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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rs1318772

Associations

Study: Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients. [PMID:21326311]
First author: Bhatnagar P
Journal: J Hum Genet
Date: 02/17/2011
Phenotype: F-cell distribution
Study population: 440 African ancestry individuals
Association P-value: 1 x 10-06
Odds ratio [95% confidence interval]: .91 [0.54-1.28] unit decrease
Gene: MCC
Risk allele: G
Minor allele frequency (controls): 0.33

Lead SNP

rs1318772
Position: chr5:112,723,567 (Open in UCSC Genome Browser)
Distance to nearest TSS: 92,931 bp
GENCODE v7 location: Intron
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:

rs26980
Position: chr5:112,770,027 (Open in UCSC Genome Browser)
Distance to lead SNP: 46,460 bp
Distance to nearest TSS: 139,391 bp
GENCODE v7 location: Coding region
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

rs348935
Position: chr5:112,829,601 (Open in UCSC Genome Browser)
Distance to lead SNP: 106,034 bp
Distance to nearest TSS: 5,489 bp
GENCODE v7 location: Exon, non-coding
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs26982
Position: chr5:112,771,342 (Open in UCSC Genome Browser)
Distance to lead SNP: 47,775 bp
Distance to nearest TSS: 805 bp
GENCODE v7 location: Exon, non-coding
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

rs348939
Position: chr5:112,824,737 (Open in UCSC Genome Browser)
Distance to lead SNP: 101,170 bp
Distance to nearest TSS: 4,921 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs17332053
Position: chr5:112,916,596 (Open in UCSC Genome Browser)
Distance to lead SNP: 193,029 bp
Distance to nearest TSS: 24,760 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.855 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs13187776
Position: chr5:112,910,850 (Open in UCSC Genome Browser)
Distance to lead SNP: 187,283 bp
Distance to nearest TSS: 19,014 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=0.922 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs17327139
Position: chr5:112,710,785 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,782 bp
Distance to nearest TSS: 80,149 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

rs36611
Position: chr5:112,755,990 (Open in UCSC Genome Browser)
Distance to lead SNP: 32,423 bp
Distance to nearest TSS: 125,354 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 / JPT: D'=1.0, r2=1.0

rs36613
Position: chr5:112,758,471 (Open in UCSC Genome Browser)
Distance to lead SNP: 34,904 bp
Distance to nearest TSS: 127,835 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

rs3763141
Position: chr5:112,896,576 (Open in UCSC Genome Browser)
Distance to lead SNP: 173,009 bp
Distance to nearest TSS: 32,505 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs13161969
Position: chr5:112,865,809 (Open in UCSC Genome Browser)
Distance to lead SNP: 142,242 bp
Distance to nearest TSS: 36,151 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.912 / JPT: D'=1.0, r2=1.0

rs13161610
Position: chr5:112,865,521 (Open in UCSC Genome Browser)
Distance to lead SNP: 141,954 bp
Distance to nearest TSS: 35,863 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.926 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs26962
Position: chr5:112,737,010 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,443 bp
Distance to nearest TSS: 106,374 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

rs2914152
Position: chr5:112,895,674 (Open in UCSC Genome Browser)
Distance to lead SNP: 172,107 bp
Distance to nearest TSS: 33,407 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs26965
Position: chr5:112,739,017 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,450 bp
Distance to nearest TSS: 108,381 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

rs255857
Position: chr5:112,743,066 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,499 bp
Distance to nearest TSS: 112,430 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

rs11739509
Position: chr5:112,650,751 (Open in UCSC Genome Browser)
Distance to lead SNP: 72,816 bp
Distance to nearest TSS: 119,786 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

rs348919
Position: chr5:112,842,837 (Open in UCSC Genome Browser)
Distance to lead SNP: 119,270 bp
Distance to nearest TSS: 48,999 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs2860483
Position: chr5:112,846,185 (Open in UCSC Genome Browser)
Distance to lead SNP: 122,618 bp
Distance to nearest TSS: 45,651 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.926, r2=0.857 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs4705554
Position: chr5:112,886,896 (Open in UCSC Genome Browser)
Distance to lead SNP: 163,329 bp
Distance to nearest TSS: 57,238 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs13182359
Position: chr5:112,721,135 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,432 bp
Distance to nearest TSS: 90,499 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs13162970
Position: chr5:112,733,357 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,790 bp
Distance to nearest TSS: 102,721 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs4705829
Position: chr5:112,870,894 (Open in UCSC Genome Browser)
Distance to lead SNP: 147,327 bp
Distance to nearest TSS: 41,236 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs458055
Position: chr5:112,799,883 (Open in UCSC Genome Browser)
Distance to lead SNP: 76,316 bp
Distance to nearest TSS: 27,844 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

rs446272
Position: chr5:112,801,861 (Open in UCSC Genome Browser)
Distance to lead SNP: 78,294 bp
Distance to nearest TSS: 29,822 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

rs414475
Position: chr5:112,808,617 (Open in UCSC Genome Browser)
Distance to lead SNP: 85,050 bp
Distance to nearest TSS: 36,578 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

rs182988
Position: chr5:112,813,566 (Open in UCSC Genome Browser)
Distance to lead SNP: 89,999 bp
Distance to nearest TSS: 41,527 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

rs13177178
Position: chr5:112,625,124 (Open in UCSC Genome Browser)
Distance to lead SNP: 98,443 bp
Distance to nearest TSS: 146,084 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

rs10519354
Position: chr5:112,689,650 (Open in UCSC Genome Browser)
Distance to lead SNP: 33,917 bp
Distance to nearest TSS: 80,887 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=0.79 / YRI: D'=0.961, r2=0.924

rs13166822
Position: chr5:112,873,608 (Open in UCSC Genome Browser)
Distance to lead SNP: 150,041 bp
Distance to nearest TSS: 43,950 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs2914151
Position: chr5:112,895,819 (Open in UCSC Genome Browser)
Distance to lead SNP: 172,252 bp
Distance to nearest TSS: 33,262 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs26984
Position: chr5:112,774,425 (Open in UCSC Genome Browser)
Distance to lead SNP: 50,858 bp
Distance to nearest TSS: 49,687 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs26989
Position: chr5:112,782,791 (Open in UCSC Genome Browser)
Distance to lead SNP: 59,224 bp
Distance to nearest TSS: 41,321 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

rs11747062
Position: chr5:112,901,836 (Open in UCSC Genome Browser)
Distance to lead SNP: 178,269 bp
Distance to nearest TSS: 27,245 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.927 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs348923
Position: chr5:112,836,838 (Open in UCSC Genome Browser)
Distance to lead SNP: 113,271 bp
Distance to nearest TSS: 54,998 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.918 / JPT: D'=1.0, r2=0.823




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 01:19:15
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