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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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 10-07
Odds ratio [95% confidence interval]: 1.39 [1.22-1.57]
Gene: GPC5
Risk allele: A
Minor allele frequency (controls): 0.17

Lead SNP

Position: chr13:92,203,813 (Open in UCSC Genome Browser)
Distance to nearest TSS: 204,881 bp
GENCODE v7 location: Intron
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 

No SNPs found for this LD threshold.

This resource uses data from:
 - The NHGRI GWAS catalog (accessed August 10, 2011)
 - The ENCODE project
 - RegulomeDB
 - The HapMap project

Contact: marc.schaub AT
Last modified: 2011-12-15 01:19:22
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