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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rs950063

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: 9 x 10-06
Odds ratio [95% confidence interval]: .08 [NR] fewer years
Gene: FAT4 - INTU
Minor allele frequency (controls): 0.39

Lead SNP

rs950063
Position: chr4:126,431,919 (Open in UCSC Genome Browser)
Distance to nearest TSS: 242,030 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - 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:

rs12643736
Position: chr4:126,426,962 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,957 bp
Distance to nearest TSS: 246,987 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.564

rs13114827
Position: chr4:126,431,339 (Open in UCSC Genome Browser)
Distance to lead SNP: 580 bp
Distance to nearest TSS: 242,610 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=1.0 / CHB: D'=1.0, r2=0.635 / JPT: D'=1.0, r2=0.744 / YRI: D'=1.0, r2=1.0

rs13102120
Position: chr4:126,433,549 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,630 bp
Distance to nearest TSS: 240,400 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 / YRI: D'=1.0, r2=0.677

rs1506352
Position: chr4:126,431,057 (Open in UCSC Genome Browser)
Distance to lead SNP: 862 bp
Distance to nearest TSS: 242,892 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

rs11726294
Position: chr4:126,430,330 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,589 bp
Distance to nearest TSS: 243,619 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=0.534

rs1588004
Position: chr4:126,435,996 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,077 bp
Distance to nearest TSS: 237,953 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.851 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs10007099
Position: chr4:126,431,574 (Open in UCSC Genome Browser)
Distance to lead SNP: 345 bp
Distance to nearest TSS: 242,375 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=0.667 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.665

rs1506365
Position: chr4:126,468,333 (Open in UCSC Genome Browser)
Distance to lead SNP: 36,414 bp
Distance to nearest TSS: 205,616 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

rs1567050
Position: chr4:126,429,271 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,648 bp
Distance to nearest TSS: 244,678 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.96 / CHB: D'=1.0, r2=0.635 / JPT: D'=1.0, r2=0.696

rs12639834
Position: chr4:126,426,695 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,224 bp
Distance to nearest TSS: 247,254 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=0.545 / JPT: D'=1.0, r2=0.696

rs2174591
Position: chr4:126,433,736 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,817 bp
Distance to nearest TSS: 240,213 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




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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