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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rs9300212

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: 8 x 10-06
Gene: ST13P9 - ALG10

Lead SNP

rs9300212
Position: chr12:33,701,166 (Open in UCSC Genome Browser)
Distance to nearest TSS: 19,645,461 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:

rs10444398
Position: chr12:33,701,333 (Open in UCSC Genome Browser)
Distance to lead SNP: 167 bp
Distance to nearest TSS: 19,645,294 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=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.887

rs6488170
Position: chr12:33,702,068 (Open in UCSC Genome Browser)
Distance to lead SNP: 902 bp
Distance to nearest TSS: 19,644,559 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 01:19:21
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