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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rs10517437

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: 4 x 10-06
Gene: SRIP1 - RPL17P19

Lead SNP

rs10517437
Position: chr4:59,008,412 (Open in UCSC Genome Browser)
Distance to nearest TSS: 417,590 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:

rs2196053
Position: chr4:59,009,319 (Open in UCSC Genome Browser)
Distance to lead SNP: 907 bp
Distance to nearest TSS: 418,497 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=0.832

rs12649436
Position: chr4:59,015,876 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,464 bp
Distance to nearest TSS: 425,054 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=0.832

rs7658369
Position: chr4:59,023,476 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,064 bp
Distance to nearest TSS: 432,654 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.925 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.832

rs1433409
Position: chr4:59,006,847 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,565 bp
Distance to nearest TSS: 416,025 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=0.819

rs4865305
Position: chr4:59,018,718 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,306 bp
Distance to nearest TSS: 427,896 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.923 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.828




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 01:19:14
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