Variant report

Variant	rs2276038
Chromosome Location	chr11:57137424-57137425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57135491..57138301-chr11:57148780..57151441,2	K562	blood:
2	chr11:57135662..57138224-chr11:57141484..57143706,3	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10896610	0.85[EUR][1000 genomes]
rs10896611	0.87[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12792781	0.82[JPT][hapmap]
rs17572970	0.82[JPT][hapmap]
rs1837974	0.86[EUR][1000 genomes]
rs2013314	0.87[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2155234	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2276039	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2276040	0.88[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2276041	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2276042	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs3781894	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3781899	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3781900	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4570598	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs4939132	0.82[JPT][hapmap]
rs4939140	0.87[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4939141	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5012051	0.82[JPT][hapmap]
rs55741081	0.82[AMR][1000 genomes]
rs55756513	0.81[AMR][1000 genomes]
rs56077100	0.87[EUR][1000 genomes]
rs59455760	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60931171	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7128371	0.82[JPT][hapmap]
rs72923914	0.82[AMR][1000 genomes]
rs879646	0.88[CEU][hapmap]
rs894450	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9667065	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2276038	OR4C11	cis	cerebellum	SCAN
rs2276038	OR5M10	cis	parietal	SCAN
rs2276038	SPRYD5	cis	cerebellum	SCAN
rs2276038	OR8H3	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57117600-57140000	Weak transcription	Right Atrium	heart
2	chr11:57132400-57137600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr11:57136200-57138400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:57136200-57138600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:57136200-57138800	Weak transcription	Right Ventricle	heart
6	chr11:57136400-57140000	Weak transcription	Left Ventricle	heart
7	chr11:57136400-57140400	Weak transcription	K562	blood
8	chr11:57136800-57138600	Enhancers	NHEK	skin
9	chr11:57137000-57137600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:57137000-57138800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:57137200-57138200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:57137200-57138400	Enhancers	HMEC	breast
13	chr11:57137400-57137800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:57137400-57137800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:57137400-57137800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:57137400-57138400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:57137400-57138600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links