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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rs10781500

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: 1 x 10-06
Gene: CARD9
Risk allele: T
Minor allele frequency (controls): 0.42

Study: Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. [PMID:19915572]
First author: Barrett JC
Journal: Nat Genet
Date: 11/15/2009
Phenotype: Ulcerative colitis
Study population: 2,361 European ancestry cases, 5,417 European ancestry controls
Replication population: 2,321 European ancestry cases, 4,818 European ancestry controls
Association P-value: 7 x 10-06
Gene: CARD9

Lead SNP

rs10781500
Position: chr9:139,269,338 (Open in UCSC Genome Browser)
Distance to nearest TSS: 23,543 bp
GENCODE v7 location: Intergenic region
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:

rs10781499
Position: chr9:139,266,405 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,933 bp
Distance to nearest TSS: 4,322 bp
GENCODE v7 location: Coding region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs10781507
Position: chr9:139,272,058 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,720 bp
Distance to nearest TSS: 20,823 bp
GENCODE v7 location: Coding region
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

rs10781510
Position: chr9:139,279,173 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,835 bp
Distance to nearest TSS: 13,708 bp
GENCODE v7 location: Coding region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.96, r2=0.921 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.91

rs4077515
Position: chr9:139,266,496 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,842 bp
Distance to nearest TSS: 4,413 bp
GENCODE v7 location: Coding region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs3829111
Position: chr9:139,269,483 (Open in UCSC Genome Browser)
Distance to lead SNP: 145 bp
Distance to nearest TSS: 23,398 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'=0.956, r2=0.875 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4567159
Position: chr9:139,277,059 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,721 bp
Distance to nearest TSS: 15,822 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=0.923 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.911

rs3812558
Position: chr9:139,269,135 (Open in UCSC Genome Browser)
Distance to lead SNP: 203 bp
Distance to nearest TSS: 23,746 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 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs10870077
Position: chr9:139,263,891 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,447 bp
Distance to nearest TSS: 2,640 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=0.961 / CHB: D'=1.0, r2=0.947 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.954

rs11794847
Position: chr9:139,271,747 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,409 bp
Distance to nearest TSS: 21,134 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




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 01:19:19
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