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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rs934299

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: 9 x 10-06
Gene: UBBP1 - THSD7B

Lead SNP

rs934299
Position: chr2:137,338,940 (Open in UCSC Genome Browser)
Distance to nearest TSS: 63,823 bp
GENCODE v7 location: Intergenic region
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:

rs1863808
Position: chr2:137,334,985 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,955 bp
Distance to nearest TSS: 67,778 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.899 / CHB: D'=1.0, r2=0.877 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs934298
Position: chr2:137,338,721 (Open in UCSC Genome Browser)
Distance to lead SNP: 219 bp
Distance to nearest TSS: 64,042 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=0.947




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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