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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rs2179965

Associations

Study: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. [PMID:17903297]
First author: Seshadri S
Journal: BMC Med Genet
Date: 09/19/2007
Phenotype: Cognitive test performance
Study population: 705 individuals(Framingham)
Association P-value: 1 x 10-06
Gene: LMO4 - RPL36AP10

Lead SNP

rs2179965
Position: chr1:88,802,012 (Open in UCSC Genome Browser)
Distance to nearest TSS: 430,614 bp
GENCODE v7 location: Intergenic region
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:

rs6682490
Position: chr1:88,825,290 (Open in UCSC Genome Browser)
Distance to lead SNP: 23,278 bp
Distance to nearest TSS: 453,892 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs12749687
Position: chr1:88,803,250 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,238 bp
Distance to nearest TSS: 431,852 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
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=1.0




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 01:19:10
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