A Genome-Wide Association Study of Hypertension and
Blood Pressure in African Americans
Adebowale Adeyemo1*, Norman Gerry2, Guanjie Chen1, Alan Herbert3, Ayo Doumatey1, Hanxia Huang1,
Jie Zhou1, Kerrie Lashley4, Yuanxiu Chen4, Michael Christman2, Charles Rotimi1*
1Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of
America, 2The Coriell Institute for Biomedical Research, Camden, New Jersey, United States of America, 3Department of Genetics and Genomics, Boston University,
Boston, Massachusetts, United States of America, 4National Human Genome Center, Howard University, Washington, D.C., United States of America
The evidence for the existence of genetic susceptibility variants for the common form of hypertension (‘‘essential
hypertension’’) remains weak and inconsistent. We sought genetic variants underlying blood pressure (BP) by conducting a
genome-wide association study (GWAS) among African Americans, a population group in the United States that is
disproportionately affected by hypertension and associated complications, including stroke and kidney diseases. Using a
dense panel of over 800,000 SNPs in a discovery sample of 1,017 African Americans from the Washington, D.C., metropolitan
region, we identified multiple SNPs reaching genome-wide significance for systolic BP in or near the genes: PMS1, SLC24A4,
YWHA7, IPO7, and CACANA1H. Two of these genes, SLC24A4 (a sodium/potassium/calcium exchanger) and CACNA1H (a
voltage-dependent calcium channel), are potential candidate genes for BP regulation and the latter is a drug target for a
class of calcium channel blockers. No variant reached genome wide significance for association with diastolic BP (top
scoring SNP rs1867226, p=5.861027) or with hypertension as a binary trait (top scoring SNP rs9791170, p=5.161027). We
replicated some of the significant SNPs in a sample of West Africans. Pathway analysis revealed that genes harboring top-
scoring variants cluster in pathways and networks of biologic relevance to hypertension and BP regulation. This is the first
GWAS for hypertension and BP in an African American population. The findings suggests that, in addition to or in lieu of
relying solely on replicated variants of moderate-to-large effect reaching genome-wide significance, pathway and network
approaches may be useful in identifying and prioritizing candidate genes/loci for further experiments.
Citation: Adeyemo A, Gerry N, Chen G, Herbert A, Doumatey A, et al. (2009) A Genome-Wide Association Study of Hypertension and Blood Pressure in African
Americans. PLoS Genet 5(7): e1000564. doi:10.1371/journal.pgen.1000564
Editor: Emmanouil T. Dermitzakis, University of Geneva Medical School, Switzerland
Received December 15, 2008; Accepted June 16, 2009; Published July 17, 2009
This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public
domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
Funding: The study was supported by grants S06GM008016-320107 to CR and S06GM008016-380111 to AA, both from the NIGMS/MBRS/SCORE Program.
Participant enrollment was carried out at the Howard University General Clinical Research Center (GCRC), which is supported by grant number 2M01RR010284
from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). Additional support was provided by the Coriell
Institute for Biomedical Sciences. This research was supported in part by the Intramural Research Program of the National Human Genome Research Institute,
National Institutes of Health, in the Center for Research in Genomics and Global Health (Z01HG200362). The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: email@example.com (AA); firstname.lastname@example.org (CR)
Genome wide association studies (GWAS) on large scale
population samples have been remarkably successful in uncovering
novel susceptibility loci for a wide range of complex human
diseases including type 2 diabetes, coronary artery disease,
dyslipidemia, breast cancer, obesity-related traits, prostate cancer
and Crohn’s disease . These notable success stories represent
significant advances in the global effort to understanding the
genetic basis of common human diseases. However, this has not
been the case for hypertension, a common human disease affecting
over one billion people worldwide  and a major contributor to
cardiac failure and chronic renal disease [3,4]. The earliest
published GWAS that specifically sought associations for hyper-
tension and/or BP traits (the Wellcome Trust Case Control
Consortium (WTCCC)  and the Diabetes Genetics Initiative
(DGI)  studies) did not find any genetic variant significantly
associated with hypertension at the genome wide level. While these
two studies have some limitations, these negative findings have
strengthened the notion that multiple rare independent variants
may account for a large fraction of BP variation , a situation in
which GWAS (designed to work best in ‘‘common disease,
common variant’’ scenarios) would be less useful. A further note is
that these studies were conducted in European populations and it
is unknown if similar studies in populations with non-European
ancestry would yield different insights.
In the present study, we conducted a GWAS of BP among
African Americans enrolled in the Washington DC metropolitan
region of the United States. In comparison with other population
groups in the United States, African Americans suffer a
disproportionate burden of hypertension and its complications. A
priori, we considered that: (1) Gene variants associated with BP
variation among normotensive individuals may not be exactly the
same set identified as those associated with persistently elevated
blood pressure (i.e. ‘‘hypertension’’); (2) Since the clinical definition
of hypertension utilizes elevation of either the systolic blood
pressure (SBP) or diastolic blood pressure (DBP), those with
hypertension are a heterogenous group comprising those with
isolated SBP elevation, those with isolated DBP elevation and
PLoS Genetics | www.plosgenetics.org1 July 2009 | Volume 5 | Issue 7 | e1000564
those with both. This heterogeneity is likely to be reflected in
genetic associations for each of these traits (SBP, DBP,
hypertension); (3) Individual response to hypertension treatment
varies greatly thereby making it a real possibility that statistical
adjustment of SBP and DBP for treatment (e.g. adding a fixed
quantity to measured BP) among treated hypertensive individuals
, may mask real associations in GWAS. (4) The evidence so far
from GWAS of hypertension and BP suggest that there may be few
or no variants with large effects, implying that p values may be
modest compared to those reported for other traits. For these
reasons, we chose to: 1) conduct a case-control association study
for hypertension; 2) conduct an association study for SBP and DBP
among normotensive individuals; 3) use pathway-based analyses of
the GWAS data to determine if the variants most strongly
associated with BP phenotypes cluster in pathways and networks
that are of biological relevance to BP regulation. Using this
strategy, we hoped to maximize the chances of discovering loci
influencing hypertension susceptibility and/or normal BP control.
Ethical approval for the study was obtained from the Howard
University Institutional Review Board (IRB). All subjects provided
written informed consent for the collection of samples and
subsequent analysis. This study was conducted according to the
principles expressed in the Declaration of Helsinki.
The subjects studied were all participants in the Howard
University Family Study (HUFS), a population based family study
of African Americans in the Washington metropolitan area. The
major objectives of the HUFS were to: 1) enroll and examine a
randomly ascertained cohort of African-American families, along
with a set of unrelated individuals, from the Washington DC
metropolitan area to study the genetic and environmental basis of
common complex diseases including hypertension, obesity and
associated phenotypes; 2) to characterize study participants for
anthropometry (including weight, height, waist and hip circum-
ferences, body composition measures) and BP; and 3) evaluate the
association between genetic variants and selected traits (hyperten-
sion, BP and obesity). Participants were sought through door-to-
door canvassing, advertisements in local print media and at health
fairs and other community gatherings. In order to maximize the
utility of this cohort for the study of multiple common traits,
families were not ascertained based on any phenotype. During a
clinical examination, demographic information was collected by
interview. Weight, height, waist circumference and hip circum-
ference were measured using standard methods as follows: Weight
was measured in light clothes on an electronic scale to the nearest
0.1 kg, and height was measured with a stadiometer to the nearest
0.1 cm. Body mass index (BMI) was computed as weight in kg
divided by the square of the height in meters. Waist circumference
was measured to the nearest 0.1 cm at the narrowest part of the
torso as seen from the anterior aspect. BP was measured in the
sitting position using an oscillometric device (Omron). Three BP
readings were taken with a ten minute interval between readings.
The reported SBP and DBP readings were the average of the
second and third readings. Pulse pressure (PP) was calculated as
the difference between the SBP and DBP. Hypertension status was
defined as SBP.=140 mmHg and/or DBP.=90 mmHg and/
or treatment with antihypertensive medication. In the overall
cohort, the frequency of hypertension was 35% and among those
that were hypertensive, 64% were on antihypertensive medication
at the time of the study.
Genome-wide genotyping was performed using the AffymetrixH
Genome-Wide Human SNP Array 6.0 . DNA samples were
prepared and hybridized following the manufacturer’s instruc-
tions. After processing, chips were scanned and genotype calls
were made using the Birdseed 2 algorithm [9,10]. All samples used
in the analysis achieved a chip wide call rate of $95%. Individual
SNPs were excluded if they had a call rate of less than 95%
(n=41,885) across all individuals, a minor allele frequency
,=0.01 (n=19,154) or had a Hardy-Weinberg equilibrium
(HWE) test p of ,161023(n=6,317). The current analysis
focused on the 808,465 autosomal SNPs that passed these filters.
The average call rate for this set of SNPs in these individuals was
99.5%. The concordance of blind duplicates was 99.74%.
Focused, lower-throughput genotyping for replication was
carried out using Sequenom Homogenous MassEXTEND or
iPLEX Gold SBE assays at the National Human Genome
Research Institute (NHGRI).
Check for population stratification
Evidence for population stratification or structure was sought by
conducting non parametric clustering of genotypes using the
AWClust algorithm . All the subjects formed one cluster with a
few outliers. Individuals identified as outliers were removed before
association analysis, which in this case resulted in the removal of 7
individuals from a sample of 1024 individuals, for a final sample
size of 1017 individuals.
Further checks were conducted during the association analysis
on the 1017 participants as follows: first, the genomic control (GC)
method was used to compute the genomic inflation factor for each
analysis and was determined to be 1.007 for hypertension, 1.001
for SBP and 0.998 for DBP, showing minimal evidence of inflation
of the test statistic due to stratification. As expected, the GC-
adjusted test statistics were virtually identical to the unadjusted
values. Second, a Q-Q plot was used to visualize the distribution of
the test statistic for each trait analysis and these again showed no
Despite intense research, the genetic risk factors for
essential hypertension and blood pressure (BP) regulation
have not been identified with consistency. We conducted
a genome wide association scan using over 800,000
genetic markers in an African American sample of 1,017
adults in the Washington, D.C., area of the United States.
We found evidence to suggest that genetic variants in
several genes, including PMS1, SLC24A4, YWHA7, IPO7,
and CACANA1H, are significantly associated with systolic
BP levels. From our previous knowledge of human
physiology, two of these genes have potential roles to
play in BP regulation. The evidence for genetic variants
influencing diastolic BP levels and hypertension status was
weaker and inconclusive. To our knowledge, this is the first
study that has used a genome-wide association approach
to study hypertension and BP in an African American
population, a minority group that experiences hyperten-
sion more frequently and more severely than other
population groups in the United States. The findings will
be useful to other researchers seeking to advance our
understanding of the genetic factors that influence BP
with the hope that these insights will eventually translate
to new and better treatment options for hypertension in
African Americans and other global populations.
GWAS for Blood Pressure in African Americans
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evidence of population stratification. Finally, principal compo-
nents (PC) were computed using the eigenstrat method . Based
on examination of the scree plot (shown in Figure S1), the first two
PCs were retained and used as covariates during the association
analysis in order to adjust for any potential residual population
Hypertension was analyzed as a binary trait (cases versus
controls) using a logistic regression model under an additive model
with adjustment for age, sex, BMI, and the first 2 PCs of the
genotypes. Given that treatment for hypertension alters BP values,
we conducted the association analysis for SBP and DBP in two
ways. First, a normotensives-only analysis was carried out using
linear regression models with age, sex, BMI, and the first 2 PCs of
the genotypes as covariates. This approach was designed to
uncover any BP associated loci without the ‘‘noise’’ effect of
treatment. Second, an analysis of the whole dataset was carried out
using the same covariates and also adjusting for the effect of
treatment. All association analyses were performed using the
PLINK software package, v1.04 . Association for the
replication sample of 980 unrelated non-diabetic West Africans
enrolled as part of the Africa America Diabetes (AADM) Study
[14,15] was done the same way. P-values for the discovery (African
American) sample and the replication (West African) samples were
combined using the Meta-Analysis Tool for genome-wide
abecasis/Metal/). The METAL algorithm calculates a z-statistic
for each marker summarizing the magnitude and direction of the
effect relative to the reference allele in each sample and then
calculates an overall z-statistic and p value from the weighted
average of the statistics. Weights are proportional to the square-
root of the sample size of each study.
SNPs that showed an association p-value less than 1e-04for each
trait were mapped to genes within 5 kB using Ensembl (http://
www.ensembl.org). The resulting gene list for the hypertension
phenotype and for SBP and DBP, each with corresponding Entrez
IDs, were entered into MetaCore (http://www.genego.com) and
tested for enrichment in Maps, Diseases, Gene Ontology (GO)
processes and GeneGO processes. MetaCore uses a hypergeo-
metric model to determine the significance of enrichment.
The subjects comprised 1017 individuals (419 men, 598
women), including 509 cases of hypertension and 508 normoten-
sive controls. Hypertensive subjects were older (mean age 54 years
versus 41 years) and heavier (mean BMI 31.7 kg/m2versus
29.3 kg/m2) than the normotensive subjects. As expected, mean
BP was higher and showed more variance among hypertensive
compared to normotensive subjects (Table 1).
The distribution of association p-values (Manhattan plot) for the
three traits is shown in Figure 1 and the QQ plots in Figure 2. The
ten top scoring SNPs for association with hypertension are shown
in Table 2. The SNP with the lowest p-value (5.1061027) for this
trait was rs9791170 located on chromosome 5. This intergenic
SNP is about 6 kbp upstream of the P4HA2 (GeneID 8974) gene.
However, it did not show genome-wide significance (Bonferroni-
corrected p=0.412) for association with hypertension; neither did
any of the other SNPs (see Table S1 for a list of the top-scoring
associations for hypertension as a binary trait).
In contrast to the hypertension results, the T allele of the
rs5743185 SNP, an intronic SNP in the PMS1 (GeneID 5378)
gene, was strongly associated with SBP (nominal p=2.09610211,
Bonferroni-corrected p=1.6961025) among normotensive indi-
viduals. Other SNPs that showed significant association with SBP
among normotensive individuals, each with a Bonferroni-correct-
ed p value of #0.05, include: rs3751664 (a non-synonymous
coding SNP in CACNA1H (GeneID 8912)), rs11160059 (an
intronic SNP inSLC24A4 (GeneID 123041)), rs17365948 (an
intronic SNP in YWHAZ (GeneID 7534)), rs12279202 (an
intronic SNP in IPO7 (GeneID 10527)) and rs1687730 (an
intergenic SNP, 12 kb from AL365365.23, a pseudogene), –
Table 3. Repeating these analyses for the whole sample, with
adjustment for treatment effects, did not change the top-scoring
characteristics of these six SNPs (as shown in Table S2). The mean
effect size on SBP associated with the at-risk alleles of these six
SNPs (estimated from the linear model adjusted for age, sex, BMI
and PCs among normotensive individuals only) was ,5–6 mmHg.
If independent, each SNP significant after Bonferroni-correction
correction would be associated with ,5% of the variance in SBP.
The full list of the top-scoring associations for SBP is shown in
Table S3. Haplotype analysis did not show any haplotype
association that reached the significance of the single locus
analyses (data not shown). Two-locus interaction analyses between
the SNPs that were significant or marginally so did not show any
significant interactions, with the lowest p-value 0.115 (between
rs17315498 and rs11160059). For DBP, the A allele of rs1867226
(an intronic SNP in PRC1 (GeneID 9055)) showed the lowest p-
value (5.861027). However, neither this nor any other association
reached genome wide significance (Table 3; see Table S4 for list of
top-scoring SNPs for DBP).
Pathway analysis revealed a number of significant pathways and
processes that are associated with SBP and DBP (Table 4).
Examination of each of these pathways and processes showed
annotations with obvious cardiovascular implications (for example,
Development_PIP3 signaling in cardiac myocytes, Transport_Potassium
transport and Development_Blood vessel morphogenesis) and several
pathways and processes that are enriched for genes involved in
hypertension and/or blood pressure regulation. As a case in point,
the top scoring pathway – Development_Role of HDAC and calcium/
clamodulin-dependent kinase (CaMK) in control of skeletal myogenesis-
(Figure 3) contains the calcium-gated channels CACNA1E and
CACNA1H, IGF-1, and AKT, each of which is known to play a
role in mechanisms of BP regulation, hypertension and/or
complications of hypertension (including left ventricular hypertro-
phy) [16–21]. The top-scoring pathways for hypertension alone
are shown in Table S5.
Table 1. Characteristics of the subjects.
CharacteristicHypertension Normotensive controls
N 509 508
Age (years) 54.1 (11.8) 42.6 (11.9)
Body mass index (BMI)31.7 (8.6) 29.3 (8.0)
Waist-hip ratio 0.88 (0.09)0.85 (0.08)
Systolic BP 144.6 (22.1) 118.0 (10.9)
Diastolic BP 88.2 (13.9) 74.5 (8.0)
Figures are mean (SD).
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Figure 1. Manhattan plot of all SNPs for the three phenotypes.
GWAS for Blood Pressure in African Americans
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A total number of 17 SNPs were carried forward for replication
in the sample of 980 unrelated non-diabetic West Africans (366
HTN cases, 614 normotensive subjects; mean age 49 (SD 12)
years, mean BMI 25.1 (SD 6) kg/m2) enrolled as part of the Africa
America Diabetes Mellitus (AADM) study [14,15]. These 17 SNPs
comprised the top-scoring seven SNPs for SBP, the top scoring
three SNPs for DBP, two SNPs that had low p-values (p,161024)
for both SBP and DBP, as well five of the top-scoring SNPs for
HTN as a dichotomous trait. Five (rs5743185, rs3751664,
rs12279202, rs11659639 and rs6543012) were monomorphic in
the West African sample. The results for the other twelve SNPs
analyzed under an additive model and with adjustment for age,
sex, BMI, ethnic group and treatment for hypertension (adjust-
ment for treatment for SBP and DBP only) are shown in Table 5.
Three SNPs (rs1867226, rs1550576 and rs8039294) were
significant at a p-value of ,0.05 among the West Africans. The
Figure 2. QQ plot for all three phenotypes. QQ plot for hypertension (blue), systolic BP (purple) and diastolic BP (red). Genomic control l was
1.007 for hypertension, 1.000 for systolic BP and 0.998 for diastolic BP.
GWAS for Blood Pressure in African Americans
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combined analysis showed that five SNPs, including rs11160059
(SLC24A4), were significantly associated with the trait and with
the same direction of effect in both samples.
Two recent GWA studies [22,23] identified the STK39 and
CDH13 genes as being significantly associated with BP. We
therefore looked for evidence for association of SNPs in these
genes with SBP and DBP in the present study. Each of these genes
showed multiple SNPs associated with SBP and DBP at a p,0.05
(Table 6). Of note, STK39 had many more significantly associated
SNPs (9/136 for SBP, 33/136 for DBP) than would be expected
by chance at a nominal p value of 0.05 (7/136). All of the STK39
SBP-associated SNPs and 24 of the 33 DBP-associated SNPs were
in the LD bins 1 and 2 (chr2:168,699,002-168,788,544) reported
in the Amish.
We also looked for in silico replication of this study’s top SBP-
associated SNPs in the Diabetes Genetics Initiative (DGI) 
GWAS, which to our knowledge, was the first published GWAS
for BP. Out of the five genes harboring the top scoring SNPs for
SBP in this study, three had variants with low p-values associated
with SBP under the same additive model in the DGI (Table S6).
Table 2. Top associated SNPs for hypertension as a binary trait.
# SNP ChrPosition (bp)Type Closest geneDistance to gene (kb) A1MAFP OR (SE)
1 rs97911705 131597526 INTERGENICP4HA26A 0.434 5.10e-07 0.58(0.11)
2 rs21462041 167140723INTERGENIC RP11-375F2.16C 0.0872.97e-062.49(0.20)
3 rs9913164 100541468INTERGENIC ADH711T 0.451 3.45e-06 1.62(0.10)
4 rs790252910 2288418INTERGENIC AL354747.1257A 0.141 6.14e-06 0.50(0.15)
5 rs155057615 56000706 INTERGENICALDH1A232T 0.1421.03e-05 0.52(0.15)
6 rs117141393 133427327 INTERGENICACPP92T 0.081 1.14e-05 2.45(0.20)
7 rs116920452 41804457 INTERGENIC LDHAL396C 0.4081.54e-05 0.64(0.10)
8 rs127482991 197249947 INTERGENIC AC096631.264C 0.132 1.66e-051.99(0.16)
9 rs2665797 1759276217UPSTREAM SMARCD23G 0.0951.73e-05 0.45(0.18)
10rs119880368 20184487INTRONIC LZTS10T 0.243 1.95e-051.66(0.12)
A1=minor allele; MAF=minor allele frequency; OR=Odds ratio for minor allele.
Table 3. Top associated SNPs for Systolic BP and Diastolic BP.
RankSNP Chr PositionType Closest gene Distance to gene (kb) Allele MAFP
1 rs57431852190446083 INTRONICPMS10T 0.14182.09E-11
2 rs168773206 16031005 INTERGENICAL365265.23 12G 0.13163.42E-09
3 rs11160059 1491877083INTRONIC SLC24A40A 0.1782 1.54E-08
4rs173659488102026053 INTRONICYWHAZ0A 0.11251.59E-08
5 rs1227920211 9388666INTRONICIPO70A 0.1231 4.80E-08
6 rs3751664 161194370 NON_SYNONYMOUS_CODING CACNA1H0T 0.10936.71E-08
7 rs11659639 1856318592INTERGENIC MC4R 127C 0.097712.13E-07
8 rs4613079 1679201458 INTRONICCDYL20T 0.1766 5.06E-07
9 rs132017446 6071844 INTERGENICF13A1 17A 0.161.12E-06
10 rs21837379 70431453 INTERGENIC RP11-274B18.315T 0.45921.21E-06
1 rs18672261589324717 INTRONICPRC10C 0.46365.80E-07
2 rs9590141 1394401623 INTERGENICABCC468A 0.1224 8.76E-07
3 rs10135446 1479479231 INTERGENICNRXN3. 79A0.1298 4.47E-06
4 rs111203131 212647829 INTRONICPTPN140A 0.16084.53E-06
5 rs168488611 235211537INTERGENICRP11-182B22.40G 0.2008 4.73E-06
6 rs11846013 1446002041 INTERGENICRPL10L188A 0.136 4.99E-06
7 rs168535743 170562457 INTERGENICMDS1 19C 0.039825.10E-06
8rs2823756 21 16664201 INTRONICAP000473.20T 0.4389 5.73E-06
9 rs8039294 1589544863INTRONIC SV2B0G 0.48286.29E-06
10 rs930119613 106645433 INTRONICFAM155A0T 0.1159 6.66E-06
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These were SLC24A4 (rs7142084, p=0.0017), IPO7 (rs7480643,
p=0.009) and PMS1 (rs3791767, p=0.014).
Unlike the growing success stories for many common complex
diseases (e.g., diabetes), our understanding of the genetic basis of
the common type of hypertension (essential hypertension) has not
been greatly advanced from the widespread use of GWAS. This is
probably due to hypertension being modulated by a larger number
of low-risk variants, each of small effect and low penetrance than
other complex diseases such as type 2 diabetes. If this is indeed the
case, GWAS analysis techniques focusing on identifying common
variants of moderate to large effects will not detect these variants,
as has been the case for the WTCCC and DGI studies. Another
indication that the usual GWAS method may not be as successful
for hypertension is the recent attempt to replicate the WTCCC
hypertension signals in 11,433 persons in the Family Blood
Pressure Program, which essentially could not replicate the
WTCC findings .
The observation of essentially null findings for hypertension
from several large-scale GWAS calls for the development of
different approaches including screening for rare variants in
genes causing rare diseases characterized by BP change. In
the most convincing study using this approach, rare variants in
three genes – SLC12A3 (NCCT), SLC12A1 (NKCC2) and
KCNJ1 (ROMK) – that alter renal salt handing were shown to
influence BP variation in the general population . In the
present study, we have used a GWAS as a discovery tool for
identifying variants influencing hypertension susceptibility and
BP variation among African Americans. Using the set of variants
prioritized from the GWAS, our secondary focus was to employ
pathway analysis to identify a set of potential genes influencing
BP through networks and pathways, rather than to identify a
locus or loci of large effect reaching genome-wide significance for
Using Bonferroni-corrected p values as the criterion for
genome-wide significance, we found significant associations with
SBP for several SNPs, comprising one intergenic SNP, four
intronic SNPs (in PMS1, SLC24A4, YWHAZ and IPO7) and one
non-synonymous coding SNP (in CACANA1H). Two of these
genes have annotations that suggest a role in BP regulation. The
gene CACNA1H (calcium channel, voltage-dependent, T type,
alpha 1H subunit), encodes a T-type member of the alpha-1
subunit family, a protein in the voltage-dependent calcium
channel complex. Calcium channels mediate the influx of calcium
ions into the cell upon membrane polarization and consist of a
complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a
1:1:1:1 ratio. The alpha-1 subunit has 24 transmembrane
segments and forms the pore through which ions pass into the
cell. The primary disease association is with childhood epilepsy
. However, one of its GO annotations is regulation of heart
contraction, which provides a plausible mechanism whereby it
could influence BP. In fact, it was first cloned from human heart
and was shown to be highly expressed in heart and kidney .
This T-type voltage-gated calcium channel protein is the target for
mibefradil , the calcium-channel blocker, used for treating
hypertension and angina pectoris under the name Posicor. It is also
a target for the calcium-channel blocking agents efonidipine,
benidipine and manidipine . The associated SNP (rs3751664)
is monomorphic in the HapMap Yoruba (YRI) sample but has a
minor allele frequency of 0.1 in the HapMap CEU sample which
is very similar to the 0.11 frequency observed in this African
American sample. This implies that it has its origin in the
European component of the African American ancestries.
Interestingly, the SNP is a non synonymous coding variant which
leads to an arginine to cysteine change in position 788 (R788C) of
the protein. This mutation is predicted to be ‘‘benign’’ by PolyPhen
, which may account for its relatively high frequency in the
HapMap CEU (0.1), HCB (0.1) and JPT (0.125) samples.
SLC24A4 (solute carrier family 24 (sodium/potassium/calcium
exchanger), member 4) codes for potassium dependent sodium/
calcium exchanger. Potassium-dependent sodium/calcium ex-
changers are thought to transport 1 intracellular calcium and 1
potassium ion in exchange for 4 extracellular sodium ions .
The associated SNP in the present study, rs11160059, is
polymorphic only in the HapMap YRI and is monomorphic in
the HapMap CEU, CHB and JPT populations. Interestingly, the
only known genetic association with this gene is with hair color
and skin pigmentation among people of European ancestry
[29,30]. However, the hair and skin color associated SNP,
rs12896399, is located 33 kb away from rs11160059 (the SBP-
associated SNP) and both SNPs are not in LD (r2=0.001 in
HapMap ASW and r2=0.0005 in HapMap YRI). Given the
limited functional data available on potassium dependent sodium/
calcium exchangers, this gene is worth investigating further as a
potential candidate gene for hypertension.
The gene PMS1 (postmeiotic segregation increased 1), encodes
a DNA mismatch repair mutL/hexB protein and mutations in this
gene cause hereditary nonpolyposis colorectal cancer type 3
(HNPCC3) either alone or in combination with mutations in other
genes involved in the HNPCC phenotype (Lynch syndrome). The
gene YWHAZ (tyrosine 3-monooxygenase/tryptophan 5-mono-
oxygenase activation protein, zeta polypeptide) codes for one of
the 14-3-3 family of proteins which mediate signal transduction by
binding to phosphoserine-containing proteins. The encoded
Table 4. Statistically significant GeneGo Pathway Maps and
Biological Processes for genes associated with SBP and DBP at
GeneGo Pathway Mapp
Development_Role of HDAC and calcium/calmodulin-dependent
kinase (CaMK) in control of skeletal myogenesis
Development_PIP3 signaling in cardiac myocytes1.179e-3
Development_IGF-RI signaling 1.407e-3
Transcription_Receptor-mediated HIF regulation3.387e-2
Signal transduction_AKT signaling 4.807e-2
Development_Ligand-independent activation of ESR1 and ESR2 5.277e-2
Signal transduction_PTEN pathway5.394e-2
GeneGo Biological Processp
Transport_Synaptic vesicle exocytosis4.525e-3
Neurophysiological process_Transmission of nerve impulse1.050e-2
DNA damage_Checkpoint 3.169e-2
Reproduction_FSH-beta signaling pathway 4.986e-2
Cell adhesion_Cell junctions5.213e-2
Development_Blood vessel morphogenesis6.740e-2
Signal transduction_Androgen receptor signaling cross-talk1.250e-1
Signal transduction_ESR1-membrane pathway 1.595e-1
GWAS for Blood Pressure in African Americans
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protein interacts with IRS1 protein, suggesting a role in regulating
insulin sensitivity. IPO7 (importin 7) codes for a protein that is a
member of a class of approximately 20 potential Ran targets that
share a sequence motif related to the Ran-binding site of importin-
beta and is one of several importin beta-like transport receptors,
that directly bind and import ribosomal proteins. However, none
of these genes is known to have any obvious or direct relationship
with BP or hypertension.
As a follow up to the initial GWAS discovery, we carried
forward a number of SNPs for replication in a West African
sample. Three SNPs showed p of ,0.05 and two others a p
between 0.05 and 0.1 in the West African sample. However,
combined analysis showed that five SNPs - rs991316, rs12748299,
rs1550576, rs11160059 (SLC24A4) and rs10135446 – showed a
low combined p-value with the same direction of association in
both samples. Our search of previously published GWAS for BP
for SNPs in the genes represented in the top-scoring SNPs for SBP
in the present study also showed that at least one SNP in each of
PMS1, SLC24A4 and IPO7 showed low p-values in the DGI
study. These findings suggest that these regions are worth further
Two recent studies provided the first strong evidence in the
literature of genetic variants associated with BP from GWAS. In
one, STK39 variants were associated with BP in the Amish
population  and in the other, CDH13 variants were associated
with BP in two European populations . We sought for
evidence that variants in these two genes may be associated with
SBP in our study of African Americans. Our findings (especially
regarding STK39) provide strong supporting evidence that these
two genes may indeed be good candidate genes for BP regulation.
For each of the genes, the association findings are supported by
strong biological evidence: the protein product of STK39 (SPAK)
interacts with cation-chloride transporters that play major roles in
renal salt excretion and the CDH13 gene codes for an adhesion
glycoprotein T-cadherin that is a regulator of vascular wall
remodeling and angiogenesis.
Figure 3. Most significant GeneGo Pathway Map for top scoring genes for SBP and DBP.
GWAS for Blood Pressure in African Americans
PLoS Genetics | www.plosgenetics.org8 July 2009 | Volume 5 | Issue 7 | e1000564
We also used pathway-based analysis to provide a means of
interpreting the subset of top-scoring SNPs located in genes. Our
findings demonstrate that this set of genes cluster in pathways and
networks that are likely to be of biological relevance to
hypertension and/or BP. A recent study  that used this
approach on the Wellcome Trust data observed some interesting
findings including pathways involved in dopamine signaling, PKA
signaling and ChREBP regulation. Indeed, despite the differences
between this study and the Wellcome Trust in terms of population
studied, study design, phenotypes and sample size, several of the
significant pathways were common to both studies (Table S5).
Thus, despite the absence of replication at the SNP association
level, some gene-based pathway maps were shared between the
two studies. This suggests that, in addition to or in lieu of relying
solely on replicated variants of moderate-to-large effect reaching
genome-wide significance, pathway and network approaches may
be useful in prioritizing candidate genes/loci for further
This study has a number of limitations. Firstly, the sample size is
modest relative to many other GWAS studies. This means that
some signals may have been missed. Secondly, due to lack of
GWAS data on African American samples, our replication
attempts were limited to a West African sample and in silico
replication in the DGI study, neither of which may be an
appropriate replication sample for African Americans. On the
other hand, this is one of the first GWAS for hypertension and BP
in a population of non-European ancestry and it increases our
resources for understanding the genetics of human hypertension.
In this regard, it is important to consider the issue of an
appropriate replication sample for an admixed population, such as
African Americans. In the absence of any previous published
GWAS of hypertension and/or BP in an African American
population, we followed the top-scoring SNPs by genotyping a
West African sample and showed that two SNPs are worth further
study. We also attempted in silico replication in a European
ancestry sample for our top SBP SNPs (assuming that these two
groups represented a significant proportion of the ancestral gene
pool of the admixed group). Furthermore, data from the HapMap
showed that four of the six SNPs were monomorphic in at least
one of these two source populations (represented by the HapMap
CEU and YRI samples), suggesting that neither one of these
samples will on its own serve as an appropriate replication sample
for an African American population. Therefore, the possibility
remains that using similar African American populations (who will
have similar allele frequencies and haplotype structures) for
replication may be optimal, as has recently been reported for
East Asian populations and type 2 diabetes . Admixture affects
allele frequencies at many loci as well as local LD patterns;
furthermore, admixed populations are often not homogenous and
may show considerable geographic variation in the degree of
Table 6. Replication of STK39 and CDH13 SNPs with SBP and DBP in this study of African American subjects.
Gene# SNPs typed
# SNPs p,0.05 Top SNPs
P# SNPs p,0.05 Top SNPsP
STK391369 rs20639580.01033 rs118905271.0261024
CDH13102049 rs11860907 5.7161024
Table 5. Replication of selected SNPs in a sample of 980 West Africans.
Chr SNP (Gene)Trait
P in African American
P in West African
MAF in African
MAF in West
5 rs9791170 HTN5.10e-07 0.1230.009 0.4340.457
4 rs991316 HTN3.45e-06 0.0814.73e-06*** 0.4510.435
1 rs12757682HTN 2.59e-05 0.4100.014 0.132 0.079
1 rs12748299 HTN 1.66e-050.715 0.0007*** 0.1320.080
15 rs1550576HTN1.03e-05 0.039 3.32e-06***0.1420.218
6 rs16877320 (PMS1)SBP 3.42e-09 0.7810.001 0.132 0.023
14 rs11160059 (SLC24A4) SBP1.54e-080.748 0.0003***0.178 0.078
8 rs17365948 (YWHAZ) SBP1.59e-080.507 0.005 0.1130.005
15 rs8039294 (SV2B) SBP 7.73e-06 0.0380.3120.483 0.354
DBP 6.29e-06 0.0920.178
14rs10135446 DBP4.47e-060.6220.002*** 0.130 0.141
13 rs9590141 DBP8.76e-070.3680.031 0.122 0.129
15 rs1867226 (PRC1)DBP5.8e-07 0.047 0.1620.464 0.376
***Same direction of association.
GWAS for Blood Pressure in African Americans
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admixture. These observations have been found to be true for
African Americans, our study population [33,34]. Therefore, the
question of replicating the findings from an admixed population
needs to be investigated further.
In summary, we have reported a GWAS for hypertension and
BP in an African American population and identified SNPs
reaching genome wide significance for SBP and suggestive
evidence of association for DBP and Hypertension. The set of
top scoring SNPs were enriched for genes in pathways with
annotations to hypertension and/or BP regulation. These findings
provide a set of candidate genes to be evaluated in-depth in future
studies. Further replication and fine mapping in multiple
populations, especially in an independent African American
samples, are needed. Given the global lack of success in identifying
susceptibility loci for essential hypertension using genome wide
linkage and association strategies, the genetic architecture
underlying BP control must be considerably more complex and
sufficiently different from those of other common complex human
diseases (e.g., diabetes). This may be the reason why the current
agnostic approaches of searching the genome of thousands of
individuals for risk loci has not yielded strong and consistent results
for hypertension and BP. Alternative strategies, e.g., complete re-
sequencing of candidate genes to identify rare variants, are clearly
Note added during the preparation of the article
While this paper was under review, two GWAS for hyperten-
sion, SBP and DBP in subjects of European descent were
published [35,36]. One of these studies  also reported finding
significant hits in the CACNB2 gene for hypertension and DBP, a
gene with a high-scoring variant for hypertension in the present
study (Table S1) and in the PMS1 gene for hypertension and SBP,
which scored highly for SBP in this study (Table 3).
genotypes in the sample.
Found at: doi:10.1371/journal.pgen.1000564.s001 (0.13 MB TIF)
Scree plot of principal components (PCs) of the
a dichotomous trait.
Top scoring SNPs for association with hypertension as
Found at: doi:10.1371/journal.pgen.1000564.s002 (0.05 MB
compared to among normotensive subjects (controls) only.
Found at: doi:10.1371/journal.pgen.1000564.s003 (0.03 MB
Top scoring SNPs for SBP among all subjects
Found at: doi:10.1371/journal.pgen.1000564.s004 (0.05 MB
Top scoring SNPs for SBP.
Found at: doi:10.1371/journal.pgen.1000564.s005 (0.05 MB
Top scoring SNPs for DBP.
Found at: doi:10.1371/journal.pgen.1000564.s006 (0.05 MB
Top scoring GeneGo pathways for top hits for
genes for top scoring SBP SNPs. HapMap CEU, YRI, and ASW
frequencies for top scoring SBP SNPs. Also shown are the DGI
study’s lowest p-values in the genes containing the top SNPs for
SBP in this study.
Found at: doi:10.1371/journal.pgen.1000564.s007 (0.03 MB
HapMap frequencies and DGI Study SBP p-values in
The authors would like to thank participants in the Howard University
Family Study (HUFS) and the HUFS field staff, in particular Sandra Epps
and Nike Hutchison. The role of the Howard University General Clinical
Research Center (GCRC) in participant enrollment is hereby acknowl-
Conceived and designed the experiments: AA NG AH YC MC CR.
Performed the experiments: NG AD HH KL YC. Analyzed the data: AA
NG GC AH AD HH JZ. Contributed reagents/materials/analysis tools:
GC. Wrote the paper: AA NG AH CR. Reviewed the manuscript: GC
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