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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rs6265

Associations

Study: Genome-wide meta-analyses identify multiple loci associated with smoking behavior. [PMID:20418890]
First author: The Tobacco and Genetics Consortium
Journal: Nat Genet
Date: 04/25/2010
Phenotype: Smoking behavior
Study population: Up to 74,035 European ancestry individuals
Replication population: Up to 68,988 participants
Association P-value: 2 x 10-08
Odds ratio [95% confidence interval]: 1.06 [1.04-1.08]
Gene: BDNF
Risk allele: C
Minor allele frequency (controls): 0.79

Study: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. [PMID:19079260]
First author: Thorleifsson G
Journal: Nat Genet
Date: 12/14/2008
Phenotype: Body mass index
Study population: 80,969 individuals
Replication population: 11,036 individuals
Association P-value: 5 x 10-10
Odds ratio [95% confidence interval]: 4.58 [3.07-6.09] % SD
Gene: BDNF
Risk allele: G
Minor allele frequency (controls): 0.85

Study: Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. [PMID:19079260]
First author: Thorleifsson G
Journal: Nat Genet
Date: 12/14/2008
Phenotype: Weight
Study population: 80,969 individuals
Replication population: 11,036 individuals
Association P-value: 2 x 10-07
Odds ratio [95% confidence interval]: 4.00 [2.47-5.53] % SD
Gene: BDNF
Risk allele: G
Minor allele frequency (controls): 0.85

Lead SNP

rs6265
Position: chr11:27,679,916 (Open in UCSC Genome Browser)
Distance to nearest TSS: 23,741 bp
GENCODE v7 location: Coding region
RegulomeDB Score: 6 - Motif (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:

rs4074134
Position: chr11:27,647,285 (Open in UCSC Genome Browser)
Distance to lead SNP: 32,631 bp
Distance to nearest TSS: 43,683 bp
GENCODE v7 location: Intron
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'=0.942, r2=0.699 / JPT: D'=0.945, r2=0.848

rs11030084
Position: chr11:27,643,725 (Open in UCSC Genome Browser)
Distance to lead SNP: 36,191 bp
Distance to nearest TSS: 40,123 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5a - ChIP-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=0.937, r2=0.709 / JPT: D'=0.942, r2=0.839

rs1488830
Position: chr11:27,636,885 (Open in UCSC Genome Browser)
Distance to lead SNP: 43,031 bp
Distance to nearest TSS: 33,283 bp
GENCODE v7 location: Intron
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'=0.834, r2=0.602 / JPT: D'=0.869, r2=0.534

rs4923457
Position: chr11:27,648,580 (Open in UCSC Genome Browser)
Distance to lead SNP: 31,336 bp
Distance to nearest TSS: 44,978 bp
GENCODE v7 location: Intron
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'=0.943, r2=0.731 / JPT: D'=0.945, r2=0.848

rs2049045
Position: chr11:27,694,241 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,325 bp
Distance to nearest TSS: 14,129 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs879048
Position: chr11:27,638,934 (Open in UCSC Genome Browser)
Distance to lead SNP: 40,982 bp
Distance to nearest TSS: 35,332 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=0.834, r2=0.602 / JPT: D'=0.869, r2=0.534

rs12419948
Position: chr11:27,666,984 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,932 bp
Distance to nearest TSS: 13,128 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.865 / JPT: D'=1.0, r2=0.95

rs11030104
Position: chr11:27,684,517 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,601 bp
Distance to nearest TSS: 11,315 bp
GENCODE v7 location: Intron
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'=1.0, r2=1.0

rs4923460
Position: chr11:27,656,789 (Open in UCSC Genome Browser)
Distance to lead SNP: 23,127 bp
Distance to nearest TSS: 23,323 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=0.942, r2=0.699 / JPT: D'=0.945, r2=0.848

rs4923461
Position: chr11:27,656,910 (Open in UCSC Genome Browser)
Distance to lead SNP: 23,006 bp
Distance to nearest TSS: 23,202 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=0.942, r2=0.699 / JPT: D'=0.945, r2=0.848

rs10501087
Position: chr11:27,670,108 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,808 bp
Distance to nearest TSS: 13,933 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.941 / CHB: D'=1.0, r2=0.865 / JPT: D'=1.0, r2=0.95

rs16917237
Position: chr11:27,702,383 (Open in UCSC Genome Browser)
Distance to lead SNP: 22,467 bp
Distance to nearest TSS: 18,570 bp
GENCODE v7 location: Intron
No regulatory annotation found
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=1.0

rs925947
Position: chr11:27,667,367 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,549 bp
Distance to nearest TSS: 12,745 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.94 / CHB: D'=1.0, r2=0.95 / JPT: D'=1.0, r2=0.949




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 01:19:20
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