C 0.0016 10 73382784 73282784 73490520 207736 ASCC1
rs10509767 None 309 G T 0.0016 10 73390520 ClOorflO4
DDIT4
DNAJB12
CBARAI
rs7917682 CBARAI 1204 G T 0.0024 10 73520486 73420486 73620821 200335 DNAJB12
rs7918099 CBARAI 1205 A G 0.0043 10 73520821 CBARAI
rs7358173 None 1153 A G 0.005 10 89569434 89469434 89669434 200000 None
rs2162361 C10orf59 718 C T 0.0028 10 89712286 89612286 89812726 200440
C10orf59
rs4934391 C10orf59 985 A G 0.0046 10 89712726
rs2032023 None 672 A C 0.005 10 112543668 112443668 112643668 200000 ADRA2A
rs10498198 RRM1 162 C G 0.0039 11 4089040 3989040 4204538 215498 STIM1 O
rs725518 RRM1 1144 C T 0.002 11 4093154 RRM1
rs720106 RRM1 1132 A G 0.0024 11 4104287
rs54816 RRM1 1005 A G 0.0034 11 4104538
rs1549488 None 556 C G 0.0047 11 4396176 4296176 4504792 208616 SSA1 vi
rs10500598 None 182 A G 0.0034 11 4396890 0R52K3P
rs10500600 OR51R1P 183 A G 0.0044 11 4404792 OR51R1P
rs4128873 GALNTL4 918 C T 0.0035 11 11507330 11407330 11607330 200000 GALNTL4
rs4078145 None 912 A T 0.0035 11 11628202 11528202 11836288 308086 GALNTL4
rs1471013 None 526 A G 0.0024 11 11705272 USP47
rs897359 None 1238 C T 0.0014 11 11727598
rs2896587 None 843 A C 0.0024 11 11734173 N
rs10500748 None 184 A T 0.0042 11 11736288
tD
rs963497 None 1341 A G 0.0047 11 21603516 21503516 21721882 218366 NELL1
tD
rs10500913 None 186 A G 0.0026 11 21621527 N
rs7112382 None 1105 A G 0.0034 11 21621882 0
rs1559759 None 559 G T 0.0036 11 35087360 34987360 35193481 206121 CD44 0
rs4756190 None 965 A G 0.0009 11 35088349 CD
rs507230 None 990 C T 0.0039 11 35093481
rs10501241 None 188 G T 0.0025 11 40660437 40560437 40760437 200000 None
rs10501242 None 189 A G 0.0017 11 40910759 40810759 41044758 233999 None
rs10501243 None 190 A G 0.0017 11 40910823
rs10501244 None 191 A T 0.0017 11 40911075 ro
rs7102885 None 1103 C T 0.0018 11 40930137
rs10501245 None 192 C T 0.0022 11 40944758
rs2298457 NUMA1 757 C T 0.0046 11 71460519 71360519 71563971 203452 RNF121
rs6592456 NUMA1 1053 C T 0.0045 11 71463971 IL18BP
NUMA1
L0C220074
FLJ20625
DKFZP564MO82
rs10501438 L0C387795 193 A G 0.0007 11 78790787 78690787 78924409 233622
L0C387795
rs528048 L0C387795 998 C T 0.0003 11 78790934 0
rs530965 L0C387795 999 C T 0.0002 11 78791409
rs481975 L0C387795 977 A C 0.0001 11 78798027
rs546868 L0C387795 1004 C T 0.0001 11 78799086
rs10501439 L0C387795 194 C T 0.0001 11 78812154
rs514536 L0C387795 993 C G 0.004 11 78824409
rs10501471 None 195 A G 0.0045 11 80051682 79951682 80152306 200624 None
rs10501472 None 196 C T 0.0037 11 80052306
rs1391533 None 474 C T 0.0048 11 80396254 80296254 80605724 309470 None
rs1566241 None 561 C T 0.0025 11 80444563
rs1608169 None 580 G T 0.0006 11 80477196 ~
rs1829764 None 602 C T 0.0003 11 80477302
rs1589574 None 573 G T 0.0012 11 80477358 N
rs2373717 None 771 A T 0.0024 11 80505724
tD
rs1542750 None 553 A G 0.0047 11 91310866 91210866 91426878 216012 None tD
rs10501763 None 200 C T 0.0035 11 91326878 0
0
rs1941437 L0C390241 638 C T 0.0022 11 91898278 91798278 91998278 200000
L0C390241 0
Ln
rs4129692 None 921 C T 0.0027 11 92979838 92879838 93181349 301511 FN5 CD
rs4129691 None 920 G T 0.0001 11 92979850 MGC5306
rs2399681 None 777 A G 0 11 92980052 PTDO12
rs2399683 None 778 C T 0 11 92980291 KIAA1731
rs7939460 KIAA1731 1207 C G 0.0012 11 93081349
rs503208 None 989 C G 0.002 11 103295656 103195656 103408638 212982 PDGFD ro
rs7127296 None 1106 A C 0.0046 11 103308638
rs875430 None 1234 C T 0.0043 11 109153307 109053307 109318071 264764 None
rs2002733 None 661 A G 0.0012 11 109154189
rs2570309 None 800 C T 0.002 11 109195092
rs1789819 None 596 C T 0.0033 11 109218071
rs10505970 FLJ36004 243 C G 0.0022 12 25536337 25436337 25637084 200747
FLJ36004
rs10505969 FLJ36004 242 A T 0.0037 12 25536631
rs10505968 FLJ36004 241 A G 0.0049 12 25537084
rs10506120 None 244 A G 0.0041 12 34126870 34026870 34226870 200000 ALG10
rs10506121 None 245 C G 0.0044 12 34290302 34190302 34390302 200000 None O
rs274460 None 810 A G 0.0029 12 58238608 58138608 58497593 358985 SLC16A7
rs3847653 None 894 C G 0.004 12 58238640
rs3897770 None 901 A C 0.0036 12 58238933
rs10506395 None 246 C T 0.0012 12 58258088
rs1391130 None 473 A G 0.0007 12 58270954
rs10506396 None 247 G T 0.0006 12 58321404
rs10506397 None 248 C T 0.0001 12 58321752
rs10506398 SLC16A7 249 C T 0.0015 12 58397593
rs1386486 TPH2 472 C T 0.0043 12 70698487 70598487 70798761 200274 TBC1D15
rs1386485 TPH2 471 A C 0.0045 12 70698634 TPH2
rs1386483 TPH2 470 A G 0.0044 12 70698761 0
rs10506650 TRHDE 251 C T 0.0036 12 70964670 70864670 71083069 218399 TRHDE N
rs4550264 TRHDE 945 A G 0.0027 12 70964827
rs10506651 TRHDE 252 A G 0.0035 12 70983069 tD
tD
rs949593 None 1323 A C 0.0046 12 71725030 71625030 71825030 200000 None N
0
0
rs1402319 None 481 C T 0.0034 12 76658608 76558608 76758608 200000 NAV3 0
Ln
rs10506761 None 254 A C 0.0034 12 76683540 76583540 76790978 207438 NAV3 CD
rs1520726 None 543 C T 0.0021 12 76690978
rs1394380 None 475 A G 0.0044 12 97055132 96955132 97155132 200000 None
rs1353761 None 455 A T 0.0014 12 101577909 101477909 101677909 200000 None
rs10507149 None 259 C T 0.0004 12 101602105 101502105 101748153 246048 PAH
rs6539051 None 1046 G T 0.0005 12 101621075
rs7311768 None 1150 A G 0.0009 12 101621739
rs10507150 None 260 C T 0.0014 12 101642141
rs6539055 None 1047 A G 0.0036 12 101648153
rs1896339 None 623 A T 0.0015 12 113829557 113729557 113949205 219648 None
rs10507255 None 263 C G 0.0015 12 113831271
rs7957333 None 1209 C T 0.0014 12 113831312
rs1863723 None 614 A G 0.0016 12 113840194
rs2021784 None 668 A C 0.0016 12 113849205
rs9315078 PSPC1 1289 A G 0.0018 13 18056452 17956452 18211924 255472 HSMPP8 0
rs2297584 PSPC1 755 A G 0.0005 13 18085758 PSPC1
rs4769900 PSPC1 969 C T 0.0007 13 18111924 ZNF237
rs1413476 L0C400099 499 A G 0.0023 13 18238020 18138020 18338020 200000 PSPC1
ZNF237
ZNF198
L0C400099
rs9315282 ZNF198 1291 A T 0.004 13 18391977 18291977 18491977 200000 ZNF198
rs1555619 None 558 C T 0.0025 13 20654983 20554983 20780871 225888 None
rs4278603 None 933 C T 0.0009 13 20655026 0
rs9316871 None 1298 C T 0.0002 13 20659921
rs9316902 None 1299 A T 0.0006 13 20680457 N
rs6490720 None 1041 A G 0.0041 13 20680871
tD
rs3002251 None 852 C T 0.0046 13 23417821 23317821 23591092 273271 PABPC3 tD
rs2497614 None 794 A C 0.0028 13 23418426 FLJ25477 0
rs2994906 None 851 C T 0.0029 13 23491092 0
0
rs9315443 L0C390393 1292 A G 0.0044 13 35109331 35009331 35231087 221756
L0C400120 L n
rs2224655 None 737 A G 0.0035 13 35117500 RFXAP CD
rs9315445 None 1293 A C 0.0034 13 35130928 SMAD9
rs10507441 None 264 A C 0.0038 13 35131087 L0C390393
rs1008913 None 2 C T 0.0011 13 41527828 41427828 41671499 243671 DNAJD1
rs9315991 None 1294 G T 0 13 41529541 FLJ10094
rs9316002 None 1295 A G 0.0011 13 41571499 ro
rs2182377 None 726 G T 0.0047 13 46385371 46285371 46485371 200000 SUCLA2
NUDT15
VDRIP
rs9318293 None 1300 C T 0.0049 13 72969141 72869141 73112529 243388 None
rs7983591 None 1213 A C 0.0008 13 72999299
rs10507828 None 266 C T 0.0041 13 73012529
rs10492637 GPC6 114 A G 0.0046 13 92224868 92124868 92324868 200000 GPC6
rs9582457 VGCNL1 1337 C T 0.0037 13 99518459 99418459 99659913 241454 VGCNL1
rs9300654 VGCNL1 1268 C T 0.0028 13 99524895 O
rs10508056 VGCNL1 267 G T 0.0026 13 99526897
rs10508058 VGCNL1 268 A G 0.0033 13 99559913
rs9301021 None 1270 C T 0.0044 13 103674248 103574248 103776948 202700 None
rs9301022 None 1271 C T 0.0032 13 103676948
rs11620131 None 422 A C 0.0005 13 107835145 107735145 108022110 286965 None
rs10492480 None 113 C T 0.0002 13 107847427
rs1410425 None 491 C T 0.0001 13 107896160
rs10492479 None 112 A G 0.0003 13 107913803
rs10492478 None 111 A C 0.0004 13 107922110
~
rs719737 None 1130 C T 0.0008 13 108048350 107948350 108148350 200000 IRS2
0
N
rs10483414 AKAP6 23 A G 0.0043 14 31055625 30955625 31173099 217474 AKAP6
rs10483416 AKAP6 24 C T 0.0015 14 31065873 tD
rs7157533 AKAP6 1115 C T 0.0017 14 31066698 tD
rs7157744 AKAP6 1116 A T 0.0016 14 31066871 N
rs1956223 AKAP6 643 A G 0.0016 14 31072068 0
rs3784203 AKAP6 887 A T 0.0018 14 31073099 0
Ln
rs10483523 LRFN5 26 A T 0.0049 14 40254131 40154131 40354131 200000 LRFN5 CD
rs10498373 None 163 A G 0.0028 14 41060504 40960504 41175621 215117 None
rs9323071 None 1310 A T 0.0024 14 41067677
rs10498374 None 164 A C 0.0024 14 41072782
rs8009697 None 1215 C T 0.0044 14 41075621
rs10483694 None 27 A G 0.0022 14 56505552 56405552 56619154 213602 None
rs10483695 None 28 A G 0.0004 14 56505597
rs178493 None 594 C T 0.0009 14 56517556
rs178497 None 595 A C 0.001 14 56519154
rs10483763 KCNH5 29 A G 0.0018 14 61556822 61456822 61658529 201707 KCNH5
rs1951805 KCNH5 642 A C 0.0021 14 61558195
rs9323431 KCNH5 1311 A C 0.0041 14 61558529
rs2056855 L0C145497 679 C T 0.0035 14 75287180 75187180 75395330 208150
KIAA1036
rs10483879 L0C145497 30 C T 0.0027 14 75288211 KIAA0759
rs2885625 L0C145497 839 A G 0.001 14 75294790 C14orf166B
rs6574333 L0C145497 1051 A G 0.0021 14 75295330 L0C145497 0
rs9323707 L0C400234 1312 A G 0.0019 14 80076248 79976248 80176248 200000 SEL1L
L0C400234
rs7177870 None 1124 C T 0.0049 15 24842209 24742209 24942209 200000 GABRA5
rs10519989 MGC14798 397 A C 0.0033 15 33246629 33146629 33346629 200000
MGC14798
rs3887013 RGMA 900 A G 0.0022 15 91343895 91243895 91456600 212705 CHD2
rs997941 RGMA 1363 A G 0.0028 15 91356600 RGMA
rs10492874 WWOX 116 C G 0.0042 16 77932158 77832158 78040235 208077 CLECSF1
rs9319518 WWOX 1304 C G 0.005 16 77940235 WWOX
0
N
rs2077576 WWOX 688 A G 0.0044 16 78118291 78018291 78218291 200000 WWOX a"'o
tD
rs4130513 WWOX 922 A G 0.0028 16 78238277 78138277 78372914 234637 WWOX tD
rs10514437 WWOX 349 C T 0.0006 16 78272387 0
rs2738646 WWOX 809 C G 0.0033 16 78272914 0
0
rs10492859 CDH13 115 A G 0.0015 16 82641499 82541499 82744597 203098 CDH13 'i'
rs759831 CDH13 1169 A C 0.0001 16 82643345 ao
rs1982608 CDH13 651 C T 0.0003 16 82644465
rs7498941 CDH13 1157 A G 0.0027 16 82644597
rs10521151 KIAA0753 405 C T 0.0034 17 6728171 6628171 6858576 230405 PITPNM3
rs10491082 L0C342531 96 C T 0.003 17 6758152 TXNL5
rs2040847 L0C342531 673 A G 0.0042 17 6758576 CGI-125 ro
SLC13A5
KIAA0753
L0C342531
L0C342531
rs7219451 KRT25D 1137 C T 0.0025 17 39330167 39230167 39479119 248952 KRT24
rs2469828 None 792 C T 0.001 17 39377625 KRT25A
rs2469816 None 790 A G 0.0043 17 39379119 KRT25B
KRT25C
KRT25D
KRT10
MGC21518
KRT12 O
KRT20
KRT23
rs10512495 None 332 C T 0.0033 17 60887422 60787422 61003496 216074 FLJ25818
rs954562 None 1334 C T 0.0026 17 60903496 FLJ12760
rs10512496 TLK2 333 C T 0.0041 17 61137732 61037732 61237732 200000 TLK2
MRC2
rs918077 None 1241 C T 0.0049 17 70762501 70662501 70862501 200000 SOX9
rs8089170 PTPRM 1222 A G 0.0047 18 7980780 7880780 8141285 260505 PTPRM
rs10502366 PTPRM 203 A T 0.0009 18 7981006
rs674823 PTPRM 1063 A G 0.0016 18 8025339 N
rs10513902 PTPRM 348 A T 0.0017 18 8040297
rs10513901 PTPRM 347 C T 0.0017 18 8041285
~ tD
rs4799483 None 974 C T 0.0038 18 34401661 34301661 34587395 285734 None N
rs1346234 None 452 G T 0.0038 18 34405689 0
rs10502700 None 211 A G 0.0038 18 34417134 0
rs4627439 None 951 G T 0.0015 18 34486191 L n
rs3744905 None 881 G T 0.0035 18 34487395 CD
rs10502772 None 212 C T 0.0042 18 37436083 37336083 37653585 317502 None
rs10502774 None 213 G T 0.0027 18 37506007
rs1865290 None 615 A T 0.0012 18 37507545
rs8092873 None 1226 A G 0.0013 18 37508323
rs9304252 None 1277 A T 0.0009 18 37534860
rs7242858 None 1140 G T 0.0037 18 37553585
rs1944404 RIT2 639 C T 0.0031 18 38784739 38684739 38885296 200557 RIT2
rs10502805 RIT2 214 C G 0.0041 18 38785296
rs1497965 None 534 A G 0.004 18 56738096 56638096 56862416 224320 None
rs10503048 None 215 C T 0.0021 18 56745407
rs720261 None 1133 A G 0.0028 18 56762416
rs931850 None 1303 A G 0.0032 18 59542803 59442803 59673654 230851 SERPINB4
rs1522722 None 547 C T 0.0019 18 59570510 SERPINB3
rs3928359 None 905 A C 0.0024 18 59573654 SERPINBII
SERPINB7 0
rs309231 None 859 C T 0.004 18 64544485 64444485 64734518 290033 FLJ20793
rs1676853 None 588 C T 0.0015 18 64598339 C18orf14
rs10503122 None 217 C T 0.0002 18 64598510
rs8092610 None 1225 C T 0.0001 18 64610859
rs2086079 None 691 A C 0.0003 18 64621145
rs10503123 None 218 A G 0.0007 18 64623492
rs6566386 None 1049 A C 0.0034 18 64634518
rs2110049 L0C388526 699 A T 0.0033 19 33056517 32956517 33203464 246947
L0C388526
rs10500226 L0C388526 177 G T 0.0011 19 33079622
rs10516700 L0C388526 375 A G 0.0005 19 33080969 0
rs10500227 L0C388526 178 A C 0 19 33102850
rs10500228 L0C388526 179 C T 0 19 33103335 N
rs9304853 L0C388526 1278 A T 0 19 33103370
rs9304854 L0C388526 1279 A C 0.0021 19 33103464
tD
rs272411 LILRAI 807 C T 0.0039 19 59803539 59703539 59986493 282954 FLJ00060 0
rs400322 LILRB4 909 A G 0.0041 19 59864390 LILRA2 0
rs1654658 None 587 A G 0.0031 19 59886493 LILRAI o
LILRB4 L n
ILT10 CD
KIR3DL3
KIR2DL3
KIR2DS2
KIR2DL1
rs4669167 None 954 C T 0.0026 2 5415069 5315069 5545029 229960 None ro
rs1453787 None 516 A G 0.0015 2 5445029
rs238634 L0C339789 775 A G 0.0035 2 8435287 8335287 8535287 200000 L0C339789
rs10518958 COMMD1 395 A G 0.0049 2 62251507 62151507 62351507 200000 COMMD1
rs10496105 PELI1 141 A G 0.0019 2 64295280 64195280 64443870 248590 VPS54
rs7563423 None 1164 A G 0.0003 2 64319936 PELI1
rs714672 None 1109 A G 0.0009 2 64320856
rs10496106 None 142 C T 0.0009 2 64321198
rs717382 None 1121 A G 0.0011 2 64321669
rs7558568 None 1162 A C 0.0008 2 64331179
rs7562080 None 1163 A G 0.0015 2 64331740 O
rs10496107 None 143 G T 0.0016 2 64343870
rs12072 REG1A 429 A G 0.005 2 79325042 79225042 79450682 225640 REG-III
rs10496213 REGL 145 A C 0.0012 2 79336691 REG1B
rs2117725 None 703 C G 0.0046 2 79350682 REG1A vi
PAP
REGL
rs723839 None 1139 C G 0.0049 2 123161810 123061810 123294482 232672 None
rs10496580 None 146 A C 0.005 2 123194482
rs3769361 GPD2 883 A G 0.003 2 157599796 157499796 157750266 250470 GPD2
rs3769368 GPD2 884 C T 0.0024 2 157613543
rs7570567 GPD2 1166 C T 0.0031 2 157621171 N
rs2288760 GPD2 753 A T 0.0041 2 157629867
rs1432573 None 507 C G 0.0047 2 157650266
tD
tD
rs10497163 None 149 G T 0.0043 2 157742506 157642506 157842506 200000 None N
0
0
rs10497189 ACVR1 150 A G 0.0048 2 158827349 158727349 159025728 298379 ACVR1 0
rs10497190 ACVR1 151 A G 0.0012 2 158841785 L n
rs10497191 ACVR1 152 A G 0.0008 2 158869762 CD
rs10497192 ACVR1 153 C T 0.0006 2 158874245
rs7605386 ACVR1 1171 C G 0.0005 2 158881484
rs9288697 ACVR1 1256 A C 0.0003 2 158897363
rs10497193 None 154 A G 0.001 2 158912223
rs6437117 None 1032 A T 0.0044 2 158925728
rs3903306 None 902 A T 0.004 2 160651226 160551226 160751264 200038 BAZ2B
rs6432539 None 1031 C T 0.0048 2 160651264 -~7
~
rs10490079 MY03B 89 C T 0.005 2 171641213 171541213 171743501 202288 MY03B
rs741283 MY03B 1154 G T 0.0024 2 171643501
rs2164857 PDE11A 719 A C 0.0049 2 178811680 178711680 178915390 203710 PDE11A
rs1438048 PDE11A 508 A C 0.0042 2 178815390
rs523437 None 997 A G 0.004 2 239685559 239585559 239785608 200049 TRAF31P1
rs567962 None 1007 C T 0.0043 2 239685608 ASB1
rs10485822 SNPH 49 C G 0.0046 20 1241412 1141412 1514846 373434 PSMF1 0
rs1884389 None 618 C T 0.002 20 1405582 C20orf46
rs1884390 None 619 C T 0.0016 20 1405818 SNPH
rs10485823 None 50 A G 0.0047 20 1414846 SDCBP2
FKBPIA
NSFLIC
PTPNSIL2
rs6076199 MGC10715 1016 A G 0.0011 20 2466755 2366755 2571778 205023 TGM6
rs6083460 MGC10715 1018 A G 0.0001 20 2471631 SNRPB
rs6083461 MGC10715 1019 A T 0 20 2471778 MGC10715
TMC2
~
rs10485601 TMC2 44 A G 0.0002 20 2589190 2489190 2689502 200312 MGC10715
rs6115181 TMC2 1023 A G 0.0005 20 2589254 TMC2
rs10485602 TMC2 45 C T 0.0015 20 2589502 NOL5A
IDH3B ~
tD
rs6019794 KCNB1 1011 C T 0.0016 20 48694867 48594867 48817052 222185 KCNB1 0
rs756529 KCNB1 1165 C T 0.0022 20 48696430 PTGIS 0
rs237459 KCNB1 772 C T 0.0026 20 48717052 0
Ln
rs2831249 None 823 A C 0.003 21 28231943 28131943 28360918 228975 C21orf94 CD
rs1974422 None 646 C T 0.0044 21 28234231
rs2831286 None 824 C T 0.0031 21 28260918
rs717205 L0C388819 1119 A G 0.0033 21 34231301 34131301 34383137 251836 ITSN1
rs2017190 L0C388819 664 C T 0.0007 21 34231309 ATP50
rs2070513 None 686 G T 0.0005 21 34274270 MRPS6
rs2834327 None 825 A T 0.0011 21 34283137 L0C388819
rs3856852 None 897 A G 0.0026 3 3206647 3106647 3306647 200000 IL5RA
TRNT1
CRBN
rs2347104 None 761 A G 0.0041 3 11875101 11775101 12014530 239429 MGC16471
rs10510408 None 310 C T 0.0024 3 11888064
rs51579 None 995 C T 0.0008 3 11888124
rs447394 None 941 G T 0.0042 3 11914530
rs9311694 None 1283 A C 0.0042 3 58997976 58897976 59235365 337389 FLJ42117
rs1913157 None 630 C G 0.0025 3 59131716 O
rs1512828 None 538 A C 0.0028 3 59135365
rs1521409 None 544 A G 0.0009 3 118178542 118078542 118307557 229015 None
rs1462840 None 523 C T 0.0037 3 118183396
rs10511365 None 316 C T 0.0028 3 118206735
rs10511366 None 317 C T 0.0036 3 118207557
rs953641 PLS1 1333 A G 0.0019 3 143748645 143648645 143941670 293025 XRN1
rs953239 TRPC1 1332 G T 0.0014 3 143767114 ATR
rs2049328 TRPC1 675 C T 0.0009 3 143769488 PLS1
rs7641514 TRPC1 1174 A G 0.0025 3 143841670 TRPC1
~
rs1523076 None 549 C T 0.0047 3 146693647 146593647 146916161 322514 None
rs2687860 None 804 A G 0.0012 3 146761400 N
rs6770324 None 1066 C T 0.0009 3 146792671
rs2140300 None 710 A G 0.0036 3 146816161
~ tD
rs475553 None 964 C T 0.0032 3 166697033 166597033 166797033 200000 None N
0
0
rs168987 STK32B 589 A C 0.0035 4 5499399 5399399 5601132 201733 STK32B o
rs2369705 STK32B 764 A G 0.0038 4 5501132 L n
CD
rs1449776 None 511 A G 0.0037 4 27434527 27334527 27595173 260646 None
rs990965 None 1355 C T 0.0032 4 27489847
rs1503466 None 537 C T 0.0016 4 27495090
rs1503465 None 536 A G 0.0016 4 27495173
rs9291304 GABRB1 1259 A G 0.0029 4 47044998 46944998 47144998 200000 GABRB1
rs10516731 None 377 A G 0.0048 4 86457178 86357178 86594911 237733 None
rs10516740 None 378 A G 0.0048 4 86494911
rs10516839 None 379 A C 0.005 4 90966734 90866734 91066734 200000 SNCA
rs10489025 L0C339979 77 A C 0.0032 4 109741503 109641503 109846552 205049
FLJ37673
rs10489026 L0C339979 78 C G 0.0012 4 109741553 L0C339979
rs7667905 L0C339979 1176 A G 0.0004 4 109745465
rs10489027 L0C339979 79 A G 0.0017 4 109746552
rs1468223 ANK2 525 C T 0.0039 4 114597479 114497479 114703481 206002 ANK2
rs362492 ANK2 879 A G 0.0034 4 114598248 0
rs3025748 ANK2 856 C T 0.0041 4 114603481
rs1376088 None 467 C T 0.0021 4 140072748 139972748 140173774 201026 None
rs1376089 None 468 A G 0.0012 4 140073568
rs1376091 None 469 A G 0.0024 4 140073774
rs920208 None 1242 A G 0.0037 4 148548703 148448703 148648703 200000 None
rs1841272 None 608 C G 0.0028 4 157383393 157283393 157509071 225678 TD02
rs10517626 TD02 385 A C 0.0027 4 157409071
rs10517654 PDGFC 386 G T 0.0023 4 158358389 158258389 158464399 206010 GLRB
rs10517655 PDGFC 387 A G 0.0008 4 158358536 PDGFC
rs6811964 PDGFC 1069 C T 0.001 4 158363081
rs10517657 PDGFC 388 A C 0.0017 4 158363655
rs7662187 PDGFC 1175 C G 0.0033 4 158364399
tD
rs9308066 None 1281 A G 0.0028 4 165245707 165145707 165345707 200000 None o
0
rs438418 None 936 A G 0.0032 5 2902174 2802174 3072326 270152 IRX2 0
rs9313016 None 1286 A C 0.0042 5 2972326 CEI L n
CD
rs1374008 None 464 A G 0.0012 5 61300470 61200470 61487098 286628 None
rs10514931 None 353 A T 0.0006 5 61300983
rs9291745 None 1260 C T 0.0009 5 61307285
rs2161499 None 717 A C 0.0017 5 61387098
rs346435 None 874 A C 0.001 5 62620128 62520128 62720128 200000 None ro
rs281455 None 817 C T 0.0044 5 67304156 67204156 67424355 220199 None
rs10515062 None 354 A T 0.0045 5 67324096
rs382190 None 889 A G 0.0028 5 67324355
rs2115127 CMYA5 702 A G 0.0045 5 79125572 79025572 79275146 249574 CMYA5
rs1643992 CMYA5 585 A T 0.0028 5 79133562
rs6453484 CMYA5 1033 C T 0.0026 5 79165786
rs9283795 CMYA5 1248 C T 0.0025 5 79166420
rs2404670 CMYA5 779 A G 0.004 5 79175146
rs10515282 None 355 C T 0.0032 5 98111861 98011861 98283284 271423 RGMB
rs1605714 None 577 C T 0.0023 5 98112838 CHD1 O
rs719246 None 1126 C T 0.0027 5 98134141
rs10515283 None 356 C T 0.0017 5 98169888
rs1979980 RGMB 650 G T 0.0041 5 98183284
rs286809 FBXL17 837 C T 0.0025 5 107534853 107434853 107737830 302977 FBXL17
rs286797 FBXL17 836 A G 0.0009 5 107559070
rs10515385 FBXL17 358 A C 0.0012 5 107604483
rs286763 FBXL17 835 C T 0.0024 5 107607518
rs2966821 FBXL17 848 A C 0.0038 5 107611102
rs2122158 FBXL17 706 C T 0.0048 5 107637830
rs10515406 None 360 A G 0.0024 5 108987234 108887234 109087234 200000
L0C391819
MAN2A1
0
N
rs383096 None 892 A G 0.004 5 125259035 125159035 125359035 200000 None
tD
rs7721549 None 1183 C T 0.0048 5 144839202 144739202 144939202 200000 None
tD
N
rs716376 None 1118 A G 0.0023 5 157527972 157427972 157652114 224142 None o
rs1614336 None 582 A C 0.0019 5 157532763 0
rs1173476 None 424 G T 0.0014 5 157537804 L n
rs1540944 None 552 A G 0.0013 5 157547994
CD
rs10515758 None 365 A G 0.0028 5 157552114
rs1157122 GABRAI 417 C T 0.0015 5 161300209 161200209 161400209 200000 GABRAI
rs10515855 None 369 C G 0.0046 5 162719997 162619997 162849780 229783 CCNG1
rs300238 None 853 A G 0.0035 5 162731265 L0C134492
rs6873695 None 1073 C T 0.005 5 162749780 HMMR
rs6601146 None 1054 G T 0.0044 5 180403167 180303167 180503167 200000 BTNL8
BTNL3
BTNL9 rs160693 None 578 C T 0.0029 6 2738529 2638529 2865713 227184 WRNIP1
rs2118940 None 704 A G 0.0019 6 2763874 SERPINB1
rs9328130 None 1314 C T 0.0022 6 2765713 SERPINB9
rs2753245 C6orf149 812 C G 0.0034 6 5203091 5103091 5326448 223357 C6orf149
rs4141760 None 926 G T 0.0006 6 5220364 FARS1
rs9328291 None 1315 A G 0.0008 6 5221747 0
rs9328292 None 1316 A G 0.0009 6 5226448
rs10484878 C6orf33 42 C T 0.004 6 52283650 52183650 52389538 205888 IL17F
rs10484877 C6orf33 41 C T 0.0036 6 52289538 MCM3
C6orf33
rs10484647 C6orf142 38 A G 0.003 6 54112210 54012210 54284342 272132 C6orf142
rs9296744 C6orf142 1262 C T 0.0014 6 54176818 TINAG
rs10484646 None 37 A C 0.0015 6 54179189
rs9296745 None 1263 C T 0.0014 6 54179227
rs10484644 None 36 A G 0.0016 6 54181892
rs6913087 None 1077 A G 0.0018 6 54183885 ~
rs2894818 None 842 A G 0.0028 6 54184342
0
N
rs10499021 None 168 A G 0.0021 6 99138965 99038965 99238965 200000 None ~
rs9322661 None 1307 C T 0.0017 6 102940065 102840065 103144877 304812 None tD
rs1578026 None 567 A G 0.0013 6 102972398 tD
rs479856 None 973 C G 0.0011 6 102986050 0
rs9322662 None 1308 C T 0.0028 6 102991994 0
rs9322664 None 1309 A G 0.0041 6 103044877 0
Ln
rs7765824 None 1188 A C 0.0042 6 119130214 119030214 119234543 204329 C6orf204
CD
rs10485389 None 43 C T 0.0035 6 119133914
rs6932535 None 1080 C T 0.0028 6 119134543
rs2328539 PLAGL1 760 A T 0.0005 6 144304399 144204399 144404399 200000 C6orf93
PLAGL1
rs10484614 STX11 35 C T 0.0003 6 144461092 144361092 144681092 320000 PLAGL1
rs1983773 STX11 652 A C 0.0008 6 144462337 SF3B5
rs6935462 None 1082 A T 0.0007 6 144493571 STX11
rs667765 None 1056 C T 0.0037 6 144581092 UTRN
rs7741672 None 1185 C T 0.0035 6 145333306 145233306 145433689 200383 None
rs6924480 None 1079 C T 0.0039 6 145333689
rs7763189 None 1186 A G 0.002 6 148125635 148025635 148232647 207012 None
rs10484683 None 39 A G 0.0034 6 148132647
rs1158619 None 418 A C 0.0015 6 160202439 160102439 160407001 304562 WTAP
rs6901166 None 1076 C T 0.0021 6 160277497 ACAT2 O
rs645851 IGF2R 1034 A G 0.0011 6 160307001 TCP1
MRPL18
PNLDC1
MAS1
IGF2R
rs713055 PARK2 1107 A G 0.0024 6 162480611 162380611 162595042 214431 PARK2
rs2849597 PARK2 828 A G 0.0005 6 162489378
rs1893556 PARK2 621 C T 0.0011 6 162494041
rs2849589 PARK2 827 C T 0.0035 6 162495042
rs654384 SDK1 1048 C T 0.0037 7 3910997 3810997 4010997 200000 SDK1
rs9969156 PHF14 1359 C T 0.0025 7 10935851 10835851 11036097 200246 PHF14 N
rs10499381 PHF14 169 C T 0.0013 7 10936071
rs10499382 PHF14 170 A T 0.004 7 10936097 tD
N tD
rs702479 None 1099 C T 0.0046 7 12548772 12448772 12648772 200000 SCIN N
ARL4A o
0
rs10486616 None 56 A G 0.004 7 33527810 33427810 33689026 261216 None L '
rs10486618 None 57 C G 0.0014 7 33569645 CD
rs10486619 None 58 C T 0.0009 7 33569830
rs7788027 None 1192 A G 0.0023 7 33589026
rs2348460 FLJ21075 762 A G 0.0025 7 47587550 47487550 47778146 290596 PKD1L1
rs7806630 FLJ21075 1194 C T 0.0028 7 47587621 FLJ21075
rs10499668 PKD1L1 172 A G 0.0015 7 47678146 HUS1
rs10224913 None 5 A C 0.0033 7 79600797 79500797 79705307 204510 None
rs6467126 None 1037 A C 0.0013 7 79603430
rs10486935 None 59 A G 0.0008 7 79603851
rs7777441 None 1191 A G 0.0008 7 79604422
rs1074388 None 410 C T 0.0016 7 79605305
rs1074389 None 411 G T 0.0012 7 79605307
rs10238431 None 7 A G 0.0046 7 82562263 82462263 82675171 212908 SEMA3E
rs10270433 None 11 A T 0.002 7 82575171
rs10487867 None 61 C T 0.0049 7 83130182 83030182 83302282 272100 SEMA3A
rs701276 None 1096 A G 0.0016 7 83142116 0
rs701294 None 1097 G T 0.0015 7 83156363
rs10239654 SEMA3A 8 C T 0.0029 7 83202282
rs1362985 None 459 A G 0.002 7 133447945 133347945 133641172 293227 FLJ32786
rs3800756 None 888 C T 0.0021 7 133519414 SLC35B4
rs1791001 None 598 C G 0.0033 7 133541172 AKR1B1
rs10487921 None 62 A G 0.0044 7 145822182 145722182 145922182 200000 CNTNAP2
rs2215798 CNTNAP2 731 A G 0.0045 7 146978322 146878322 147111287 232965
CNTNAP2
rs10488348 CNTNAP2 65 C T 0.0025 7 146999108
rs2708264 CNTNAP2 806 G T 0.004 7 147011287
rs7011065 CSMD1 1095 G T 0.0044 8 4124065 4024065 4225908 201843 CSMD1 N
rs813585 CSMD1 1227 C G 0.0023 8 4125908
tD
rs10503725 MSCP 222 C T 0.0016 8 23418475 23318475 23519248 200773 ENTPD4 tD
rs4593549 MSCP 949 A G 0.0012 8 23418670 MSCP o
rs7819907 MSCP 1196 C T 0.0009 8 23418915 0
rs9314268 MSCP 1288 C T 0.001 8 23418973 0
rs10503726 MSCP 223 C T 0.002 8 23419204 L n
rs4872143 MSCP 982 C T 0.0044 8 23419248 CD
rs4242477 None 931 A T 0.0044 8 52768802 52668802 52870650 201848 None
rs10504127 None 226 A G 0.0039 8 52770650
rs10504596 None 228 C T 0.0039 8 76738283 76638283 76838283 200000 HNF4G
rs1914927 None 631 A C 0.004 8 78745117 78645117 78849973 204856 None
rs2139321 None 708 A G 0.0026 8 78749516
rs1607534 None 579 A C 0.0016 8 78749973
rs7001645 RIMS2 1092 C G 0.0031 8 105079933 104979933 105180574 200641 RIMS2
rs10505054 RIMS2 233 C T 0.0042 8 105080007
rs9297344 RIMS2 1264 A C 0.004 8 105080574
rs723107 None 1138 A G 0.0038 8 105731815 105631815 105831815 200000 LRP12
rs1521775 None 546 A G 0.0017 8 106000463 105900463 106164864 264401 None
rs285866 None 831 A G 0 8 106020040
rs285790 None 829 C T 0.0002 8 106033280 O
rs285839 None 830 A G 0.0018 8 106048055
rs1460582 None 522 C T 0.0048 8 106064864
rs9283944 None 1249 A G 0.0046 8 107290692 107190692 107412262 221570 None
rs9297381 None 1265 C T 0.0024 8 107290914
rs6469061 None 1038 C T 0.0014 8 107312223
rs905556 None 1239 C T 0.0011 8 107312262
rs10505428 ZHX2 239 A G 0.0032 8 123812929 123712929 123912929 200000 ZHX2
rs945658 None 1320 G T 0.005 9 1606639 1506639 1726435 219796 None
rs1323256 None 440 C T 0.0029 9 1608419
rs1323224 None 439 A G 0.0011 9 1626435
0
N
rs438405 RCL1 935 A C 0.0019 9 4814607 4714607 4941661 227054 AK3L1
rs10511460 RCL1 318 C G 0.0016 9 4817222 RCL1 tD
rs456044 RCL1 946 C T 0.0006 9 4841661 tD
N
rs719673 None 1129 A G 0.0006 9 4947650 4847650 5083082 235432 RCL1 00
rs2381194 None 773 C T 0.0003 9 4949331 JAK2 0
rs1327493 JAK2 444 C G 0.0015 9 4983082 L n
N
CD
rs10511581 L0C401492 319 A G 0.0038 9 13405530 13305530 13560671 255141
L0C401492
rs10491751 None 98 C T 0.0015 9 13434932
rs9298688 None 1266 C T 0.0003 9 13459833
rs987290 None 1353 A G 0.0039 9 13460671
rs2060850 FLJ31810 683 A G 0.0032 9 28091541 27991541 28191541 200000 FLJ31810
rs10491884 FLJ31810 106 C T 0.0044 9 28552149 28452149 28652149 200000
FLJ31810
~
rs2589628 TMC1 801 C T 0.003 9 70811449 70711449 70911449 200000 TRPM3
TMC1
rs2769613 None 815 C T 0.0035 9 83364910 83264910 83464995 200085 FRMD3
rs2841475 None 826 C T 0.004 9 83364995
rs1034097 C9orf97 14 C G 0.004 9 95766284 95666284 95962814 296530 C9orflO2
rs3176757 XPA 866 C T 0.0029 9 95816896 C9orf97
rs953199 L0C392371 1331 G T 0.0014 9 95862814 XPA
L0C392371 0
rs4742820 GRIN3A 962 A G 0.0036 9 99774423 99674423 99930334 255911 NR4A3
rs1323435 GRIN3A 442 A G 0.0029 9 99812015 STX17
rs1323434 GRIN3A 441 A G 0.0026 9 99812131 TXNDC4
rs10512285 GRIN3A 330 C T 0.0023 9 99812872 GRIN3A
rs1337710 GRIN3A 448 A G 0.005 9 99830334
rs2416864 NT008470 783 C T 0.001 9 120630058 120530058 120791463 261405 FBXW2
rs10513404 NT008470 343 C T 0.0008 9 120643278 PSMD5
rs1318392 OR1J4 438 A G 0.0007 9 120658438 PHF19
rs1411270 OR1N2 492 C G 0.0027 9 120691463 TRAF1 N
NT008470
0R1J4 tD
OR1N2 tD
N
0
rs10521366 RPS6KA6 408 C T 0.0039 X 82124827 82024827 82224827 200000 RPS6KA6
0
0
rs724981 None 1143 C T 0.0044 X 82335552 82235552 82435552 200000 None L n
~
-------------------------------------------------------------------------------
-----------
dbSNPrsID: SNP identification number in NCBI dbSNP database build 124
Gene locus: Gene positioned in the physical position pointed by the SNP
according to
NCBI Human Genome Build 35
Sequence ID: Sequence identification number
Allele A: Alternate SNP allele or its complementary nucleotide in the position
indicated by dbSNP rs ID and basepair position ro
Allele B: Alternate SNP allele or its complementary nucleotide in the position
indicated by dbSNP rs ID and basepair position
P-value: P-value from haplotype sharing analysis
Position: Basepair Position, SNP physical position according to NCBI Human
Genome
Build 35
Gene_content: Haplotype gene content, genes positioned within 100Kbp
up/downstream from
the physical position of the SNPs bordering the haplotype genomic region
found using NCBI MapViewer, based on NCBI Human Genome Build 35
Table 4. Haplotype genomic regions with the strongest association with HT in
the
haplotype sharing analysis (HaploRec + HPM) with 5 SNPs.
d I G I S IAIAI P I C I P I S I E I E I G O
b I e I e 11111 I h I o I t I n I X I e
S I n I q 11111 v I r I s I a I d I t I n
N I e I u lelel a I o I i I r I I e I e
P I I e 11111 1 I m I t I t I I n I
I 1 I n lelel u I o I i I I I s I c
r I o I c I I I e I s I o I I I i I o
s I c I e IAIBI I o I n I I I o I n
I u I I I I I m I I I I n I t
1 I s I 1 I I I I e I I I I I e
D I I D I I I I I I I I I n
I I I I I I I I I I I t
-------------------------------------------------------------------------------
-------------
rs515279 None 994 A G 0.0049 1 4554061 4454061 4684310 230249 SHREW1
rs10489134 None 81 C G 0.0015 1 4562378 N
rs10489133 None 80 C T 0.0049 1 4584310
tD
rs4660918 RAD54L 952 C T 0.0041 1 46443714 46343714 46618723 275009 TSPAN-1 tD
rs10489769 MGC22960 86 A G 0.0039 1 46518723 FLJ20277 0
RAD54L 0
MUF1 0
UQCRH Li "
MGC22960 CD
FAAH
rs9326028 SSBP3 1313 C T 0.0034 1 54462646 54362646 54630375 267729 L0C200008
rs10489809 SSBP3 87 C T 0.0002 1 54469422 MRPL37
rs7524749 SSBP3 1160 C T 0 1 54491264 SSBP3
rs2076571 SSBP3 687 C T 0.001 1 54530120
rs10489566 SSBP3 85 C G 0.0014 1 54530375
rs542873 DAB1 1002 A G 0.0046 1 57426550 57326550 57526550 200000 DAB1
rs531496 None 1000 C T 0.0018 1 61002405 60902405 61148550 246145 None
rs10493297 None 117 G T 0.0009 1 61003143
rs602295 None 1012 A T 0.0004 1 61004714
rs310159 None 861 C T 0.001 1 61032913
rs10493298 None 118 C T 0.0049 1 61048550
rs1281611 None 435 C T 0.0019 1 82610585 82510585 82769142 258557 None
rs1986902 None 653 A G 0.0006 1 82611768
rs1281590 None 434 A G 0.0007 1 82616264 0
rs10489861 None 88 C T 0.003 1 82669142
rs721599 None 1136 C G 0.0022 1 83240652 83140652 83342288 201636 None
rs10487981 None 63 C T 0.0047 1 83242288
rs477862 COL24A1 972 C T 0.0049 1 86193890 86093890 86337825 243935 COL24A1
rs474106 COL24A1 961 A G 0.0005 1 86194307
rs473232 COL24A1 959 C T 0.0004 1 86194386
rs10493787 COL24A1 122 C G 0.0004 1 86195125
rs10518362 COL24A1 393 A G 0.0005 1 86195653
rs10518360 COL24A1 392 C T 0.0023 1 86237825
~
rs10494009 None 123 C G 0.0033 1 104422787 104322787 104587618 264831
L0C388656
rs1928326 None 635 C T 0.0024 1 104482567 L0C440598 N
rs6586445 None 1052 A C 0.0024 1 104485930
rs1928322 None 634 A G 0.0043 1 104487618 tD
tD
rs2861427 None 834 G T 0.0028 1 185715978 185615978 186091821 475843 None o
rs2861426 None 833 C T 0.0012 1 185716050 0
rs1912914 None 628 A G 0.0006 1 185776923 0
rs2175550 None 724 A G 0.0004 1 185811059 L n
rs1912941 None 629 C T 0.0003 1 185837726 CD
rs4845303 None 980 A T 0.0002 1 185884000
rs6428195 None 1030 C G 0.0002 1 185892552
rs1935654 None 636 C T 0.0003 1 185952796
rs1935659 None 637 A G 0.0003 1 185956354
rs1578704 None 568 A G 0.0002 1 185968869
rs1578705 None 569 A G 0.0002 1 185968934 ro
rs10494628 None 128 C T 0.0003 1 185991821
rs10494627 None 127 C T 0.0005 1 186233469 186133469 186375070 241601 None
rs9287136 None 1252 C T 0.0021 1 186275070
rs1572474 None 562 A G 0.0047 1 188318629 188218629 188658913 440284 None
rs1338034 None 449 C T 0.0037 1 188358939
rs10494658 None 129 A C 0.0036 1 188421032
rs833961 None 1231 C G 0.0008 1 188449185
rs10494659 None 130 C T 0.0001 1 188451130
rs2785762 None 816 C G 0.0016 1 188453606
rs10494660 None 131 C T 0.0009 1 188458950
rs7536312 None 1161 A G 0.0004 1 188459017 O
rs10494661 None 132 A T 0.0008 1 188459839
rs10494662 None 133 C T 0.0008 1 188507286
rs10494663 None 134 A G 0.0001 1 188507735
rs6683269 None 1057 C T 0.0001 1 188507895
rs10494664 None 135 A C 0 1 188509177
rs9287120 None 1251 C G 0.0003 1 188558913
rs10494673 None 136 C T 0.0016 1 188804177 188704177 188904177 200000 RGS18
rs647908 USH2A 1040 G T 0.0046 1 212493121 212393121 212656039 262918 USH2A
rs9308440 XM372814 1282 G T 0.0023 1 212548330
rs1992099 USH2A 654 A G 0.0034 1 212556039
0
rs1112903 None 412 A G 0.0048 1 235664628 235564628 235810329 245701 None N
rs7521497 None 1159 C T 0.0012 1 235703668
rs2105233 None 696 A G 0.0014 1 235710329 tD
~ tD
rs6734151 None 1060 A G 0.0021 2 5420431 5320431 5520431 200000 None N
0
0
rs1012566 None 4 G T 0.0016 2 11933881 11833881 12033881 200000 LPIN1 0
Ln
rs6708911 None 1059 C G 0.002 2 12005429 11905429 12106921 201492 LPIN1 CD
rs966391 None 1346 A G 0.0039 2 12006921
rs7582749 QPCT 1167 C G 0.0025 2 37510988 37410988 37702284 291296 PRKCN
rs2287094 QPCT 752 C T 0.0012 2 37511339 QPCT
rs10490445 None 91 G T 0.001 2 37529135
rs2192947 None 728 A G 0.0013 2 37602284
rs6745501 COMMD1 1061 C T 0.0031 2 62188424 62088424 62319430 231006 COMMD1
rs10518958 COMMD1 395 A G 0.0022 2 62188624 L0C388954
rs10496096 COMMD1 140 C G 0.0012 2 62219430
rs10496095 None 139 A C 0.0046 2 62325264 62225264 62425264 200000 COMMD1
L0C388954
B3GNT1
rs1997454 None 656 A G 0.0014 2 76683211 76583211 76798833 215622 None
rs7592517 None 1168 C T 0.0035 2 76688934
rs2139502 None 709 A G 0.0039 2 76698500
rs1519991 None 542 A C 0.0045 2 76698833 0
rs1921734 None 632 C T 0.0045 2 77222252 77122252 77565585 443333 None
rs1837426 None 607 A G 0.0005 2 77306805
rs1866565 None 616 C T 0 2 77325905
rs10496205 None 144 A G 0 2 77405362
rs290039 None 845 C T 0.0019 2 77465585
rs1487042 None 530 A G 0.0002 2 77842706 77742706 77957830 215124 None
rs994214 None 1357 C T 0.0003 2 77856897
rs10520195 None 399 A G 0.0001 2 77857830
rs2861215 None 832 C T 0.0009 2 77958447 77858447 78058447 200000 None
rs12072 REG1A 429 A G 0.0041 2 79262160 79162160 79373809 211649 UNQ429 n0,
rs10496213 REGL 145 A C 0.0022 2 79273809 REG1B a"'o
REG1A tD
REGL tD
PAP o
0
rs2109312 None 697 C T 0.0031 2 128292061 128192061 128392154 200093 WDR33 0
rs2109313 None 698 A G 0.0024 2 128292154 POLR2D 'i'
MGC4268 ao
rs6756311 None 1065 A G 0.005 2 138714811 138614811 138814811 200000 None
rs9287536 LRP1B 1253 C T 0.0032 2 141139308 141039308 141239308 200000 LRP1B
rs967295 None 1347 A C 0.0036 2 145854184 145754184 145985484 231300 None ro
rs10496976 None 148 C T 0.0043 2 145885484
rs6746500 None 1062 C T 0.0032 2 146491334 146391334 146591334 200000
L0C442053
rs10490387 L0C130576 90 C T 0.005 2 149883856 149783856 149983856 200000
L0C130576
rs9288697 ACVR1 1256 A C 0.0034 2 158520326 158420326 158620326 200000 ACVR1
rs1370656 PDE11A 463 A C 0.0022 2 178433505 178333505 178558300 224795 PDE11A
rs2164857 PDE11A 719 A C 0.0011 2 178434643
rs1438048 PDE11A 508 A C 0.001 2 178438353
rs10497488 PDE11A 155 A C 0.0007 2 178446084
rs1370655 PDE11A 462 C T 0.0048 2 178458300 O
rs10497895 L0C344471 157 C T 0.004 2 208752799 208652799 208933065 280266
L0C389072
rs10497893 CRYGEP1 156 A C 0.0006 2 208803303 L0C344471
rs796287 CRYGB 1210 G T 0.0027 2 208833065 CRYGEP1
CRYGD
CRYGC
L0C442066
CRYGB
CRYGA
L0C389073
L0C130429
IDH1
rs10497952 ERBB4 159 C T 0.0022 2 212548864 212448864 212648864 200000 ERBB4 N
Ln
CD
rs2222182 None 734 G T 0.005 2 215314636 215214636 215426661 212025 L0C402117
tD
rs9288498 None 1254 A C 0.0044 2 215314796 L0C391481 tD
rs9288499 None 1255 C T 0.0036 2 215315184 BARD1 N
rs1040217 L0C391481 16 A G 0.0037 2 215326661 00
0
rs1649882 SP100 586 G T 0.0017 2 231160817 231060817 231260817 200000 L0C93349
L n
SP100 CD
HMG1L3
rs161912 None 583 A G 0.004 3 7796996 7696996 7913242 216246 GRM7
rs45840 None 948 C T 0.0015 3 7797471
rs161927 None 584 A G 0.0022 3 7813242
rs10514689 None 352 A G 0.0025 3 35284798 35184798 35463148 278350 L0C442078
rs7625092 L0C389105 1173 A G 0.0022 3 35361572 L0C389105
rs1160577 L0C389105 420 A C 0.0019 3 35363086
rs1160578 L0C389105 421 C T 0.0035 3 35363148
rs3849526 FLJ42117 895 A T 0.002 3 58829160 58729160 58929160 200000 FLJ42117
rs9311694 None 1283 A C 0.0003 3 59015681 58915681 59115681 200000 FLJ42117
rs1913157 None 630 C G 0 3 59149421 59049421 59370772 321351 None
rs1512828 None 538 A C 0 3 59153070
rs2165999 None 720 C T 0.0005 3 59239357
rs10510805 None 312 C T 0.0013 3 59244082 0
rs7613873 None 1172 A G 0.0044 3 59270772
rs1473857 None 528 A G 0.002 3 103118335 103018335 103337290 318955 MGC15606
rs771829 L0C152225 1181 C T 0.0003 3 103174504 MAIL
rs1514471 L0C152225 540 A G 0 3 103179898 L0C152225
rs1513120 L0C152225 539 C T 0 3 103180369
rs10511192 L0C152225 314 C T 0 3 103196322
rs771765 None 1180 A G 0.0004 3 103221763
rs978697 None 1352 C T 0.0031 3 103237290
rs1521409 None 544 A G 0.002 3 118340331 118240331 118468524 228193 None
rs1462840 None 523 C T 0.0035 3 118345185 ~
rs10511365 None 316 C T 0.0034 3 118368524
0
N
rs3846211 None 893 A G 0.0045 3 187789243 187689243 187920935 231692 CRYGS
rs9290835 None 1258 A T 0.0014 3 187801488 FLJ10560 tD
rs1029353 AHSG 13 C T 0.0035 3 187820935 DNAJBII tD
AHSG N
0
FETUB
HRG o
L0C442099 L n
KNG1 CD
rs2370156 None 766 C G 0.004 4 34858973 34758973 35098967 339994 None
rs7679959 None 1178 C G 0.0015 4 34922573
rs10517338 None 381 C G 0.0005 4 34939974
rs959297 None 1338 A T 0.0009 4 34979810
rs1480972 None 529 A G 0.0033 4 34998967 ro
rs9291304 GABRB1 1259 A G 0.0026 4 46970384 46870384 47070384 200000 GABRB1
~
rs10488850 None 74 C T 0.0013 4 55298473 55198473 55452010 253537 KIT
rs10488849 None 73 C T 0.0009 4 55351790
rs10488848 None 72 A C 0.002 4 55352010
rs10517413 None 382 C G 0.0041 4 58498976 58398976 58606986 208010 None
rs3905283 None 903 A C 0.0042 4 58506986
rs6821362 None 1070 A G 0.0049 4 61614979 61514979 61760388 245409 None
rs10517518 None 383 C T 0.0032 4 61624182
rs767645 None 1177 A T 0.0006 4 61660160 O
rs10517519 None 384 A T 0.0035 4 61660388
rs293443 None 847 C T 0.0039 4 69411859 69311859 69511859 200000 L0C345378
L0C441018
rs10516708 None 376 C T 0.0038 4 85194717 85094717 85340203 245486 None
rs1827814 None 601 C T 0.0017 4 85212132
rs725997 None 1145 C G 0.0011 4 85212727
rs2017802 None 666 C T 0.0021 4 85240203
rs10489026 L0C339979 78 C G 0.0019 4 109640337 109540337 109745336 204999
L0C339979
rs7667905 L0C339979 1176 A G 0.0003 4 109644249 L0C391681
rs10489027 L0C339979 79 A G 0.0013 4 109645336
0
N
rs10516557 SEC24B 373 A G 0.0048 4 110753010 110653010 110944263 291253 SEC24B
rs10516558 SEC24B 374 C T 0.0029 4 110807600 L0C389217 tD
rs2089273 None 693 A T 0.0011 4 110821552 FLJ20647
tD
rs10488910 FLJ20647 75 A G 0.0026 4 110844263 0
0
rs4833470 None 979 C T 0.005 4 112145059 112045059 112269892 224833 L0C391686
0
rs10488914 None 76 A G 0.0021 4 112169892 L n
N
CD
rs1376089 None 468 A G 0.0035 4 139853546 139753546 139953546 200000 L0C152594
rs10517654 PDGFC 386 G T 0.0042 4 158138367 158038367 158243059 204692 PDGFC
rs10517655 PDGFC 387 A G 0.0021 4 158138514
rs6811964 PDGFC 1069 C T 0.0044 4 158143059
rs9308065 None 1280 A G 0.0036 4 165020972 164920972 165125685 204713 None
rs9308066 None 1281 A G 0.0019 4 165025685
~
rs10517877 None 389 C T 0.0044 4 167437519 167337519 167541111 203592 TLL1
rs10517878 None 390 C T 0.0025 4 167437549
rs4691246 None 956 C T 0.002 4 167437606
rs10517879 None 391 G T 0.0035 4 167441111
rs10512675 None 336 C G 0.0019 5 2739258 2639258 2839258 200000 IRX2
CEI
rs10512672 None 335 G T 0.0005 5 2855065 2755065 3117980 362915 IRX2
rs438418 None 936 A G 0.0004 5 2902436 CEI 0
rs9313016 None 1286 A C 0.0005 5 2972588 L0C391734
rs9313018 None 1287 A G 0.0034 5 3017980 L0C442129
rs995553 None 1358 C G 0.0048 5 8881383 8781383 9008403 227020 None
rs10512984 None 341 C G 0.0045 5 8908403
rs7724797 None 1184 A C 0.004 5 31131278 31031278 31239623 208345 L0C391774
rs12658568 None 433 A G 0.0031 5 31139623 CDH6
rs2115127 CMYA5 702 A G 0.0039 5 79077255 78977255 79226829 249574 PAPD4
rs1643992 CMYA5 585 A T 0.0042 5 79085245 CMYA5
rs6453484 CMYA5 1033 C T 0.0014 5 79117469 ~
rs9283795 CMYA5 1248 C T 0.0007 5 79118103
rs2404670 CMYA5 779 A G 0.005 5 79126829 N
Ln
CD
rs1605714 None 577 C T 0.0032 5 98064521 97964521 98235041 270520 L0C402222 tD
rs719246 None 1126 C T 0.0017 5 98085824 RGMB tD
rs10515283 None 356 C T 0.0002 5 98121571 CHD1 0
rs1979980 RGMB 650 G T 0.0024 5 98134967 0
rs2302981 RGMB 758 A G 0.0039 5 98135041 0
Ln
rs724719 L0C391819 1142 C T 0.0033 5 108775429 108675429 109038917 363488
L0C285638 CD
rs10515401 L0C391819 359 A G 0.0024 5 108856709 PJA2
rs10515406 None 360 A G 0.0022 5 108938917 L0C391819
rs383096 None 892 A G 0.0036 5 125210718 125110718 125310718 200000 None
rs1007400 KIAA1985 1 C T 0.0023 5 148362828 148262828 148570256 307428
KIAA1985 ro
rs384979 L0C255187 896 C T 0.0008 5 148439460 L0C255187
rs10515622 L0C255187 364 G T 0.0006 5 148468253 ABLIM3
rs1363522 L0C255187 460 C T 0.0005 5 148469763
rs1422586 None 502 C T 0.0014 5 148470256
rs4704935 None 957 A T 0.0022 5 155387010 155287010 155487010 200000 None
rs249882 None 795 C T 0.0022 5 155572134 155472134 155705573 233439 SGCD
rs30280 None 857 C G 0.0045 5 155605573
rs10484199 None 32 A G 0.0007 5 157430213 157330213 157603797 273584 L0C345471
rs716376 None 1118 A G 0 5 157479655
rs1614336 None 582 A C 0.0003 5 157484446 O
rs1173476 None 424 G T 0.0007 5 157489487
rs1540944 None 552 A G 0.0049 5 157499677
rs10515758 None 365 A G 0.0039 5 157503797
rs10515768 None 366 A G 0.0044 5 158017072 157917072 158129553 212481 EBF
rs824848 None 1230 A G 0.0013 5 158019033
rs6881040 None 1075 A G 0.0019 5 158028752
rs403334 None 910 A C 0.0023 5 158029229
rs10515769 None 367 C T 0.0043 5 158029553
rs4128400 None 916 C G 0.0036 5 161087892 160987892 161187892 200000 GABRA6
L0C441113
rs1157122 GABRAI 417 C T 0.0003 5 161251892 161151892 161419863 267971 GABRAI
N
rs2279020 GABRAI 750 C T 0.002 5 161255467
rs4144483 GABRAI 927 A G 0.0035 5 161256450 tD
rs10515836 None 368 C T 0.0045 5 161319863
tD
N
rs4128628 None 917 C T 0.0041 5 178971483 178871483 179071483 200000 L0C441120
0
RUFY1 0
HNRPH1
L0C285679 CD
L0C389352
CANX
rs10516146 MAML1 372 A G 0.0042 5 179099580 178999580 179199580 200000
L0C285679
L0C389352
CANX
MAML1
LTC4S
MGAT4B
SQSTM1
L0C51149
rs511574 PHACTR1 992 G T 0.0018 6 12824508 12724508 12973311 248803 PHACTR1
rs6922482 PHACTR1 1078 C T 0.0022 6 12873311
rs8541 None 1232 C T 0.0021 6 13398217 13298217 13509896 211679 PHACTR1
rs202020 None 667 C G 0.0032 6 13409896 TBC1D7
GFOD1
O
rs10484858 BPAG1 40 C T 0.0038 6 56571971 56471971 56769232 297261 DST
rs6941626 DST 1084 C T 0.0033 6 56607148
rs10498811 DST 166 A G 0.0047 6 56669232
rs9320728 None 1305 C T 0.004 6 120323232 120223232 120423232 200000 None
rs9321214 None 1306 C T 0.0029 6 130524915 130424915 130677705 252790 L3MBTL3
rs6569665 SAMD3 1050 C T 0.0036 6 130575427 SAMD3
rs6934450 SAMD3 1081 A G 0.0043 6 130577705
rs10484614 STX11 35 C T 0.0006 6 144522215 144422215 144742215 320000 SF3B5
rs1983773 STX11 652 A C 0.0004 6 144523460 MRPL42P3
rs6935462 None 1082 A T 0.0005 6 144554694 STX11
rs667765 None 1056 C T 0.0041 6 144642215 L0C285741
UTRN
Ln
m
rs6938409 UTRN 1083 A G 0.0047 6 144958637 144858637 145087523 228886 UTRN tD
rs1830271 UTRN 603 C T 0.0027 6 144963781 tD
rs951573 UTRN 1328 A G 0.0019 6 144987523 0
0
rs2758778 None 813 A G 0.0045 6 153099916 152999916 153266436 266520 SYNE1 0
rs633596 None 1028 C T 0.0023 6 153157601 MYCT1 'i'
rs3823082 VIP 890 C T 0.0047 6 153166436 VIP ao
rs2146162 ACAT2 711 C T 0.0049 6 160151513 160051513 160251513 200000 SOD2
WTAP
ACAT2
TCP1
MRPL18
PNLDC1
rs1998167 None 657 A G 0.0035 6 166688847 166588847 166789073 200226 MGC35308
rs1998168 None 658 A G 0.0025 6 166689073 C6orf83
L0C401284
BRP44L
rs2235280 RPS6KA2 740 A G 0.0042 6 166856907 166756907 166956907 200000 BRP44L
RPS6KA2
rs6462545 SDK1 1036 A G 0.0044 7 3852653 3752653 4039900 287247 SDK1
rs10485860 SDK1 52 C T 0.0026 7 3863524
rs654384 SDK1 1048 C T 0.0023 7 3939900 O
rs1178363 None 426 A G 0.0034 7 17951650 17851650 18113337 261687 L0C402463
rs1178328 L0C402463 425 G T 0.0024 7 18006698
rs6461373 None 1035 G T 0.0018 7 18006935
rs10486419 L0C402463 54 C T 0.0037 7 18013337
rs4719652 None 958 C T 0.005 7 21031040 20931040 21131040 200000 L0C340274
rs9638787 DNAH11 1342 C G 0.0038 7 21423805 21323805 21619605 295800 SP4
rs10226107 DNAH11 6 A G 0.0016 7 21452680 DNAH11
rs2177520 DNAH11 725 C G 0.0027 7 21471062
rs10499538 DNAH11 171 A G 0.0012 7 21471340
rs7793951 DNAH11 1193 C G 0.0018 7 21473279
rs970604 DNAH11 1348 A G 0.0018 7 21478560 N
rs10485971 DNAH11 53 A C 0.0019 7 21519605
tD
rs10486618 None 57 C G 0.0019 7 33600653 33500653 33789384 288731 BMPER
tD
rs10486619 None 58 C T 0.0005 7 33600838 N
rs7788027 None 1192 A G 0.001 7 33620034 00
rs315853 None 863 A G 0.0023 7 33689384 0
Ln
rs2348460 FLJ21075 762 A G 0.0047 7 47620010 47520010 47891917 371907 MGC16075
CD
rs7806630 FLJ21075 1194 C T 0.003 7 47620081 FLJ21075
rs10499668 PKD1L1 172 A G 0.0011 7 47710606 PKD1L1
rs3176499 HUS1 865 A G 0.0036 7 47791917 HUS1
MGC33329
L0C136288
rs717707 ABCA13 1123 C T 0.005 7 48206690 48106690 48306690 200000 ABCA13
rs921909 None 1244 A T 0.0044 7 50018956 49918956 50118956 200000 L0C340228
rs1581590 None 572 C G 0.0041 7 53880000 53780000 54011504 231504 None
rs10499727 None 173 C T 0.0027 7 53897460
rs10499728 None 174 A G 0.0028 7 53904808
rs953160 None 1330 A G 0.003 7 53911397
rs956316 None 1336 C T 0.0033 7 53911504
rs10487817 None 60 A G 0.0049 7 105552534 105452534 105701508 248974 PBEF1
rs10499961 None 175 C T 0.0025 7 105563140
rs2014402 None 663 A G 0.0049 7 105578138 0
rs2519681 None 798 C T 0.0042 7 105578447
rs179861 None 599 C T 0.0037 7 105600903
rs719917 None 1131 C T 0.0043 7 105601508
rs1365358 None 461 A G 0.002 7 135363114 135263114 135569609 306495 None
rs10270360 L0C401406 10 A G 0.0005 7 135407033
rs730694 L0C401406 1149 C T 0 7 135407458
rs10488406 None 66 C T 0 7 135408567
rs2114337 None 701 A G 0.0004 7 135412215
rs10488407 None 67 C T 0.004 7 135469609
rs10500165 CNTNAP2 176 A G 0.0049 7 145980635 145880635 146107522 226887
CNTNAP2
rs4537227 CNTNAP2 944 A G 0.0037 7 146007522
0
N
rs1599405 None 576 A T 0.0048 7 155187279 155087279 155287279 200000 SHH
L0C389602
tD
rs7814546 None 1195 C T 0.0046 8 12730375 12630375 12856234 225859 FLJ23749 0
rs2068280 None 685 G T 0.0035 8 12736493 L0C340357 0
rs4831837 None 978 A G 0.0025 8 12756234 FLJ36980 0
Ln
rs1346277 SGCZ 453 A G 0.0022 8 14204068 14104068 14347492 243424 SGCZ CD
rs10503493 SGCZ 219 G T 0.0019 8 14247492
rs823603 None 1229 A C 0.0036 8 16861200 16761200 16967896 206696 FGF20
rs823600 None 1228 G T 0.0038 8 16861804 L0C286097
rs963080 None 1340 A G 0.0038 8 16867896
rs1464252 None 524 C T 0.0045 8 60472233 60372233 60572233 200000 None
rs10504292 None 227 A G 0.0037 8 60586442 60486442 60686442 200000 None
rs10504596 None 228 C T 0.0026 8 76850876 76750876 76950876 200000 None
rs10504677 PKIA 229 G T 0.0047 8 79623737 79523737 79755531 231794 PKIA
rs2062233 PKIA 684 A G 0.0046 8 79655531 CGI-62
rs416011 None 928 C T 0.0018 8 88602922 88502922 88769709 266787 None
rs10504835 None 231 A G 0.0025 8 88616896
rs10504836 None 232 A C 0.0043 8 88669709
O
rs1160054 None 419 A G 0.0048 8 106006662 105906662 106106662 200000 None
rs10505087 ZFPM2 234 C T 0.004 8 106877254 106777254 106988057 210803 ZFPM2
rs6990997 ZFPM2 1091 C T 0.0027 8 106881703
rs7007352 None 1093 C T 0.0032 8 106888057
rs9297381 None 1265 C T 0.0024 8 107403507 107303507 107524855 221348
L0C346887
rs6469061 None 1038 C T 0.001 8 107424816
rs905556 None 1239 C T 0.0009 8 107424855
rs1789967 None 597 G T 0.0027 8 107526431 107426431 107626431 200000 None
rs10505137 L0C392262 235 C T 0.0034 8 111210785 111110785 111342982 232197
L0C392262
rs10505138 L0C392262 236 A T 0.003 8 111211034 N
rs2060688 L0C392262 682 C T 0.001 8 111220823
rs10505139 L0C392262 237 C T 0.0018 8 111220849 tD
rs10505140 L0C392262 238 A G 0.0009 8 111223708 tD
rs921382 L0C392262 1243 C G 0.0011 8 111236214 N
rs4735150 L0C392262 960 C T 0.0025 8 111236704 00
rs2198044 L0C392262 729 A G 0.0023 8 111242982 0
Ln
rs1412254 None 495 G T 0.0028 9 1500230 1400230 1602232 202002 None CD
rs10491859 None 104 C T 0.0034 9 1500299
rs10491858 None 103 A G 0.0041 9 1500495
rs10491857 None 102 C T 0.005 9 1502232
rs456044 RCL1 946 C T 0.0032 9 4841661 4741661 4941661 200000 L0C392282
RCL1
L0C441384
rs719673 None 1129 A G 0.0015 9 4947650 4847650 5088639 240989 RCL1
rs2381194 None 773 C T 0.0008 9 4949331 L0C441384
rs1327493 JAK2 444 C G 0.0009 9 4983082 JAK2
rs2225125 JAK2 739 A G 0.0034 9 4988639
rs1374172 None 466 A C 0.0049 9 12018131 11918131 12121256 203125 None
rs2077861 None 690 A G 0.0036 9 12018387
rs1446253 None 509 C G 0.0032 9 12021256
rs947144 ADAMTSL1 1321 A G 0.0046 9 18643380 18543380 18771452 228072 ADAMTSL1
rs10511661 ADAMTSL1 320 A G 0.0026 9 18644351 0
rs1412672 ADAMTSL1 497 C G 0.0039 9 18670679
rs776760 ADAMTSL1 1189 A G 0.0037 9 18671452
rs10491828 FLJ31810 101 G T 0.003 9 28030600 27930600 28191541 260941 FLJ31810
rs1452353 FLJ31810 512 A G 0.0009 9 28030937
rs1343456 FLJ31810 450 C T 0.0012 9 28039518
rs10511820 FLJ31810 321 G T 0.0005 9 28045603
rs2383761 FLJ31810 774 A G 0.0006 9 28054538
rs1452356 FLJ31810 513 C T 0.0003 9 28057491
rs7853840 FLJ31810 1197 A G 0.0015 9 28058081
rs7858580 FLJ31810 1198 A G 0.0009 9 28059562
rs10511821 FLJ31810 322 A G 0.002 9 28064589
rs1452357 FLJ31810 514 C T 0.003 9 28090846
rs993038 FLJ31810 1356 C G 0.0021 9 28091281 N
rs2060850 FLJ31810 683 A G 0.0012 9 28091541
tD
rs10511824 FLJ31810 323 A G 0.005 9 28195162 28095162 28295162 200000 FLJ31810
tD
N
O
rs10491883 FLJ31810 105 C T 0.0044 9 28552256 28452256 28718807 266551
FLJ31810 0
rs10511829 FLJ31810 324 C G 0.0048 9 28618807 0
Ln
rs10512162 None 327 A G 0.0042 9 85091455 84991455 85237345 245890 None CD
rs2769613 None 815 C T 0.0046 9 85137345
rs2814726 None 818 C T 0.0048 9 85244200 85144200 85353684 209484 None
rs10512167 None 328 C T 0.0046 9 85253684
rs2417359 None 784 A G 0.0024 9 102187111 102087111 102287111 200000 None ro
rs10513402 None 342 C T 0.0043 9 122244490 122144490 122497997 353507 MRRF
rs950104 None 1324 A G 0.0006 9 122244779 PTGS1
rs2416863 NT008470 782 C T 0.0002 9 122332531 OR1J1
rs2416864 NT008470 783 C T 0 9 122333567 OR1J2
rs1318392 OR1J4 438 A G 0.0001 9 122361947 OR1J4
rs1411270 L0C138882 492 C G 0.0001 9 122394972 OR1N1
rs1831369 OR1N2 604 A G 0.0002 9 122395096 OR1N2
rs1411271 OR1N2 493 C G 0.0003 9 122395332 OR1L8
rs1411272 OR1N2 494 C T 0.0005 9 122395904 OR1H1P
rs1041355 None 17 A G 0.0011 9 122397215 OR1Q1
rs1024288 None 9 C G 0.0025 9 122397449 OR1B1
rs2149931 None 713 C T 0.0039 9 122397997 O
rs7912369 None 1203 A G 0.0018 10 1995604 1895604 2238650 343046 L0C439946
rs1010784 None 3 C G 0.0011 10 2013899 L0C399707
rs1335311 None 447 C G 0.0001 10 2014269
rs10508220 None 272 A G 0.0001 10 2014591 vi
rs1335310 None 446 C T 0.0001 10 2074135
rs2026493 None 670 A G 0.0006 10 2114063
rs4880556 None 983 A G 0.0031 10 2138650
rs10508229 None 274 A G 0.0021 10 2381642 2281642 2483152 201510 L0C399708
rs10508230 None 275 A G 0.002 10 2383152 L0C387630
~
rs649537 FBX018 1043 A C 0.0047 10 5985678 5885678 6098078 212400 GDI2
rs668498 FBX018 1058 C T 0.003 10 5998078 ANKRD16 i
FBX018
IL15RA tD
LOC399713 0
IL2RA iv
0
0
rs10508410 None 276 C G 0.0029 10 10710236 10610236 10814839 204603 None o
rs10508411 None 277 A G 0.0029 10 10711607 L '
rs10508412 None 278 C T 0.0028 10 10713082 CD
rs960791 None 1339 A T 0.0032 10 10714839
rs10508562 CACNB2 283 C T 0.0044 10 18845512 18745512 18953283 207771 CACNB2
rs10508563 CACNB2 284 A C 0.003 10 18852597 NOPD1
rs7081811 CACNB2 1101 A G 0.0018 10 18853283
rs10508771 None 286 A T 0.0042 10 32532098 32432098 32764642 332544 L0C441550
rs3006608 None 854 C T 0.0026 10 32532124 L0C441551 -~7
rs10508773 EPC1 287 C T 0.004 10 32615450 L0C439953
rs950132 EPC1 1325 C T 0.0022 10 32664642 EPC1
rs4445583 None 939 C T 0.0002 10 52173015 52073015 52472683 399668 FLJ31958
rs10508933 ACF 289 C G 0 10 52240121 L0C439978
rs10509071 None 295 A G 0.0001 10 52257286 L0C441561
rs4567398 ACF 947 C T 0.0011 10 52286928 L0C399773
rs10490967 None 94 A G 0.003 10 52372683 ACF
rs10509012 PCDH15 290 G T 0.0013 10 55796840 55696840 56066306 369466 PCDH15
rs1832879 PCDH15 605 C T 0.0009 10 55878340 0
rs2026414 PCDH15 669 A G 0.0008 10 55878742
rs9299552 PCDH15 1267 C T 0.0004 10 55911196
rs10509013 PCDH15 291 A G 0.0022 10 55957107
rs1781451 PCDH15 593 C T 0.0045 10 55966306
rs1900493 None 624 A G 0.0036 10 56783626 56683626 57184485 500859 L0C389970
rs7908118 None 1202 C T 0.001 10 56883032
rs2050318 None 676 G T 0.0006 10 56934746
rs10509034 None 292 C T 0.001 10 56962466
rs997418 None 1361 A G 0.0015 10 56976835
rs1413668 None 500 A G 0.0028 10 56985141
rs10509035 None 293 G T 0.0019 10 57015785 0
rs4336940 None 934 A G 0.0021 10 57039123
rs10509036 None 294 A G 0.0031 10 57040245 N
rs2244956 None 743 C G 0.0049 10 57084485
tD
rs4474385 ANK3 942 A T 0.0032 10 61563083 61463083 61696196 233113 ANK3 ~
rs10509123 ANK3 296 A C 0.0006 10 61563151 0
rs10509124 ANK3 297 C T 0.0005 10 61563739 0
rs3213829 ANK3 869 G T 0.0004 10 61563904 0
rs4948254 ANK3 987 A T 0.0013 10 61569339 L n
rs4245585 ANK3 932 C T 0.004 10 61596196 CD
rs1904620 CTNNA3 625 A G 0.005 10 68721550 68621550 68821550 200000 CTNNA3
rs987312 None 1354 A G 0.0033 10 85304655 85204655 85469801 265146 None
rs10509478 None 307 A T 0.004 10 85369801
rs10509408 MINPP1 306 C T 0.0042 10 89300261 89200261 89408314 208053 MINPP1
rs1408377 MINPP1 487 C T 0.0017 10 89300642
rs2147287 None 712 A G 0.0016 10 89308314
rs2209672 None 730 A G 0.0022 10 92020205 91920205 92120599 200394 None
rs10509597 None 308 A C 0.0031 10 92020599
rs7069564 None 1100 C T 0.0028 10 112887060 112787060 112987060 200000 ADRA2A
rs2468826 None 789 C T 0.0042 11 18127264 18027264 18227264 200000 L0C113174
SAA3P
MRGX3
MRGX4 O
SAA4
SAA2
rs10500911 None 185 A C 0.0033 11 21568879 21468879 21742888 274009 NELL1
rs963497 None 1341 A G 0.0006 11 21595783
rs10500913 None 186 A G 0.0002 11 21613794
rs7112382 None 1105 A G 0.0003 11 21614149
rs7107412 None 1104 C T 0.0011 11 21642613
rs1459865 None 521 A G 0.0036 11 21642888
rs4086865 None 913 C T 0.005 11 25968769 25868769 26068769 200000 None
~
rs1346099 None 451 C G 0.0047 11 35066313 34966313 35187935 221622 PDHX
rs1425800 None 504 C T 0.0029 11 35066493 CD44 N
rs353589 None 876 A G 0.0023 11 35077802
rs353587 None 875 A G 0.0013 11 35079237 tD
rs1559759 None 559 G T 0.0004 11 35079627
tD
rs4756190 None 965 A G 0.0001 11 35080616 N
rs507230 None 990 C T 0.0002 11 35085748 0
rs634096 None 1029 C T 0.0017 11 35087935 0
Ln
rs10501486 None 197 C T 0.0046 11 80347478 80247478 80558705 311227 None CD
rs1391533 None 474 C T 0.0006 11 80347594
rs1608169 None 580 G T 0.0006 11 80428536
rs1829764 None 602 C T 0.0012 11 80428642
rs2373717 None 771 A T 0.0009 11 80457064
rs10501487 None 198 A T 0.0042 11 80458705
rs1941437 L0C390241 638 C T 0.0036 11 91849773 91749773 91951009 201236
L0C440062
rs10501790 L0C440062 201 C T 0.0042 11 91851009
~
rs721346 None 1135 A C 0.0021 11 103242667 103142667 103376131 233464 PDGFD
rs1400549 None 479 C T 0.001 11 103245119
rs503208 None 989 C G 0.0002 11 103263149
rs7127296 None 1106 A C 0.0034 11 103276131
rs1789819 None 596 C T 0.0048 11 109185632 109085632 109368427 282795
L0C260340
rs715312 None 1112 C T 0.0026 11 109222549
rs666899 None 1055 A G 0.002 11 109239458
rs10488748 None 70 A G 0.0046 11 109268427
O
rs10502283 L0C338661 202 C T 0.0031 11 123258475 123158475 123358896 200421
OR6M2P
rs1054041 L0C338661 409 C T 0.0049 11 123258896 OR6M3P
L0C338661
0R8D4
0R4D5
OR6T1
OR10S1
rs10492107 PRKWNK1 107 A G 0.0026 12 842330 742330 972280 229950 PRKWNK1
rs2051852 PRKWNK1 678 C T 0.0023 12 872280 HSN2
RAD52
ELKS
rs7954090 ELKS 1208 C T 0.0022 12 1034157 934157 1134157 200000 ELKS n0,
Ln
CD
rs10492194 None 108 C T 0.0035 12 16806772 16706772 16907436 200664 None tD
rs7296019 None 1148 A C 0.0039 12 16807436 tD
N
0
rs7135355 None 1108 G T 0.0023 12 58108434 58008434 58238327 229893 None 0
rs276002 None 814 A G 0.0001 12 58138327 0
Ln
rs274460 None 810 A G 0 12 58238608 58138608 58421404 282796 SLC16A7 ao
rs3847653 None 894 C G 0 12 58238640
rs3897770 None 901 A C 0 12 58238933
rs10506395 None 246 C T 0 12 58258088
rs1391130 None 473 A G 0.0004 12 58270954
rs10506396 None 247 G T 0.0019 12 58321404
rs11175617 None 415 A C 0.0039 12 63677987 63577987 63777987 200000 L0C400046
WIF1
rs10506645 TPH2 250 A G 0.0046 12 70671767 70571767 70884135 312368 TBC1D15
rs4760754 TPH2 966 A C 0.001 12 70675106 TPH2
rs1487275 TPH2 531 A C 0.0002 12 70696559
rs1386486 TPH2 472 C T 0 12 70698487
rs1386485 TPH2 471 A C 0 12 70698634
rs1386483 TPH2 470 A G 0.0001 12 70698761
rs7977245 None 1212 C T 0 12 70784135
rs2687491 None 803 A G 0.0017 12 70901536 70801536 71001536 200000 L0C283392
TRHDE O
rs1394380 None 475 A G 0.0022 12 97055132 96955132 97178944 223812 None
rs1842328 None 609 C T 0.0025 12 97078944
rs10507103 EB-1 255 C T 0.002 12 97866110 97766110 97968064 201954 EB-1
rs10507104 EB-1 256 A G 0.0014 12 97868064
rs2888378 EB-1 840 A G 0.0007 12 97978643 97878643 98106090 227447 EB-1
rs2372643 EB-1 768 A G 0.0005 12 97988506
rs2372644 EB-1 769 A C 0.0017 12 97993228
rs4762559 EB-1 967 C T 0.0013 12 98001108
rs10507107 EB-1 257 C G 0.0025 12 98006090
rs2270861 DRIM 747 C T 0.0026 12 100238849 100138849 100345515 206666 DRIM
rs2373444 DRIM 770 C T 0.0039 12 100245515
ARL1
tD
rs6539051 None 1046 G T 0.0048 12 101621075 101521075 101721075 200000
L0C283432
tD
N
rs9316335 None 1296 G T 0.0048 13 20856918 20756918 20960207 203289 L0C440127
0
rs9316337 None 1297 C T 0.0043 13 20860207 L0C387904 0
GRK6PS
L0C387905 CD
FLJ25952
rs1555619 None 558 C T 0.0033 13 21754983 21654983 21880939 225956 None
rs9316871 None 1298 C T 0.0013 13 21759921
rs9316902 None 1299 A T 0.0011 13 21780457
rs6490720 None 1041 A G 0.0026 13 21780871
rs6490721 None 1042 G T 0.0047 13 21780939
rs9315991 None 1294 G T 0.0013 13 42629541 42529541 42729541 200000 DNAJD1
FLJ10094
rs9318485 None 1301 A G 0.004 13 76935786 76835786 77075376 239590 SCEL
rs9318486 None 1302 A C 0.0009 13 76965059
rs4884068 None 984 C G 0.0004 13 76965482
rs1323618 None 443 A G 0.0024 13 76975376
rs2086428 FARP1 692 C T 0.0025 13 97797872 97697872 97915213 217341 FARP1
rs7330217 FARP1 1152 A G 0.0027 13 97799173 STK24
rs2892734 FARP1 841 A G 0.003 13 97815213 0
rs10508138 None 269 C T 0.0025 13 103749582 103649582 103871158 221576 None
rs728555 None 1147 A G 0.0011 13 103755724
rs9300909 None 1269 A G 0.0008 13 103756340
rs9284215 None 1250 C T 0.0027 13 103757709
rs10508139 None 270 C T 0.004 13 103771158
rs11620131 None 422 A C 0.0012 13 108935145 108835145 109122110 286965 None
rs10492480 None 113 C T 0.0007 13 108947427
rs1410425 None 491 C T 0 13 108996160
rs10492479 None 112 A G 0 13 109013803
rs10492478 None 111 A C 0.0002 13 109022110
rs719737 None 1130 C T 0.0044 13 109148350 109048350 109248350 200000 IRS2 N
Ln
CD
rs10483355 STRN3 22 A G 0.0033 14 30472655 30372655 30611516 238861 COCH tD
rs10483354 STRN3 21 A C 0.0012 14 30500092 STRN3 ~ tD
rs1977130 STRN3 647 C T 0.0032 14 30511516 AP4S1 0
0
rs243294 NPAS3 786 A G 0.0004 14 32793167 32693167 32942075 248908 NPAS3 0
rs2173802 NPAS3 723 A G 0 14 32817425 L n
rs1886781 NPAS3 620 A G 0 14 32818656 CD
rs716193 NPAS3 1117 G T 0 14 32824348
rs8007568 NPAS3 1214 C G 0 14 32834319
rs10483435 NPAS3 25 G T 0 14 32842075
rs10483694 None 27 A G 0.0022 14 57585264 57485264 57685309 200045 UBA52P3
rs10483695 None 28 A G 0.0018 14 57585309 ro
rs7152153 None 1110 C T 0.005 14 76265708 76165708 76513050 347342 CYCSP1
rs4435183 KIAA0759 938 C T 0.0038 14 76323852 LAMR1P3
rs2056855 L0C145497 679 C T 0.0028 14 76366892 KIAA1036
rs10483879 L0C145497 30 C T 0.0028 14 76367923 KIAA0759
rs2885625 L0C145497 839 A G 0.0005 14 76374502 C14orf166B
rs6574333 L0C145497 1051 A G 0.0009 14 76375042 RPL22P2
rs741854 None 1155 A G 0.0015 14 76413050 RPLPIPI
rs8010717 L0C388001 1217 C T 0.0044 14 79480194 79380194 79581032 200838 NRXN3
rs8010105 L0C388001 1216 A G 0.0015 14 79480345 L0C388001
rs8014855 L0C388001 1218 C T 0.0019 14 79481032
O
rs9323707 L0C400234 1312 A G 0.0022 14 81155960 81055960 81255960 200000 SEL1L
EEF1A1P2
rs1257920 None 431 A T 0.0039 14 97760147 97660147 97860147 200000 None
rs976451 EML1 1351 G T 0.0034 14 99415166 99315166 99515166 200000 EML1
L0C341965
RPS2P3
rs2224585 MGC4645 736 A G 0.0023 14 99938712 99838712 100058306 219594
SLC25A29
rs1951522 MGC4645 641 C T 0.0029 14 99958306 C14orf68
WARS
NDUFB3P4
L0C440198 N
MGC4645
tD
rs4778334 None 971 A G 0.0041 15 20592297 20492297 20692297 200000 CYFIP1
tD
NIPA2 N
NIPA1 0
L0C400320 0
L0C339003 L n
CD
rs1458885 None 520 A C 0.0017 15 33249052 33149052 33496024 346972 NANOGP8
rs10519989 MGC14798 397 A C 0.0003 15 33317865 L0C441722
rs318360 None 867 A G 0.003 15 33396024 L0C390572
L0C440272
LOC441723
MGC14798
rs3825847 BG1 891 C T 0.002 15 76250541 76150541 76350541 200000 KIAA1055
CIB2
IDH3A
BG1
DNAJA4
rs10520640 None 401 C G 0.0049 15 85153480 85053480 85285010 231530 None
rs1452459 None 515 A G 0.005 15 85185010
rs7601 PRC1 1170 C T 0.0025 15 89310596 89210596 89426322 215726 FURIN
rs6496742 PRC1 1044 C T 0.0006 15 89324040 FES
rs11857612 PRC1 428 C T 0.0018 15 89326322 MAN2A2 0
MGC45386
SMAP-1
MGC14386
PRC1
VPS33B L0C390638
rs1400786 SLC03A1 480 A C 0.0032 15 90387143 90287143 90487143 200000 SLC03A1
rs7178880 None 1125 A G 0.0035 15 90512987 90412987 90621604 208617 SLC03A1
rs10520704 None 403 A G 0.0026 15 90521604
~
rs9302552 None 1274 A C 0.0046 16 62071933 61971933 62173509 201576 None
rs10500474 None 181 A G 0.0036 16 62073509 n0,
rs2077576 WWOX 688 A G 0.003 16 76896265 76796265 76996265 200000 WWOX a"'o
tD
rs4130513 WWOX 922 A G 0.0013 16 77016251 76916251 77195856 279605 WWOX 00 tD
rs10514437 WWOX 349 C T 0.0006 16 77050361 0
rs2738646 WWOX 809 C G 0.0016 16 77050888 0
rs1397927 WWOX 477 A G 0.0035 16 77095856 0
Ln
rs10514506 CDYL2 350 A G 0.004 16 79278578 79178578 79404911 226333 CDYL2 ao
rs8047401 CDYL2 1221 C T 0.0017 16 79304514
rs10514507 CDYL2 351 C G 0.0031 16 79304695
rs3100179 CDYL2 860 A T 0.0045 16 79304911
rs2469825 None 791 A C 0.0042 17 36095188 35995188 36359516 364328 SMARCE1
rs2462957 None 788 C T 0.004 17 36095487 MGC45562 ro
rs2429555 None 785 C G 0.0027 17 36137973 KRT24
rs4132126 KRT25D 925 A G 0.0044 17 36205780 KRT25A
rs7219451 KRT25D 1137 C T 0.0024 17 36210528 KRT25B
rs2469828 None 792 C T 0.0008 17 36257986 KRT25C
rs2469816 None 790 A G 0.002 17 36259480 KRT25D
rs9303297 None 1275 C T 0.0041 17 36259516 KRT10
MGC21518
KRT12
KRT20
KRT23
rs551920 L0C388458 1006 C G 0.0022 18 4261385 4161385 4390528 229143 L0C388458
rs523436 L0C388458 996 A G 0.0014 18 4285384 O
rs627777 L0C388458 1026 C T 0.0009 18 4290528
rs10502579 None 205 C T 0.0035 18 27824861 27724861 28111131 386270 KIAA1012
rs627346 L0C390848 1025 A G 0.0023 18 27910954 L0C342705
rs10502582 None 206 A T 0.0007 18 27991040 RNF125
rs10502583 None 207 G T 0.0019 18 28011131 L0C390848
L0C440491
RNF138
MEP1B
C18orf11
rs4627439 None 951 G T 0.0031 18 34488202 34388202 34588202 200000 None
rs10502772 None 212 C T 0.0036 18 37438094 37338094 37634376 296282 NPM1P1 N
rs10502774 None 213 G T 0.002 18 37508018
rs1865290 None 615 A T 0.0017 18 37509556 tD
rs8092873 None 1226 A G 0.0018 18 37510334 00 00 tD
rs9304251 None 1276 G T 0.0031 18 37534376 N
0
0
rs8091714 None 1224 A C 0.0042 18 51803567 51703567 51915280 211713 None o
rs1978502 None 648 C G 0.002 18 51815225 L n
rs1978503 None 649 A G 0.0013 18 51815280 CD
rs1403302 None 483 C G 0.0043 18 59525016 59425016 59745607 320591 SERPINB4
rs952857 None 1329 G T 0.0043 18 59525552 SERPINB3
rs1522723 SERPINBII 548 C T 0.003 18 59535960 SERPINBII
rs1395266 SERPINBII 476 C T 0.0002 18 59541312 SERPINB7
rs931850 None 1303 A G 0 18 59544814 SERPINB2
rs1522722 None 547 C T 0 18 59572521 SERPINBIO
rs10503087 None 216 A C 0.0014 18 59627434
rs1701586 None 590 A G 0.0036 18 59645607
rs1573400 None 564 A G 0.003 18 65077486 64977486 65180058 202572 None
rs572166 None 1008 A G 0.0016 18 65078530
rs998156 None 1365 A C 0.0033 18 65078841
rs481598 None 976 A T 0.0049 18 65080058
rs1457856 None 518 C T 0.0034 19 57649297 57549297 57749935 200638 ZNF610
rs2168792 None 721 C G 0.0017 19 57649935 L0C400713
L0C284373
ZNF528 0
ZNF534
L0C441862
ZNF578
L0C388558
rs2058318 L0C440544 680 C G 0.0039 19 61554788 61454788 61655118 200330
L0C440544
rs2058319 L0C440544 681 C T 0.0032 19 61555118 ZNF542
ZNF582
ZNF583
FLJ14011
rs3971706 MGC9913 908 A G 0.0039 19 61697881 61597881 61797881 200000 ZNF583 ~
FLJ14011
MGC9913 N
ZNF471
ZFP28 tD
FLJ26175 tD
N
0
rs1294690 FKBPIA 436 A G 0.0046 20 1319697 1219697 1520408 300711 SNPH 0
rs6042018 None 1013 C T 0.0006 20 1332298 SDCBP2 0
rs6042209 None 1014 A G 0.0001 20 1354212 FKBPIA L n
rs1884389 None 618 C T 0 20 1358582 NSFLIC CD
rs1884390 None 619 C T 0.0002 20 1358818 PTPNS1L3
rs10485823 None 50 A G 0.0007 20 1367846 L0C441937
rs715217 PTPNS1L3 1111 A G 0.0015 20 1420408 PTPNS1L2
SIRPB1
rs6108011 None 1021 A G 0.0043 20 7500504 7400504 7670826 270322 None ro
rs6108015 None 1022 C G 0.0016 20 7515858
rs6086141 None 1020 C T 0.0031 20 7570826
~
rs1408872 None 488 A G 0.0044 20 37804766 37704766 37904766 200000 None
rs10485825 None 51 C T 0.0038 20 61608092 61508092 61729912 221820 KCNQ2
rs186332 PTK6 613 C T 0.0048 20 61629912 EEF1A2
C20orf149
PTK6
SRMS
MGC5356
PRIC285
L0C200213 O
GMEB2
L0C388807
rs2825583 None 820 C T 0.0039 21 19734374 19634374 19893599 259225 None
rs2825601 None 821 A G 0.0011 21 19766620
rs2825610 None 822 G T 0.0009 21 19793455
rs1489734 None 532 A G 0.0038 21 19793599
-------------------------------------------------------------------------------
-----------
dbSNPrsID: SNP identification number in NCBI dbSNP database build 124
Gene locus: Gene positioned in the physical position pointed by the SNP
according to
NCBI Human Genome Build 35
Sequence ID: Sequence identification number
Allele A: Alternate SNP allele or its complementary nucleotide in the position
indicated by dbSNP rs ID and basepair position N
Allele B: Alternate SNP allele or its complementary nucleotide in the position
Ln
indicated by dbSNP rs ID and basepair position tD
P-value: P-value from haplotype sharing analysis 0
Position: Basepair Position, SNP physical position according to NCBI Human
Genome N
Build 35 0
Gene content: Haplotype gene content, genes positioned within 100Kbp
up/downstream from
- o
the physical position of the SNPs bordering the haplotype genomic region L '
found using NCBI MapViewer, based on NCBI Human Genome Build 35
~
Table 5. Haplotype blocks (n = 14) with the strongest association with HT
based on
HaploRec + HPM analysis.
O
dbSNPrsID Genelocus SequenceID Chr Riskallele Variants Chi-square P-value
-------------------------------------------------------------------------------
--------
rs4845303 None 980 1 A A/T 23.70 <1.OE-5 rs6428195 None 1030 1 C C/G
rs1935659 None 637 1 G A/G
rs1997454 None 656 2 A A/G 19.73 1.OOE-05
rs2139502 None 709 2 G A/G
rs1519991 None 542 2 C A/C
rs1521409 None 544 3 A A/G 23.54 <1.OE-5
rs10511365 None 316 3 C C/T
rs10511366 None 317 3 T C/T
0
N
rs7679959 None 1178 4 C C/G 21.37 <1.OE-5 Ln
rs10517338 None 381 4 G C/G tD
rs959297 None 1338 4 A A/T tD
N
0
rs2278677 T 749 6 G A/G 21.29 <1.OE-5 0
rs3886091 None 899 6 C C/G o
rs1998167 None 657 6 A A/G L n
rs1998168 None 658 6 G A/G
rs2235280 RPS6KA2 740 6 G A/G
rs10521062 None 404 9 A A/C 18.40 0.00002
rs10512296 None 331 9 A A/G
rs1924001 None 633 9 C C/G
rs2417359 None 784 9 G A/G ro
rs10508933 ACF 289 10 G C/G 19.56 1.OOE-05 rs10509071 None 295 10 G A/G
rs10490967 None 94 10 A A/G
rs10508771 None 286 10 T A/T 18.76 0.00001
rs3006608 None 854 10 C C/T
rs10508773 EPC1 287 10 C C/T
rs950132 EPC1 1325 10 C C/T
rs1386486 TPH2 472 12 C C/T 19.54 1.OOE-05
rs1386485 TPH2 471 12 A A/C
rs1386483 TPH2 470 12 G A/G O
rs7977245 None 1212 12 T C/T
rs276002 None 814 12 A A/G 18.81 0.00001
rs274460 None 810 12 A A/G
rs1245383 None 430 14 G A/G 18.77 0.00001
rs2133829 None 707 14 C C/T
rs2173738 None 722 14 T C/T
rs2050528 None 677 14 T C/T
rs202970 None 671 14 C C/T
rs1395266 SERPINBII 476 18 T C/T 23.73 <1.OE-5 rs931850 None 1303 18 A A/G
rs1522722 None 547 18 C C/T 0
N
Ln
OD
rs2221511 SERPINBII 733 18 A A/G 22.42 <1.OE-5 tD
rs4940595 SERPINBII 986 18 T G/T tD
rs1522723 SERPINBII 548 18 C C/T N
rs1395266 SERPINBII 476 18 C C/T o
0
rs2825555 None 819 21 A A/G 23.77 <1.OE-5
rs2825583 None 820 21 T C/T
CD
rs2825601 None 821 21 G A/G
rs2825610 None 822 21 G G/T
rs1489734 None 532 21 A A/G
-------------------------------------------------------------------------------
-------
dbSNPrsID: SNP identification number in NCBI dbSNP database build 124
Gene_locus: Gene positioned in the physical position pointed by the SNP
according to
NCBI Human Genome Build 35 ro
Sequence_ID: Sequence identification number
Chr: Chromosome
Risk_allele: Allele in at-risk haplotype
Variants: Variant alleles present in the SNP
Chi-square: Chi-square value based on 2x2 table (haplotype present (not-
present) in
cases and controls)
P-value: P-value corresponding the chi-square value with 1 df
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Table 6. Genes associated with HT according to point wise
or haplotype analyses (n = 722).
Chromosome I Gene
----------------------------------------------------------
1 DAB1
1 APG4C
1 CAPON
1 COL24A1
1 COL24A1
1 DPT
1 EAT2
1 FAAH
1 FAF1
1 FLJ20277
1 FLJ32825
1 GADD45A
1 GNG12
1 L0C116123
1 L0C128153
1 L0C200008
1 L0C284680
1 L0C388656
1 L0C391046
1 L0C391046
1 L0C399701
1 L0C400758
1 L0C440598
1 MAST2
1 MGC22960
1 MGC29875
1 MGC8902
1 MRPL37
1 MUF1
1 POGK
1 PRKCL2
1 RAD54L
1 RGS18
1 RGS7
1 SEC22L1
1 SHREW1
1 SIAT7C
1 SIPA1L2
1 SSBP3
1 SSBP3
1 TARBP1
1 TSPAN-1
1 UQCRH
1 USH2A
1 USH2A
1 XM372814
2 COMMD1
2 CRYGEP1
2 ERBB4
2 L0C130576
2 MY03B
2 REGL
2 SP100
2 ACVR1
2 ACVR1
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2 AOX2
2 ASB1
2 B3GNT1
2 BARD1
2 BAZ2B
2 CRYGA
2 CRYGB
2 CRYGC
2 CRYGD
2 CTNNA2
2 FLJ13110
2 FSHR
2 GORASP2
2 GPD2
2 HMG1L3
2 IDH1
2 LANCL1
2 LHCGR
2 L0C130429
2 L0C339789
2 L0C344471
2 L0C388954
2 L0C389072
2 L0C389073
2 L0C391481
2 L0C402117
2 L0C442053
2 L0C442066
2 L0C93349
2 LPIN1
2 LRP1B
2 LTBP1
2 MGC4268
2 PAP
2 PDE11A
2 PDE11A
2 PELI1
2 POLR2D
2 PRKCE
2 PRKCN
2 QPCT
2 REG-III
2 REG1A
2 REG1B
2 TLK1
2 TRAF31P1
2 UNQ429
2 VPS54
2 WDR33
3 L0C152225
3 AHSG
3 ATR
3 CRBN
3 CRYGS
3 DGKG
3 DNAJBII
3 FETUB
3 FLJ10560
3 FLJ12604
3 FLJ42117
3 GRM7
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3 HRG
3 IL5RA
3 KCNAB1
3 KNG1
3 L0C152225
3 L0C389105
3 L0C389105
3 L0C442078
3 L0C442099
3 MAIL
3 MGC15606
3 MGC16471
3 MRPL47
3 PLS1
3 SCHIP1
3 TRAD
3 TRNT1
3 TRPC1
3 XRN1
4 L0C339979
4 PDGFC
4 ANK2
4 ANK2
4 FLJ20647
4 FLJ37673
4 GABRB1
4 GABRB1
4 GLRB
4 KIAA0882
4 KIT
4 L0C152594
4 L0C255130
4 L0C339979
4 L0C345378
4 L0C389217
4 L0C391681
4 L0C391686
4 L0C441018
4 PDGFC
4 SEC24B
4 SNCA
4 STK32B
4 TD02
4 TLL1
5 ABLIM3
5 ADAMTS12
5 BTNL3
5 BTNL8
5 BTNL9
5 CANX
5 CCNG1
5 CDH6
5 CEI
5 CHD1
5 CMYA5
5 CMYA5
5 CTNND2
5 EBF
5 FBXL17
5 FLJ10904
5 GABRAI
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GABRAI
5 GABRA6
5 HMMR
5 HNRPH1
5 IL12B
5 IRX2
5 KIAA1061
5 KIAA1985
5 L0C134492
5 L0C255187
5 L0C255187
5 L0C285638
5 L0C285679
5 L0C345471
5 L0C389285
5 L0C389352
5 L0C391734
5 L0C391774
5 L0C391819
5 L0C391858
5 L0C402222
5 L0C441113
5 L0C441120
5 L0C442129
5 L0C51149
5 LTC4S
5 MAML1
5 MAN2A1
5 MGAT4B
5 NDFIP1
5 PAPD4
5 PJA2
5 RGMB
5 RUFY1
5 SGCD
5 SGCD
5 SQSTM1
6 STX11
6 ACAT2
6 BA13
6 BPAG1
6 BRP44L
6 C6orf142
6 C6orf149
6 C6orf157
6 C6orf204
6 C6orf33
6 C6orf65
6 C6orf83
6 C6orf93
6 CRISP2
6 DST
6 FARS1
6 GFOD1
6 IGF2R
6 IL17F
6 L3MBTL3
6 L0C285741
6 L0C389370
6 L0C401255
6 L0C401284
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6 MAS1
6 MCM3
6 MGC35308
6 MRPL18
6 MRPL42P3
6 MYCT1
6 PARK2
6 PARK2
6 PHACTR1
6 PLAGL1
6 PNLDC1
6 RPS6KA2
6 SAMD3
6 SEC5L1
6 SERPINB1
6 SERPINB9
6 SF3B5
6 SLC35F1
6 SOD2
6 SYNE1
6 T
6 TBC1D7
6 TBC1D7
6 TCBA1
6 TCP1
6 TINAG
6 UTRN
6 VIP
6 WRNIP1
6 WTAP
6 UTRN
7 DNAH11
7 ABCA13
7 AKR1B1
7 ARL4
7 ARL4A
7 BMPER
7 CNTNAP2
7 CNTNAP2
7 DGKI
7 DNAH11
7 FLJ21075
7 FLJ32786
7 HDAC9
7 HIC
7 HUS1
7 L0C136288
7 L0C340228
7 L0C340274
7 L0C389602
7 L0C401406
7 L0C402463
7 L0C402640
7 MGC16075
7 MGC33329
7 OSBPL3
7 PBEF1
7 PHF14
7 PHF14
7 PKD1L1
7 PKD1L1
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7 SCIN
7 SDK1
7 SEMA3A
7 SEMA3E
7 SHH
7 SLC35B4
7 SP4
7 UNQ739
8 SGCZ
8 ZFPM2
8 ASAH1
8 CGI-62
8 CSMD1
8 EFA6R
8 ENTPD4
8 FGF20
8 FLJ23749
8 FLJ36980
8 HNF4G
8 L0C286097
8 L0C340357
8 L0C346887
8 L0C392262
8 LRP12
8 MATN2
8 MSCP
8 PKIA
8 PSD3
8 RBPMS
8 RIMS2
8 RRM2B
8 ZHX2
9 NT008470
9 OR1J4
9 ADAMTSL1
9 AK3L1
9 C9orf102
9 C9orf97
9 ECM2
9 FBXW2
9 FLJ31810
9 FLJ31810
9 FRMD3
9 GRIN3A
9 JAK2
9 LOC138882
9 L0C392282
9 LOC392371
9 LOC401492
9 LOC441384
9 MRRF
9 NR4A3
9 NTRK2
9 OR1B1
9 OR1H1P
9 OR1J1
9 OR1J2
9 OR1J4
9 OR1L8
9 OR1N1
9 OR1N2
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9 OR1Q1
9 PHF19
9 PSMD5
9 PTGS1
9 RCL1
9 RCL1
9 STX17
9 TMC1
9 TRAF1
9 TRPM3
9 TXNDC4
9 XPA
CTNNA3
10 L0C389938
10 PCDH15
10 ACF
10 ADRA2A
10 ADRA2A
10 ANK3
10 ANK3
10 ANKRD16
10 ASCC1
10 ClOorflO4
10 ClOorf35
10 ClOorf49
10 ClOorf59
10 ClOorf64
10 CACNB2
10 CACNB2
10 CBARAI
10 CTNNA3
10 CXXC6
10 DDIT4
10 DNA2L
10 DNAJB12
10 EPC1
10 FBX018
10 FBX018
10 FLJ31958
10 GDI2
10 HNRPH3
10 IL15RA
10 IL2RA
10 L0C387630
10 L0C389970
10 L0C399707
10 L0C399708
10 L0C399713
10 L0C399773
10 L0C439946
10 L0C439953
10 L0C439978
10 L0C441550
10 L0C441551
10 L0C441561
10 MAWBP
10 MCM10
10 MINPP1
10 MPP7
10 MY03A
10 NEUROG3
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NOPD1
10 NY-BR-1
10 OPTN
10 PARD3
10 RUFY2
11 NUMA1
11 CD44
11 DKFZP564MO82
11 FAT3
11 FAT3
11 FLJ20625
11 FN5
11 GALNTL4
11 GAS2
11 IL18BP
11 KIAA1731
11 L0C113174
11 L0C220074
11 L0C260340
11 L0C260340
11 L0C338661
11 L0C338661
11 L0C387795
11 L0C390241
11 L0C390263
11 L0C440062
11 MGC5306
11 MRGX3
11 MRGX4
11 NELL1
11 NUMA1
11 OR10S1
11 0R4D5
11 OR51R1P
11 0R52K3P
11 OR6M2P
11 OR6M3P
11 OR6T1
11 0R8D4
11 PDGFD
11 PDHX
11 PTDO12
11 RNF121
11 RRM1
11 SAA2
11 SAA3P
11 SAA4
11 SSA1
11 STIM1
11 USP47
12 EB-1
12 TPH2
12 ALG10
12 ARL1
12 DRIM
12 DRIM
12 EB-1
12 ELKS
12 FLJ36004
12 HSN2
12 L0C283392
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12 L0C283432
12 L0C390359
12 L0C400019
12 L0C400046
12 NAV3
12 NAV3
12 PAH
12 PRKWNK1
12 RAD52
12 SLC16A7
12 TBC1D15
12 TPH2
12 TRHDE
12 VPS29
12 WIF1
13 DNAJD1
13 FARP1
13 FARP1
13 FLJ10094
13 FLJ25477
13 FLJ25952
13 GPC6
13 GRK6PS
13 HSMPP8
13 IRS2
13 L0C387904
13 L0C387905
13 L0C390393
13 L0C400099
13 L0C400120
13 L0C440127
13 NUDT15
13 PABPC3
13 PSPC1
13 RFXAP
13 SCEL
13 SMAD9
13 STK24
13 SUCLA2
13 VDRIP
13 VGCNL1
13 ZNF198
13 ZNF237
14 L0C145497
14 L0C388001
14 L0C400234
14 NPAS3
14 AKAP6
14 AP4S1
14 C14orf166B
14 C14orf68
14 COCH
14 CYCSPI
14 EEF1A1P2
14 EML1
14 KCNH5
14 KIAA0759
14 KIAA1036
14 LAMRIP3
14 L0C341965
14 L0C388001
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14 L0C440198
14 LRFN5
14 MGC4645
14 NDUFB3P4
14 NPAS3
14 NRXN3
14 RPL22P2
14 RPLPIPI
14 RPS2P3
14 SEL1L
14 SLC25A29
14 STRN3
14 STRN3
14 UBA52P3
14 WARS
15 MGC14798
15 ADAM10
15 ARNT2
15 ARRDC4
15 BG1
15 CHD2
15 CIB2
15 CYFIP1
15 DNAJA4
15 FES
15 FURIN
15 GABRA5
15 IDH3A
15 KIAA1055
15 L0C339003
15 L0C390561
15 L0C390572
15 L0C390638
15 L0C400320
15 L0C440272
15 L0C441722
15 L0C441723
15 MAN2A2
15 MEIS2
15 MGC14386
15 MGC14798
15 MGC45386
15 MTHFS
15 NANOGP8
15 NIPA1
15 NIPA2
15 NTRK3
15 pp9099
15 PRC1
15 RASGRF1
15 RGMA
15 SIAT8B
15 SLC03A1
15 SMAP-1
15 VPS33B
16 CDYL2
16 WWOX
16 CDH13
16 CLECSF1
16 RRN3
16 WWOX
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17 CGI-125
17 FLJ12760
17 FLJ25818
17 KIAA0753
17 KRT10
17 KRT12
17 KRT20
17 KRT20
17 KRT23
17 KRT24
17 KRT25A
17 KRT25B
17 KRT25C
17 KRT25D
17 L0C342531
17 L0C342531
17 MGC21518
17 MGC21518
17 MGC45562
17 MRC2
17 PITPNM3
17 SLC13A5
17 SMARCE1
17 SOX9
17 TLK2
17 TXNL5
18 L0C388458
18 SERPINBII
18 C18orf10
18 C18orf11
18 C18orf14
18 FLJ20793
18 KIAA1012
18 KIAA1328
18 L0C342705
18 L0C390848
18 L0C440491
18 MEP1B
18 NET01
18 NPM1P1
18 PTPRM
18 RIT2
18 RIT2
18 RNF125
18 RNF138
18 SERPINBIO
18 SERPINB2
18 SERPINB3
18 SERPINB4
18 SERPINB7
19 FLJ00060
19 FLJ14011
19 FLJ26175
19 GRLF1
19 ILT10
19 KIR2DL1
19 KIR2DL3
19 KIR2DS2
19 KIR3DL3
19 LILRAI
19 LILRA2
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19 LILRB4
19 L0C284373
19 L0C388526
19 L0C388558
19 L0C400713
19 L0C440544
19 L0C441862
19 MGC9913
19 ZFP28
19 ZNF471
19 ZNF528
19 ZNF534
19 ZNF542
19 ZNF578
19 ZNF582
19 ZNF583
19 ZNF610
20 SNPH
20 C20orf149
20 C20orf46
20 EEF1A2
20 FKBPIA
20 GMEB2
20 IDH3B
20 KCNB1
20 KCNQ2
20 L0C200213
20 L0C388807
20 L0C441937
20 MGC10715
20 MGC5356
20 NOL5A
20 NSFLIC
20 PRIC285
20 PROCR
20 PSMF1
20 PTGIS
20 PTK6
20 PTPNSIL2
20 PTPNS1L3
20 SDCBP2
20 SIRPB1
20 SNPH
20 SNRPB
20 SRMS
20 TGM6
20 TMC2
20 TMC2
21 ATP50
21 C21orf94
21 ITSN1
21 ITSN1
21 L0C388819
21 MRPS6
22 DGCR2
22 FBLN1
X RPS6KA6
---------------------------------------------
Gene name according to HUGO Gene Nomenclature
Committee (HGNC)
Table 7. A multivariate logistic model predicting the risk of hypertension,
including O
haplotypes and individual SNP markers.
-------------------------------------------------------------------------------
-------------
A
t
r
p i
r s
e k
d
i H A
c T 1
t G
o e o e C
N
r G n r 1 0 L'
OD
e e e F e o
v n g s r f ~ tD
a e c e e f P
0
r S o n i q i 9 0
i 1 E n o n u c 5 v 10
a o Q t t e i % a 'I n
b c C e y S n e 1 OD
1 u h I n p N c n 0 C u
e s r D t e P y t R I e
-------------------------------------------------------------------------------
-------------
Haplotype*
rs1521409 None 3 544 None A A/G 6,27,130 -6.904 0.001 [0.000,0.028] <0.001
rs10511365 None 3 316 C C/T ro
rs10511366 None 3 317 T C/T
~
Haplotype
rs10508771 None 10 286 L0C441550 T A/T 139,23,1 9.045 8477 [87.2,823831]
<0.001
rs3006608 None 10 854 L0C441551 C C/T
rs10508773 EPC1 10 287 L0C439953 C C/T
rs950132 EPC1 10 1325 EPC1 C C/T
Haplotype
rs2221511 SERPINBII 18 733 SERPINB4 A A/G 118,37,8 -3.421 0.033 [0.004,0.242]
0.001
rs4940595 SERPINBII 18 986 SERPINB3 T G/T O
rs1522723 SERPINBII 18 548 SERPINBII C C/T
rs1395266 SERPINBII 18 476 SERPINB7 C C/T
SNP-marker**
rs1992906 None 5 655 G A/G 138,22,3 4.154 63.7 [6.61,614] <0.001
rs10270360 L0C401406 7 10 G A/G 47,90,26 2.593 13.4 [3.12,57.3] <0.001
rs1318392 OR1J4 9 438 G A/G 47,86,30 -3.299 0.037 [0.007,0.195] <0.001
rs2209672 None 10 730 A A/G 33,94,36 -3.032 0.048 [0.011,0.216] <0.001
rs503208 None 11 989 G C/G 78,68,17 2.619 13.7 [3.15,59.81 <0.001
Constant 7.473 1760.389 0.003
-------------------------------------------------------------------------------
-------------
~
SNP identification number according to NCBI dbSNP database build 124.
Gene locus, gene locus as reported by NCBI dbSNP database build 124 , ~
The 8-variable model predicts 91.4 % of HT cases correctly.
The statistics are based on 163 subjects of which 81 were HT cases and 82
controls. o
* Haplotypes coded as 0, if no haplotype, 1 if one haplotype and 2 if two
haplotypes o
** Genotypes coded as 0, if major allele homozygote, 1 if heterozygote and 2
if minor o
allele homozygote 0
Haplotype gene content, genes positioned within 100Kbp up/downstream from the
physical o
position of the SNPs bordering the haplotype genomic region found using NCBI
MapViewer L '
~
OD
HT = haplotype
OR = Odds ration in multivariate logistic model
95% CI = 95% confidence interval for odds ratio
~
Table 8. A multivariate logistic model predicting the risk of hypertension
including
haplotypes,individual SNP markers and phenotypic measurements. O
-------------------------------------------------------------------------------
-------------
A
t
r
p i
r s
e k
d
i H A
c T 1
t G 1
o e o e C
r G n r 1 0
N
e e e F e
v n g s r f tD
a e c e e f P o 0
r S o n i q i 9 0
i 1 E n o n u c 5 v 0
a o Q t t e i % a o
b c C e y S n e 1 L '
1 u h I n p N c n 0 C u OD
e s r D t e P y t R I e
-------------------------------------------------------------------------------
-------------
Haplotype*
rs1521409 None 3 544 None A A/G 6,27,130 -3.629 0.026 [0.004, 0.177] <0.001
rs10511365 None 3 316 C C/T ro
rs10511366 None 3 317 T C/T
Haplotype
rs2221511 SERPINBII 18 733 SERPINB4 A A/G 118,37,8 -1.828 0.161 [0.054, 0.478]
0.001
rs4940595 SERPINBII 18 986 SERPINB3 T G/T
rs1522723 SERPINBII 18 548 SERPINBII C C/T
rs1395266 SERPINBII 18 476 SERPINB7 C C/T
SNP-marker**
rs1997454 None 2 656 G A/G 103,53,7 -1.194 0.303 [0.112, 0.821] 0.019
rs10270360 L0C401406 7 10 G A/G 47,90,26 1.379 3.97 [1.65, 9.56] 0.002
rs1318392 OR1J4 9 438 G A/G 47,86,30 -2.035 0.131 [0.049, 0.348] <0.001 O
rs2209672 None 10 730 A A/G 33,94,36 -1.608 0.200 [0.075, 0.533] 0.001
rs503208 None 11 989 G C/G 78,68,17 1.392 4.03 [1.73, 9.38] 0.001
BMI (kg/m2) n.a. 0.248 1.281 [1.067, 1.537] 0.008
Obesity in the family n.a. 1.508 4.52 [1.49, 13.7] 0.008
Constant -2.542 0.079 0.376
-------------------------------------------------------------------------------
-------------
SNP identification number according to NCBI dbSNP database build 124.
Gene locus, gene locus as reported by NCBI dbSNP database build 124
The 9-variable model predicts 87.1 % of HT cases correctly. ~
The statistics are based on 163 subjects of which 81 were HT cases and 82
controls.
* Haplotypes coded as 0, if no haplotype, 1 if one haplotype and 2 if two
haplotypes , ~
** Genotypes coded as 0, if major allele homozygote, 1 if heterozygote and 2
if minor allele
homozygote o
n.a. denotes not applicable o
Haplotype gene content, genes positioned within 100Kbp up/downstream from the
physical o
position of the SNPs bordering the haplotype genomic region found using NCBI
MapViewer 0
HT = Haplotype o
OR = Odds ratio in multivariate logistic model L '
95% CI = 95% confidence interval for odds ratio OD
~
Table 9. Linear regression model for systolic and diastolic blood pressure
using individual
SNP markers O
-------------------------------------------------------------------------------
------------
SBP DBP
Variable Closest gene* Sequence ID Coefficient P-value Coefficient P-value
-------------------------------------------------------------------------------
------------
Drug treatment 8.403 0.001 4.695 0.02
rs1860933 L0C391839, SPINK5 1366 -4.673 <0.001
rs4236780 STARS, ANGPTI 1367 -5.659 <0.001
rs2000112 OR1N2, OR1L8 660 -4.481 0.001
rs931850 SERPINB11, SERPINB7 1303 -5.084 0.001
rs2192947 QPCT, CDC42EP3 728 3.656 0.001
rs9328292 C6orf149, FARS1 1316 -3.486 <0.001
rs1409367 5100A7, 5100A6 490 -6.839 <0.001
rs1893814 ODZ4, PRCP 622 3.747 <0.001
rs2263356 PHF2, BARX1 746 3.209 <0.001 N
rs6826647 TLL1, SPOCK3 1368 -2.786 <0.001 Ln
rs1913157 FLJ42117, LOC339902 630 -2.721 <0.001 tD
tD
Constant 139.698 <0.001 101.901 <0.001
0
Adjusted R2 0.247 0.301 0
-------------------------------------------------------------------------------
------------
0
SBP, systolic blood pressure L n
DBP, diastolic blood pressure
Closest gene up and downstream according to NCBI MapViewer
Sequence ID, sequence identification number
~
Table 10. Associations of selected SNP markers with the mean systolic blood
pressure
in mmHg. O
Homozygote for Homozygote for a
minor allele Heterozygote major allele
SNP marker Closest gene* SeqID Mean SD N Mean SD N Mean SD N P-value
-------------------------------------------------------------------------------
---------------
rs6826647 TLL1 1368 134.6 17.7 55 131.7 15.1 129 129.3 14.2 64 0.067
SPOCK3
rs1409367 5100A7 490 149.5 18.6 5 146.8 6.4 5 131.3 15.1 213 0.008
S100A6
rs9328292 C6orf149 1316 124.7 16.7 36 132.0 13.9 108 134.8 16.1 73 0.001
FARS1 0
N
rs1395266 SERPINB3 476 124.6 10.2 16 127.2 14.3 65 135.2 16.1 150 0.009
SERPINB11** tD
SERPINB7 tD
O
rs1893814 ODZ4 622 132.1 16.1 21 135.0 17.3 90 129.7 14.2 115 0.522 0
PRCP 10
Ln
rs931850 SERPINBII 1303 125.1 10.3 15 127.2 14.0 75 135.2 16.0 151 0.014
SERPINB7
rs1860933 L0C391839 1366 137.1 17.7 60 130.8 14.5 97 128.0 14.7 69 0.001
SPINK5
rs1386483 TBC1D15 470 135.7 16.2 63 130.5 14.6 119 130.3 16.3 66 0.049
TPH2** ro
L0C283392
~
rs4236780 STARS 1367 124.6 13.1 21 129.4 15.7 105 135.0 15.2 123 0.004
ANGPTI
rs1913157 FLJ42117 630 133.9 9.3 20 127.9 13.4 107 134.8 17.3 122 0.788
L0C339902
rs2263356 PHF2 746 133.8 18.4 19 135.5 14.7 67 129.7 14.8 129 0.281
BARX1
O
rs2000112 OR1N2 660 126.5 12.3 19 127.2 15.9 76 133.8 14.8 132 0.047
OR1L8
-------------------------------------------------------------------------------
-------------
* Closest gene up and downstream according to NCBI MapViewer.
** the marker is intragenic for this gene.
P-value: statistical significance of the linear component of variation across
the three
genotypes from ANOVA model.
Seq. ID: sequence identification number.
~
0
N
Ln
tD
~ J
~ tD
N
0
0
0
Ul
F-'
~I
Table 11. Associations of selected SNP markers with the mean diastolic blood
pressure
in mmHg. O
Homozygote for Homozygote for
minor allele Heterozygote major allele
SNP marker Closest gene* SeqID Mean SD N Mean SD N Mean SD N P-value
-------------------------------------------------------------------------------
-------------
rs6826647 TLL1 1368 89.0 11.8 55 85.9 9.2 129 82.6 8.6 64 <0.001
SPOCK3
rs1409367 5100A7 490 101.4 12.1 5 90.1 6.0 5 85.6 9.5 213 <0.001
S100A6
rs9328292 C6orf149 1316 80.4 9.4 36 85.7 9.3 108 88.3 10.0 73 <0.001
FARS1 0
N
rs1395266 SERPINB3 Ln
SERPINB11** 476 80.0 7.4 16 83.5 9.1 65 87.7 10.2 150 0.003 0
SERPINB7 N tD
N
O
rs1893814 ODZ4 622 90.5 11.0 21 87.4 10.2 90 83.6 9.3 115 0.004 0
PRCP 10
Ln
rs931850 SERPINBII 1303 80.5 7.4 15 83.3 9.0 75 87.7 10.2 151 0.006
SERPINB7
rs1860933 L0C391839 1366 88.3 10.6 60 85.2 9.2 97 84.1 9.2 69 0.013
SPINK5
rs1386483 TBC1D15 470 89.1 11.2 63 84.4 9.5 119 85.0 8.9 66 0.019
TPH2** ro
L0C283392
~
rs4236780 STARS 1367 82.5 8.0 21 84.6 10.3 105 87.3 9.7 123 0.040
ANGPTI
rs1913157 FLJ42117 630 83.3 5.3 20 84.0 10.1 107 87.8 10.0 122 0.060
L0C339902
rs2263356 PHF2 746 88.2 10.2 19 89.1 10.0 67 83.9 9.6 129 0.072
BARX1
O
rs2000112 OR1N2 660 83.2 7.4 19 84.2 9.1 76 86.4 9.9 132 0.169
OR1L8
-------------------------------------------------------------------------------
-----------
* Closest gene up and downstream according to NCBI MapViewer
** the marker is intragenic for this gene
P-value: statistical significance of the linear component of variation across
the three
genotypes from ANOVA model
Seq ID: sequence identification number
~
0
N
Ln
tD
~ J
tD
N
0
0
0
Ul
F-'
~I
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114
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