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



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: 7 x 10-06
Odds ratio [95% confidence interval]: .32 [NR] unit decrease
Gene: CACNA2D1
Risk allele: A
Minor allele frequency (controls): 0.33

Lead SNP

Position: chr7:81,847,651 (Open in UCSC Genome Browser)
Distance to nearest TSS: 185,262 bp
GENCODE v7 location: Intron
No regulatory annotation found

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: chr7:81,825,697 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,954 bp
Distance to nearest TSS: 163,308 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.957, r2=0.842 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

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 01:19:18
SCGPM logo A project of the Center for Genomics and Personalized Medicine at Stanford University. Stanford logo