Variant report

Variant	rs1503139
Chromosome Location	chr6:54724405-54724406
allele	C/T
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:
5	chr6:54721521..54725055-chr6:54731692..54735464,4	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1021836	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12194012	0.87[LWK][hapmap]
rs2397171	1.00[YRI][hapmap]
rs6459029	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]

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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54712600-54725000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:54713200-54725600	Weak transcription	Gastric	stomach
3	chr6:54713400-54726400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:54715400-54731200	Weak transcription	Hela-S3	cervix
5	chr6:54721200-54724600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:54721200-54727000	Weak transcription	Fetal Kidney	kidney
7	chr6:54721200-54727000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:54721200-54730000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:54721400-54724800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:54721400-54725000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:54721400-54725200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:54721400-54726200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:54721600-54726400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:54722400-54724600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:54722400-54724800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:54723000-54725800	Weak transcription	Stomach Mucosa	stomach
17	chr6:54723000-54726000	Weak transcription	Fetal Intestine Large	intestine
18	chr6:54724000-54725800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:54724200-54724600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:54724200-54726200	Enhancers	NHEK	skin
21	chr6:54724200-54726800	Enhancers	HMEC	breast
22	chr6:54724200-54727400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:54724400-54724600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:54724400-54725400	Enhancers	Brain Germinal Matrix	brain
25	chr6:54724400-54725600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:54724400-54725600	Weak transcription	Fetal Intestine Small	intestine
27	chr6:54724400-54725800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:54724400-54725800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links