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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rs448720

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: 5 x 10-06
Gene: RNU6-1 - PIAS1

Lead SNP

rs448720
Position: chr15:68,198,911 (Open in UCSC Genome Browser)
Distance to nearest TSS: 281,263 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (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:

rs8035326
Position: chr15:68,208,533 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,622 bp
Distance to nearest TSS: 271,641 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 2b - ChIP-seq peak + any motif + matched DNase Footprint + DNaseI-seq peak (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=1.0

rs440341
Position: chr15:68,210,959 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,048 bp
Distance to nearest TSS: 269,215 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (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=1.0

rs379281
Position: chr15:68,210,700 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,789 bp
Distance to nearest TSS: 269,474 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
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=1.0

rs338338
Position: chr15:68,201,422 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,511 bp
Distance to nearest TSS: 278,752 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=0.887 / CHB: D'=1.0, r2=0.928 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs410554
Position: chr15:68,198,499 (Open in UCSC Genome Browser)
Distance to lead SNP: 412 bp
Distance to nearest TSS: 281,675 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=1.0

rs2448136
Position: chr15:68,211,991 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,080 bp
Distance to nearest TSS: 268,183 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

rs430610
Position: chr15:68,198,622 (Open in UCSC Genome Browser)
Distance to lead SNP: 289 bp
Distance to nearest TSS: 281,552 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

rs338340
Position: chr15:68,202,957 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,046 bp
Distance to nearest TSS: 277,217 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.88 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs7163687
Position: chr15:68,193,949 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,962 bp
Distance to nearest TSS: 286,225 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=0.924 / JPT: D'=1.0, r2=0.935 / YRI: D'=1.0, r2=1.0

rs383144
Position: chr15:68,204,581 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,670 bp
Distance to nearest TSS: 275,593 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

rs449761
Position: chr15:68,210,579 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,668 bp
Distance to nearest TSS: 269,595 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

rs11853797
Position: chr15:68,200,578 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,667 bp
Distance to nearest TSS: 279,596 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=0.945 / 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 01:19:23
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