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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rs6599077

Associations

Study: Genome-wide association of sleep and circadian phenotypes. [PMID:17903308]
First author: Gottlieb DJ
Journal: BMC Med Genet
Date: 09/19/2007
Phenotype: Sleep duration
Study population: 738 individuals(Framingham)
Association P-value: 1 x 10-07
Gene: MYRIP

Lead SNP

rs6599077
Position: chr3:40,096,618 (Open in UCSC Genome Browser)
Distance to nearest TSS: 183,615 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:

rs9863428
Position: chr3:40,099,571 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,953 bp
Distance to nearest TSS: 180,662 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=0.944 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs9832726
Position: chr3:40,097,576 (Open in UCSC Genome Browser)
Distance to lead SNP: 958 bp
Distance to nearest TSS: 182,657 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs7637811
Position: chr3:40,096,412 (Open in UCSC Genome Browser)
Distance to lead SNP: 206 bp
Distance to nearest TSS: 183,821 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 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4676560
Position: chr3:40,097,649 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,031 bp
Distance to nearest TSS: 182,584 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=0.947 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs6766178
Position: chr3:40,098,109 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,491 bp
Distance to nearest TSS: 182,124 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 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.959

rs6763643
Position: chr3:40,097,991 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,373 bp
Distance to nearest TSS: 182,242 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 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.942 / YRI: D'=1.0, r2=1.0

rs9848462
Position: chr3:40,097,204 (Open in UCSC Genome Browser)
Distance to lead SNP: 586 bp
Distance to nearest TSS: 183,029 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 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs6782134
Position: chr3:40,100,692 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,074 bp
Distance to nearest TSS: 179,541 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.945 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4676563
Position: chr3:40,105,092 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,474 bp
Distance to nearest TSS: 175,141 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.95 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs9860449
Position: chr3:40,094,033 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,585 bp
Distance to nearest TSS: 186,200 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 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs9860463
Position: chr3:40,094,062 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,556 bp
Distance to nearest TSS: 186,171 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 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs9311232
Position: chr3:40,105,850 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,232 bp
Distance to nearest TSS: 174,383 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.943 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.945 / YRI: D'=1.0, r2=0.96

rs9867011
Position: chr3:40,105,468 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,850 bp
Distance to nearest TSS: 174,765 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.95 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs10510706
Position: chr3:40,100,257 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,639 bp
Distance to nearest TSS: 179,976 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.95 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs11706046
Position: chr3:40,104,137 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,519 bp
Distance to nearest TSS: 176,096 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.95 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4676562
Position: chr3:40,105,039 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,421 bp
Distance to nearest TSS: 175,194 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.948 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4676566
Position: chr3:40,108,636 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,018 bp
Distance to nearest TSS: 171,597 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.945 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.961

rs9853925
Position: chr3:40,107,295 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,677 bp
Distance to nearest TSS: 172,938 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.95 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.965

rs11920120
Position: chr3:40,094,795 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,823 bp
Distance to nearest TSS: 185,438 bp
GENCODE v7 location: Intron
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=1.0

rs9809788
Position: chr3:40,103,734 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,116 bp
Distance to nearest TSS: 176,499 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.95 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.965

rs9311231
Position: chr3:40,105,683 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,065 bp
Distance to nearest TSS: 174,550 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.95 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.949 / 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 01:19:13
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