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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rs2242944

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: 8 x 10-20
Odds ratio [95% confidence interval]: 1.39 [1.28-1.49]
Gene: FLJ45139 - RPL23AP12
Minor allele frequency (controls): 0.63

Lead SNP

rs2242944
Position: chr21:40,465,178 (Open in UCSC Genome Browser)
Distance to nearest TSS: 90,134 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (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:

rs2242945
Position: chr21:40,467,423 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,245 bp
Distance to nearest TSS: 87,889 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'=0.952, r2=0.906 / JPT: D'=0.942, r2=0.841 / YRI: D'=1.0, r2=1.0

rs2836880
Position: chr21:40,466,239 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,061 bp
Distance to nearest TSS: 89,073 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=0.954 / JPT: D'=1.0, r2=0.896 / YRI: 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 01:19:25
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