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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rs10989661

Associations

Study: Genome-wide and candidate gene association study of cigarette smoking behaviors. [PMID:19247474]
First author: Caporaso N
Journal: PLoS One
Date: 02/27/2009
Phenotype: Smoking behavior
Study population: 4,611 individuals (2,617 smokers)
Association P-value: 6 x 10-06
Odds ratio [95% confidence interval]: 1.68 [NR]
Gene: PPP3R2 - ZYG11AP1
Minor allele frequency (controls): 0.74

Lead SNP

rs10989661
Position: chr9:104,622,868 (Open in UCSC Genome Browser)
Distance to nearest TSS: 396,125 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:

rs10989654
Position: chr9:104,603,023 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,845 bp
Distance to nearest TSS: 415,970 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.938 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.896

rs10819996
Position: chr9:104,590,378 (Open in UCSC Genome Browser)
Distance to lead SNP: 32,490 bp
Distance to nearest TSS: 428,615 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.896

rs10512291
Position: chr9:104,603,846 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,022 bp
Distance to nearest TSS: 415,147 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.896

rs10989647
Position: chr9:104,595,027 (Open in UCSC Genome Browser)
Distance to lead SNP: 27,841 bp
Distance to nearest TSS: 423,966 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.91 / JPT: D'=1.0, r2=0.896

rs10989657
Position: chr9:104,613,466 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,402 bp
Distance to nearest TSS: 405,527 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=0.94 / CHB: D'=1.0, r2=0.91 / JPT: D'=1.0, r2=1.0

rs13288852
Position: chr9:104,621,961 (Open in UCSC Genome Browser)
Distance to lead SNP: 907 bp
Distance to nearest TSS: 397,032 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.936 / CHB: D'=1.0, r2=0.896 / JPT: D'=1.0, r2=0.887

rs10819999
Position: chr9:104,606,759 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,109 bp
Distance to nearest TSS: 412,234 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.94 / CHB: D'=1.0, r2=0.91 / JPT: D'=1.0, r2=0.896

rs10989632
Position: chr9:104,573,511 (Open in UCSC Genome Browser)
Distance to lead SNP: 49,357 bp
Distance to nearest TSS: 445,482 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=1.0 / JPT: D'=0.893, r2=0.798

rs10989636
Position: chr9:104,584,492 (Open in UCSC Genome Browser)
Distance to lead SNP: 38,376 bp
Distance to nearest TSS: 434,501 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.91 / JPT: D'=0.893, r2=0.798

rs10989637
Position: chr9:104,585,858 (Open in UCSC Genome Browser)
Distance to lead SNP: 37,010 bp
Distance to nearest TSS: 433,135 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.936 / CHB: D'=1.0, r2=1.0 / JPT: D'=0.893, r2=0.798

rs10989638
Position: chr9:104,586,404 (Open in UCSC Genome Browser)
Distance to lead SNP: 36,464 bp
Distance to nearest TSS: 432,589 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=1.0 / JPT: D'=0.893, r2=0.798

rs10989639
Position: chr9:104,591,829 (Open in UCSC Genome Browser)
Distance to lead SNP: 31,039 bp
Distance to nearest TSS: 427,164 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.91 / JPT: D'=1.0, r2=0.896

rs10989646
Position: chr9:104,594,589 (Open in UCSC Genome Browser)
Distance to lead SNP: 28,279 bp
Distance to nearest TSS: 424,404 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.94 / CHB: D'=1.0, r2=0.91 / JPT: D'=1.0, r2=0.896

rs10989648
Position: chr9:104,597,417 (Open in UCSC Genome Browser)
Distance to lead SNP: 25,451 bp
Distance to nearest TSS: 421,576 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.932 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.887

rs10819998
Position: chr9:104,604,852 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,016 bp
Distance to nearest TSS: 414,141 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.91 / JPT: D'=1.0, r2=0.896

rs1337689
Position: chr9:104,607,773 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,095 bp
Distance to nearest TSS: 411,220 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.91 / JPT: D'=1.0, r2=0.896

rs10989660
Position: chr9:104,620,990 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,878 bp
Distance to nearest TSS: 398,003 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.91 / JPT: D'=1.0, r2=1.0

rs10989662
Position: chr9:104,624,043 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,175 bp
Distance to nearest TSS: 394,950 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.91 / JPT: 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 01:19:19
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