Variant report

Variant	rs12192659
Chromosome Location	chr6:54726327-54726328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54718921..54722891-chr6:54723074..54726787,4	MCF-7	breast:
2	chr6:54718981..54722041-chr6:54724023..54729682,8	MCF-7	breast:
3	chr6:54596752..54599206-chr6:54723703..54726514,2	MCF-7	breast:
4	chr6:54583465..54585924-chr6:54724133..54726618,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456176	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs10807484	0.82[AMR][1000 genomes]
rs10807485	0.82[AMR][1000 genomes]
rs10948866	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs1155749	0.88[CHB][hapmap]
rs12191299	0.82[AMR][1000 genomes]
rs12191386	0.82[AMR][1000 genomes]
rs12194667	0.83[AMR][1000 genomes]
rs12208341	0.83[EUR][1000 genomes]
rs12208348	0.83[EUR][1000 genomes]
rs12211168	0.83[EUR][1000 genomes]
rs1393776	0.81[CHB][hapmap]
rs1472679	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs171224	0.88[CHB][hapmap]
rs181155	0.88[CHB][hapmap]
rs1963697	0.81[CHB][hapmap]
rs2179786	0.87[CHB][hapmap]
rs2207025	0.81[CHB][hapmap]
rs2207026	0.83[CHB][hapmap]
rs239781	0.87[CHB][hapmap]
rs239783	0.87[CHB][hapmap]
rs239790	0.87[CHB][hapmap]
rs239794	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs239796	0.87[CHB][hapmap]
rs239801	0.88[CHB][hapmap]
rs239815	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs239837	0.87[CHB][hapmap]
rs2816810	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs2816812	0.87[CHB][hapmap]
rs3996950	0.80[EUR][1000 genomes]
rs421957	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs6459034	0.87[CHB][hapmap]
rs6908745	0.83[AMR][1000 genomes]
rs6918402	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6926997	0.81[CHB][hapmap]
rs6937970	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7741915	0.87[CHB][hapmap]
rs7752349	0.83[EUR][1000 genomes]
rs7761336	0.88[CHB][hapmap]
rs7765721	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs924712	0.88[CHB][hapmap]
rs931766	0.89[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes]
rs9349740	0.81[CHB][hapmap]
rs9370345	0.80[CHB][hapmap]
rs9382403	0.81[CHB][hapmap]
rs971526	0.89[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs973205	0.89[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs988913	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54713400-54726400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:54715400-54731200	Weak transcription	Hela-S3	cervix
3	chr6:54721200-54727000	Weak transcription	Fetal Kidney	kidney
4	chr6:54721200-54727000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:54721200-54730000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:54721600-54726400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:54724200-54726800	Enhancers	HMEC	breast
8	chr6:54724200-54727400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:54724600-54726600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:54725400-54731400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:54725600-54726400	Genic enhancers	Fetal Intestine Small	intestine
12	chr6:54725600-54729800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:54725600-54737400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:54725600-54737600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:54725800-54727000	Weak transcription	Gastric	stomach
16	chr6:54725800-54727200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:54725800-54727200	Enhancers	Stomach Mucosa	stomach
18	chr6:54725800-54730000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:54725800-54730000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:54725800-54730000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:54726000-54726400	Enhancers	Fetal Intestine Large	intestine
22	chr6:54726000-54726600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:54726200-54726600	Enhancers	Small Intestine	intestine
24	chr6:54726200-54726800	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr6:54726200-54727000	Weak transcription	NHEK	skin
26	chr6:54726200-54727400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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