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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rs1427407

Associations

Study: A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15. [PMID:17767159]
First author: Menzel S
Journal: Nat Genet
Date: 09/02/2007
Phenotype: F-cell distribution
Study population: 179 adults in upper and lower 5%
Replication population: 90 adults
Association P-value: 6 x 10-31
Odds ratio [95% confidence interval]: 13.10 [NR] % of variance explained
Gene: BCL11A
Minor allele frequency (controls): 0.14

Lead SNP

rs1427407
Position: chr2:60,718,043 (Open in UCSC Genome Browser)
Distance to nearest TSS: 22,145 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5a - ChIP-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:

rs766432
Position: chr2:60,719,970 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,927 bp
Distance to nearest TSS: 24,072 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.855 / CHB: D'=1.0, r2=0.947 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.942, r2=0.758

rs4671393
Position: chr2:60,720,951 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,908 bp
Distance to nearest TSS: 25,053 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.855 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.942, r2=0.758




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 01:19:12
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