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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rs9674544

Associations

Study: Genome-wide association study reveals multiple loci associated with primary tooth development during infancy. [PMID:20195514]
First author: Pillas D
Journal: PLoS Genet
Date: 02/26/2010
Phenotype: Primary tooth development (number of teeth)
Study population: 5,752 European descent related individuals
Association P-value: 2 x 10-08
Odds ratio [95% confidence interval]: .27 [NR] % variance explained
Gene: IGF2BP1
Risk allele: G
Minor allele frequency (controls): 0.46

Study: Genome-wide association study reveals multiple loci associated with primary tooth development during infancy. [PMID:20195514]
First author: Pillas D
Journal: PLoS Genet
Date: 02/26/2010
Phenotype: Primary tooth development (time to first tooth eruption)
Study population: 5,919 European descent related individuals
Association P-value: 8 x 10-07
Odds ratio [95% confidence interval]: .25 [NR] % variance explained
Gene: IGF2BP1
Risk allele: G
Minor allele frequency (controls): 0.46

Lead SNP

rs9674544
Position: chr17:47,084,711 (Open in UCSC Genome Browser)
Distance to nearest TSS: 9,856 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + 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:

rs11079851
Position: chr17:47,092,310 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,599 bp
Distance to nearest TSS: 21,508 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=0.921 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.92 / YRI: D'=1.0, r2=0.934

rs1994969
Position: chr17:47,080,431 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,280 bp
Distance to nearest TSS: 10,657 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=0.921 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: 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 01:19:24
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