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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rs1227756

Associations

Study: Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. [PMID:20708005]
First author: Chalasani N
Journal: Gastroenterology
Date: 08/10/2010
Phenotype: Non-alcoholic fatty liver disease histology (lobular)
Study population: 236 non-Hispanic Caucasian women
Association P-value: 2 x 10-07
Odds ratio [95% confidence interval]: .57 [NR] unit increase
Gene: COL13A1
Risk allele: G
Minor allele frequency (controls): 0.46

Lead SNP

rs1227756
Position: chr10:71,588,504 (Open in UCSC Genome Browser)
Distance to nearest TSS: 110,504 bp
GENCODE v7 location: Intron
RegulomeDB Score: 2b - ChIP-seq peak + any motif + matched DNase Footprint + 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:

rs1227753
Position: chr10:71,587,887 (Open in UCSC Genome Browser)
Distance to lead SNP: 617 bp
Distance to nearest TSS: 109,887 bp
GENCODE v7 location: Intron
RegulomeDB Score: 2b - ChIP-seq peak + any motif + matched DNase Footprint + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.959 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.928




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 01:19:20
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