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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rs3027409

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: 7 x 10-06
Odds ratio [95% confidence interval]: 1.73 [NR]
Gene: MAOA - MAOB
Minor allele frequency (controls): 0.95

Lead SNP

rs3027409
Position: chrX:43,607,033 (Open in UCSC Genome Browser)
Distance to nearest TSS: 95,976 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:

rs1800464
Position: chrX:43,571,197 (Open in UCSC Genome Browser)
Distance to lead SNP: 35,836 bp
Distance to nearest TSS: 485,349 bp
GENCODE v7 location: Coding region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs3027392
Position: chrX:43,551,400 (Open in UCSC Genome Browser)
Distance to lead SNP: 55,633 bp
Distance to nearest TSS: 465,552 bp
GENCODE v7 location: Intron
RegulomeDB Score: 3a - ChIP-seq peak + any motif + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs7052785
Position: chrX:43,609,617 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,584 bp
Distance to nearest TSS: 93,392 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 / YRI: D'=1.0, r2=0.941

rs3027404
Position: chrX:43,596,221 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,812 bp
Distance to nearest TSS: 7,540 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs3027405
Position: chrX:43,596,329 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,704 bp
Distance to nearest TSS: 7,432 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs3027406
Position: chrX:43,602,401 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,632 bp
Distance to nearest TSS: 11,771 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: 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 01:19:25
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