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

Return Home

rs910696

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: 3 x 10-06
Odds ratio [95% confidence interval]: .08 [NR] more cigarettes per day
Gene: PTPRU - MATN1
Minor allele frequency (controls): 0.31

Lead SNP

rs910696
Position: chr1:30,567,596 (Open in UCSC Genome Browser)
Distance to nearest TSS: 57,136 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:

rs1746272
Position: chr1:30,572,812 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,216 bp
Distance to nearest TSS: 62,352 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=0.822 / JPT: D'=1.0, r2=0.946 / YRI: D'=1.0, r2=0.678

rs1694315
Position: chr1:30,573,108 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,512 bp
Distance to nearest TSS: 62,648 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=0.916 / CHB: D'=1.0, r2=0.862 / JPT: D'=1.0, r2=0.907 / YRI: D'=1.0, r2=0.717

rs1694321
Position: chr1:30,570,287 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,691 bp
Distance to nearest TSS: 59,827 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=0.957 / CHB: D'=1.0, r2=0.862 / JPT: D'=1.0, r2=0.907 / YRI: D'=1.0, r2=0.717

rs1746273
Position: chr1:30,572,429 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,833 bp
Distance to nearest TSS: 61,969 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=0.954 / CHB: D'=0.94, r2=0.836 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.685

rs6691680
Position: chr1:30,576,228 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,632 bp
Distance to nearest TSS: 65,768 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=0.899

rs6658945
Position: chr1:30,577,720 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,124 bp
Distance to nearest TSS: 67,260 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'=0.949, r2=0.857 / JPT: D'=0.83, r2=0.595

rs6666739
Position: chr1:30,577,594 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,998 bp
Distance to nearest TSS: 67,134 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'=0.946, r2=0.894 / JPT: D'=0.846, r2=0.716




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 01:19:10
SCGPM logo A project of the Center for Genomics and Personalized Medicine at Stanford University. Stanford logo