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: Variants in FAM13A are associated with chronic obstructive pulmonary disease. [PMID:20173748]
First author: Cho MH
Journal: Nat Genet
Date: 02/21/2010
Phenotype: Chronic obstructive pulmonary disease
Study population: 2,940 white cases, 1,380 white controls
Replication population: 502 non-Hispanic Caucasian cases, 504 non-Hispanic Caucasian controls, 1,100 probands, 2,698 relatives
Association P-value: 1 x 10-11
Odds ratio [95% confidence interval]: 1.32 [1.19-1.47]
Gene: FAM13A
Minor allele frequency (controls): 0.48

Lead SNP

Position: chr4:89,883,979 (Open in UCSC Genome Browser)
Distance to nearest TSS: 94,137 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 

SNPs in the linkage disequilibrium region sorted by decreasing amount of evidence supporting a functional role for the SNP:

Position: chr4:89,885,714 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,735 bp
Distance to nearest TSS: 92,402 bp
GENCODE v7 location: Intron
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=0.928

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 01:19:14
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