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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rs9399137

Associations

Study: Sequence variants in three loci influence monocyte counts and erythrocyte volume. [PMID:19853236]
First author: Ferreira MA
Journal: Am J Hum Genet
Date: 10/22/2009
Phenotype: Hematology traits
Study population: 2,538 Australian individuals, 3,477 Dutch individuals
Replication population: 1,543 Australian and European individuals
Association P-value: 1 x 10-09
Odds ratio [95% confidence interval]: .16 [0.10-0.22] s.d. decrease
Gene: HBS1L - MYB
Risk allele: T
Minor allele frequency (controls): 0.74

Study: A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15. [PMID:17767159]
First author: Menzel S
Journal: Nat Genet
Date: 09/02/2007
Phenotype: F-cell distribution
Study population: 179 adults in upper and lower 5%
Replication population: 90 adults
Association P-value: 3 x 10-36
Odds ratio [95% confidence interval]: 15.80 [NR] % of variance explained
Gene: HBS1L - MYB
Minor allele frequency (controls): 0.23

Lead SNP

rs9399137
Position: chr6:135,419,018 (Open in UCSC Genome Browser)
Distance to nearest TSS: 96,605 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found

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:

rs7775698
Position: chr6:135,418,635 (Open in UCSC Genome Browser)
Distance to lead SNP: 383 bp
Distance to nearest TSS: 96,988 bp
GENCODE v7 location: Intergenic region
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 / CHB: D'=1.0, r2=0.881 / JPT: D'=1.0, r2=1.0

rs9389268
Position: chr6:135,419,631 (Open in UCSC Genome Browser)
Distance to lead SNP: 613 bp
Distance to nearest TSS: 95,992 bp
GENCODE v7 location: Intergenic region
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 / CHB: D'=1.0, r2=0.88 / JPT: D'=1.0, r2=1.0

rs9376090
Position: chr6:135,411,228 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,790 bp
Distance to nearest TSS: 104,395 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=0.944 / CHB: D'=1.0, r2=0.881 / JPT: D'=1.0, r2=0.947

rs7776054
Position: chr6:135,418,916 (Open in UCSC Genome Browser)
Distance to lead SNP: 102 bp
Distance to nearest TSS: 96,707 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=0.881 / 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 01:19:17
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