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

Return Home

rs7743761

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: 5 x 10-304
Gene: DHFRP2 - HLA-S

Lead SNP

rs7743761
Position: chr6:31,336,100 (Open in UCSC Genome Browser)
Distance to nearest TSS: 11,164 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:

rs6457401
Position: chr6:31,334,852 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,248 bp
Distance to nearest TSS: 9,916 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 2a - ChIP-seq peak + matched TF motif + matched Dnase Footprint + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=0.945 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs6457402
Position: chr6:31,334,864 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,236 bp
Distance to nearest TSS: 9,928 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'=1.0, r2=0.927 / CHB: D'=1.0, r2=0.942 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs9501572
Position: chr6:31,333,820 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,280 bp
Distance to nearest TSS: 8,884 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

rs9501374
Position: chr6:31,332,332 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,768 bp
Distance to nearest TSS: 7,396 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=0.943 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs13215664
Position: chr6:31,337,311 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,211 bp
Distance to nearest TSS: 12,375 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=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 01:19:16
SCGPM logo A project of the Center for Genomics and Personalized Medicine at Stanford University. Stanford logo