Variant report

Variant	rs3125260
Chromosome Location	chr6:54846044-54846045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10456176	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10948866	0.88[CHB][hapmap]
rs1108887	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1108888	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1115159	0.82[CHB][hapmap]
rs1155749	0.82[CHB][hapmap]
rs12192659	0.81[CHB][hapmap]
rs1354288	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1393775	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1393776	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1472679	0.88[CHB][hapmap]
rs1503147	0.82[CHB][hapmap]
rs1580891	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1580892	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs171224	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs181155	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1963697	1.00[CHB][hapmap]
rs2134537	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2134538	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2174115	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2179786	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2207025	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2207026	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs239781	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs239783	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs239790	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs239796	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs239801	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs239837	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2816810	0.82[JPT][hapmap]
rs2816812	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3125261	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3125263	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3125267	0.84[EUR][1000 genomes]
rs3125269	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4141552	0.82[CHB][hapmap]
rs4712083	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6459034	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6918402	0.81[CHB][hapmap]
rs6926997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6937970	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs7453866	0.82[CHB][hapmap]
rs7741915	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7761336	0.82[CHB][hapmap]
rs7765721	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs924712	0.82[CHB][hapmap]
rs931766	0.88[CHB][hapmap]
rs9349740	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9370345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9382403	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs971526	0.88[CHB][hapmap]
rs973205	0.88[CHB][hapmap]
rs980821	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs980822	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs988913	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv5309	chr6:54834971-54855729	Enhancers Active TSS Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
3	nsv603134	chr6:54841672-54851340	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54845000-54847000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:54845400-54846600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:54845400-54847200	Enhancers	HMEC	breast
4	chr6:54845400-54847200	Enhancers	NHEK	skin
5	chr6:54845600-54846200	Enhancers	Hela-S3	cervix
6	chr6:54845600-54846800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:54845600-54846800	Enhancers	NHLF	lung
8	chr6:54845600-54847000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:54845800-54847000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:54845800-54847000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:54846000-54846400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links