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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rs30187

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: 2 x 10-27
Gene: ERAP1
Risk allele: T
Minor allele frequency (controls): 0.33

Lead SNP

rs30187
Position: chr5:96,124,330 (Open in UCSC Genome Browser)
Distance to nearest TSS: 15,300 bp
GENCODE v7 location: Coding 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:

rs27529
Position: chr5:96,126,308 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,978 bp
Distance to nearest TSS: 13,322 bp
GENCODE v7 location: Coding 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=1.0

rs26510
Position: chr5:96,125,910 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,580 bp
Distance to nearest TSS: 13,720 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - 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=1.0

rs27710
Position: chr5:96,126,197 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,867 bp
Distance to nearest TSS: 13,433 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - 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=1.0

rs246453
Position: chr5:96,123,336 (Open in UCSC Genome Browser)
Distance to lead SNP: 994 bp
Distance to nearest TSS: 16,294 bp
GENCODE v7 location: Intron
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=0.962

rs30379
Position: chr5:96,122,260 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,070 bp
Distance to nearest TSS: 556 bp
GENCODE v7 location: Intron
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=0.96

rs30380
Position: chr5:96,122,281 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,049 bp
Distance to nearest TSS: 577 bp
GENCODE v7 location: Intron
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=0.952 / YRI: D'=1.0, r2=0.962

rs469758
Position: chr5:96,121,715 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,615 bp
Distance to nearest TSS: 750 bp
GENCODE v7 location: Intron
No regulatory annotation found
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=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 01:19:15
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