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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rs10865331

Associations

Study: Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. [PMID:21743469]
First author: Evans DM
Journal: Nat Genet
Date: 07/10/2011
Phenotype: Ankylosing spondylitis
Study population: 3,023 European ancestry cases, 8,779 European ancestry controls
Replication population: 2,111 European ancestry cases, 4,483 European ancestry controls
Association P-value: 7 x 10-34
Gene: B3GNT2 - TMEM17
Risk allele: A
Minor allele frequency (controls): 0.37

Study: Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci. [PMID:20062062]
First author: Reveille JD
Journal: Nat Genet
Date: 01/10/2010
Phenotype: Ankylosing spondylitis
Study population: 2,053 European descent cases, 5,140 European descent controls
Replication population: 898 British cases, 1,518 British controls
Association P-value: 2 x 10-19
Odds ratio [95% confidence interval]: 1.27 [1.18-1.37]
Gene: B3GNT2 - TMEM17
Risk allele: A
Minor allele frequency (controls): 0.40

Lead SNP

rs10865331
Position: chr2:62,551,472 (Open in UCSC Genome Browser)
Distance to nearest TSS: 139,734 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:

rs4672505
Position: chr2:62,560,332 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,860 bp
Distance to nearest TSS: 130,874 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 2b - ChIP-seq peak + any motif + matched DNase Footprint + DNaseI-seq peak (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

rs13024541
Position: chr2:62,555,737 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,265 bp
Distance to nearest TSS: 135,469 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-seq peak (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

rs11679753
Position: chr2:62,552,321 (Open in UCSC Genome Browser)
Distance to lead SNP: 849 bp
Distance to nearest TSS: 138,885 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=0.954 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs6759003
Position: chr2:62,559,205 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,733 bp
Distance to nearest TSS: 132,001 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=0.86 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.963




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 01:19:12
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