Linking Disease Associations with Regulatory Information in the Human Genome - Companion website
Marc A. Schaub, Alan P. Boyle, Anshul Kundaje, Serafim Batzoglou, Michael Snyder, Stanford University

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rs11968814

Associations

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: 9 x 10-07
Odds ratio [95% confidence interval]: 1.17 [0.70-1.64] unit decrease
Gene: B3GAT2 - OGFRL1
Risk allele: A
Minor allele frequency (controls): 0.16

Lead SNP

rs11968814
Position: chr6:71,776,971 (Open in UCSC Genome Browser)
Distance to nearest TSS: 110,838 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found

Linkage disequilibrium region

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:

rs10945292
Position: chr6:71,869,340 (Open in UCSC Genome Browser)
Distance to lead SNP: 92,369 bp
Distance to nearest TSS: 32,531 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs11970269
Position: chr6:71,779,034 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,063 bp
Distance to nearest TSS: 112,901 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.765

rs12110901
Position: chr6:71,799,922 (Open in UCSC Genome Browser)
Distance to lead SNP: 22,951 bp
Distance to nearest TSS: 133,789 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / YRI: D'=0.829, r2=0.56

rs6916241
Position: chr6:71,841,491 (Open in UCSC Genome Browser)
Distance to lead SNP: 64,520 bp
Distance to nearest TSS: 50,931 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

rs6916069
Position: chr6:71,841,399 (Open in UCSC Genome Browser)
Distance to lead SNP: 64,428 bp
Distance to nearest TSS: 51,023 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

rs11965581
Position: chr6:71,815,049 (Open in UCSC Genome Browser)
Distance to lead SNP: 38,078 bp
Distance to nearest TSS: 148,916 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.585

rs9969061
Position: chr6:71,862,393 (Open in UCSC Genome Browser)
Distance to lead SNP: 85,422 bp
Distance to nearest TSS: 30,029 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs6927030
Position: chr6:71,864,929 (Open in UCSC Genome Browser)
Distance to lead SNP: 87,958 bp
Distance to nearest TSS: 28,120 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs7767341
Position: chr6:71,613,238 (Open in UCSC Genome Browser)
Distance to lead SNP: 163,733 bp
Distance to nearest TSS: 52,895 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0




Credits:
This resource uses data from:
 - The NHGRI GWAS catalog (accessed August 10, 2011)
 - The ENCODE project
 - RegulomeDB
 - The HapMap project

Contact: marc.schaub AT cs.stanford.edu
Last modified: 2011-12-15 01:19:16
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