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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rs9657451

Associations

Study: Common genetic variation and performance on standardized cognitive tests. [PMID:20125193]
First author: Cirulli ET
Journal: Eur J Hum Genet
Date: 02/03/2010
Phenotype: Cognitive test performance
Study population: Up to 1,086 individuals
Association P-value: 2 x 10-06
Gene: FLJ45872

Lead SNP

rs9657451
Position: chr8:138,905,296 (Open in UCSC Genome Browser)
Distance to nearest TSS: 787,594 bp
GENCODE v7 location: Intron
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:

rs4909716
Position: chr8:138,903,347 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,949 bp
Distance to nearest TSS: 785,645 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs2221844
Position: chr8:138,927,680 (Open in UCSC Genome Browser)
Distance to lead SNP: 22,384 bp
Distance to nearest TSS: 809,978 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5a - ChIP-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.863 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.915, r2=0.802

rs4909718
Position: chr8:138,923,146 (Open in UCSC Genome Browser)
Distance to lead SNP: 17,850 bp
Distance to nearest TSS: 805,444 bp
GENCODE v7 location: Intron
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=0.863 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.855

rs1511832
Position: chr8:138,923,517 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,221 bp
Distance to nearest TSS: 805,815 bp
GENCODE v7 location: Intron
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=0.863 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.855

rs1511830
Position: chr8:138,922,247 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,951 bp
Distance to nearest TSS: 804,545 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=0.863 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.918




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 01:19:19
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