Study: Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients. [PMID:21326311]
First author: Bhatnagar P
Journal: J Hum Genet
Date: 02/17/2011
Phenotype: F-cell distribution
Study population: 440 African ancestry individuals
Association P-value: 6 x 10-06
Odds ratio [95% confidence interval]: .85 [0.50-1.20] unit decrease
Gene: SAR1AP3 - PRDM5
Risk allele: G
Minor allele frequency (controls): 0.43
rs10017284
Position: chr4:121,513,215
(Open in UCSC Genome Browser)
Distance to nearest TSS: 506,480 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium threshold:
- In all HapMap 2 populations: r2≥0.8 r2≥0.9 r2=1.0
- In the HapMap 2 CEU population r2≥0.8 r2≥0.9 r2=1.0
SNPs in the linkage disequilibrium region sorted by decreasing amount of evidence supporting a functional role for the SNP:
rs1603392
Position: chr4:121,517,978
(Open in UCSC Genome Browser)
Distance to lead SNP: 4,763 bp
Distance to nearest TSS: 511,243 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.964
rs1532055
Position: chr4:121,489,983
(Open in UCSC Genome Browser)
Distance to lead SNP: 23,232 bp
Distance to nearest TSS: 483,248 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.591
rs1603391
Position: chr4:121,518,005
(Open in UCSC Genome Browser)
Distance to lead SNP: 4,790 bp
Distance to nearest TSS: 511,270 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.964
rs13121680
Position: chr4:121,503,934
(Open in UCSC Genome Browser)
Distance to lead SNP: 9,281 bp
Distance to nearest TSS: 497,199 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.963
rs10020594
Position: chr4:121,537,169
(Open in UCSC Genome Browser)
Distance to lead SNP: 23,954 bp
Distance to nearest TSS: 530,434 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.764 / JPT: D'=1.0, r2=0.669 / YRI: D'=0.961, r2=0.857
rs10005792
Position: chr4:121,527,272
(Open in UCSC Genome Browser)
Distance to lead SNP: 14,057 bp
Distance to nearest TSS: 520,537 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=0.945, r2=0.847 / JPT: D'=1.0, r2=0.939
rs10518365
Position: chr4:121,536,939
(Open in UCSC Genome Browser)
Distance to lead SNP: 23,724 bp
Distance to nearest TSS: 530,204 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.775 / JPT: D'=1.0, r2=0.65 / YRI: D'=1.0, r2=0.964
rs6840627
Position: chr4:121,517,688
(Open in UCSC Genome Browser)
Distance to lead SNP: 4,473 bp
Distance to nearest TSS: 510,953 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.962
rs11733175
Position: chr4:121,504,784
(Open in UCSC Genome Browser)
Distance to lead SNP: 8,431 bp
Distance to nearest TSS: 498,049 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0
rs1496256
Position: chr4:121,516,847
(Open in UCSC Genome Browser)
Distance to lead SNP: 3,632 bp
Distance to nearest TSS: 510,112 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.887 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0
rs1496262
Position: chr4:121,540,662
(Open in UCSC Genome Browser)
Distance to lead SNP: 27,447 bp
Distance to nearest TSS: 533,927 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.775 / JPT: D'=1.0, r2=0.65 / YRI: D'=0.888, r2=0.788
rs1488072
Position: chr4:121,495,658
(Open in UCSC Genome Browser)
Distance to lead SNP: 17,557 bp
Distance to nearest TSS: 488,923 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.591
rs10032714
Position: chr4:121,516,476
(Open in UCSC Genome Browser)
Distance to lead SNP: 3,261 bp
Distance to nearest TSS: 509,741 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.964
rs11098574
Position: chr4:121,487,559
(Open in UCSC Genome Browser)
Distance to lead SNP: 25,656 bp
Distance to nearest TSS: 480,824 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.853 / JPT: D'=1.0, r2=0.547
rs11098579
Position: chr4:121,538,689
(Open in UCSC Genome Browser)
Distance to lead SNP: 25,474 bp
Distance to nearest TSS: 531,954 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.853
rs9992150
Position: chr4:121,542,845
(Open in UCSC Genome Browser)
Distance to lead SNP: 29,630 bp
Distance to nearest TSS: 536,110 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.754 / JPT: D'=1.0, r2=0.642 / YRI: D'=0.88, r2=0.692
rs17342461
Position: chr4:121,540,763
(Open in UCSC Genome Browser)
Distance to lead SNP: 27,548 bp
Distance to nearest TSS: 534,028 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.853
rs1353470
Position: chr4:121,527,386
(Open in UCSC Genome Browser)
Distance to lead SNP: 14,171 bp
Distance to nearest TSS: 520,651 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.952 / JPT: D'=1.0, r2=0.953 / YRI: D'=0.961, r2=0.857
Credits:This resource uses data from:
- The NHGRI GWAS catalog (accessed August 10, 2011)
- The ENCODE project
- RegulomeDB
- The HapMap project
A project of the Center for Genomics and Personalized Medicine at Stanford University.
RegulomeDB (TM) Copyright ©2011 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. The RegulomeDB project at Stanford University is supported by a Genome Research Resource Grant from the US National Human Genome Research Institute, part of the US National Institutes of Health.