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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rs11086243

Associations

Study: Common variation in GPC5 is associated with acquired nephrotic syndrome. [PMID:21441931]
First author: Okamoto K
Journal: Nat Genet
Date: 03/27/2011
Phenotype: Nephrotic syndrome (acquired)
Study population: 195 Japanese cases, 1,546 Japanese controls
Replication population: 662 Japanese cases, 4,919 Japanese controls
Association P-value: 3 x 10-06
Odds ratio [95% confidence interval]: 1.37 [1.20-1.57]
Gene: SRMP1 - PREX1
Risk allele: T
Minor allele frequency (controls): 0.23

Lead SNP

rs11086243
Position: chr20:46,779,235 (Open in UCSC Genome Browser)
Distance to nearest TSS: 209,206 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:

rs6066649
Position: chr20:46,779,442 (Open in UCSC Genome Browser)
Distance to lead SNP: 207 bp
Distance to nearest TSS: 208,999 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.912

rs6066651
Position: chr20:46,780,313 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,078 bp
Distance to nearest TSS: 208,128 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.954, r2=0.909

rs6063215
Position: chr20:46,777,514 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,721 bp
Distance to nearest TSS: 210,927 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.832

rs6094991
Position: chr20:46,779,102 (Open in UCSC Genome Browser)
Distance to lead SNP: 133 bp
Distance to nearest TSS: 209,339 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'=0.953, r2=0.908

rs11700186
Position: chr20:46,778,574 (Open in UCSC Genome Browser)
Distance to lead SNP: 661 bp
Distance to nearest TSS: 209,867 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'=0.952, r2=0.866

rs6066645
Position: chr20:46,778,325 (Open in UCSC Genome Browser)
Distance to lead SNP: 910 bp
Distance to nearest TSS: 210,116 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=0.835

rs6066646
Position: chr20:46,778,604 (Open in UCSC Genome Browser)
Distance to lead SNP: 631 bp
Distance to nearest TSS: 209,837 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=0.835

rs11700195
Position: chr20:46,778,503 (Open in UCSC Genome Browser)
Distance to lead SNP: 732 bp
Distance to nearest TSS: 209,938 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=0.835

rs6063216
Position: chr20:46,777,647 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,588 bp
Distance to nearest TSS: 210,794 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=0.832

rs6063218
Position: chr20:46,778,984 (Open in UCSC Genome Browser)
Distance to lead SNP: 251 bp
Distance to nearest TSS: 209,457 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=0.879




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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