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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rs1018326

Associations

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 10-06
Odds ratio [95% confidence interval]: 1.24 [1.15-1.33]
Gene: UBE2E3 - ITGA4
Risk allele: C
Minor allele frequency (controls): 0.45

Lead SNP

rs1018326
Position: chr2:182,007,800 (Open in UCSC Genome Browser)
Distance to nearest TSS: 256,487 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)

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:

rs7588217
Position: chr2:181,988,909 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,891 bp
Distance to nearest TSS: 275,378 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.814 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.915 / YRI: D'=0.963, r2=0.894

rs6731186
Position: chr2:181,977,953 (Open in UCSC Genome Browser)
Distance to lead SNP: 29,847 bp
Distance to nearest TSS: 286,334 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=0.814 / CHB: D'=1.0, r2=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.963, r2=0.894

rs13010713
Position: chr2:181,996,045 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,755 bp
Distance to nearest TSS: 268,242 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.884 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.963, r2=0.928




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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