Variant report

Variant	rs72954849
Chromosome Location	chr6:54721259-54721260
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54718981..54722041-chr6:54724023..54729682,8	MCF-7	breast:
2	chr6:54718921..54722891-chr6:54723074..54726787,4	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10807486	0.86[EUR][1000 genomes]
rs12199500	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12203166	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12203906	0.90[AMR][1000 genomes]
rs12203996	0.90[AMR][1000 genomes]
rs12205593	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12211620	1.00[AMR][1000 genomes]
rs72954818	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72954824	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72954829	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72954852	0.95[EUR][1000 genomes]
rs72957593	0.90[AMR][1000 genomes]
rs72967427	1.00[AFR][1000 genomes]
rs72967428	1.00[AFR][1000 genomes]
rs7744880	0.90[AMR][1000 genomes];0.90[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	chr6:54720200-54721400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:54720400-54721400	Enhancers	Stomach Mucosa	stomach
7	chr6:54720400-54722200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:54720400-54723000	Enhancers	Fetal Intestine Large	intestine
9	chr6:54720400-54723200	Enhancers	Fetal Intestine Small	intestine
10	chr6:54720800-54721400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:54720800-54721400	Genic enhancers	HMEC	breast
12	chr6:54720800-54722400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:54720800-54722400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr6:54720800-54722600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr6:54721000-54721400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr6:54721000-54721400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:54721000-54721600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:54721200-54721400	Enhancers	Duodenum Mucosa	Duodenum
19	chr6:54721200-54721400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr6:54721200-54721600	Genic enhancers	NHEK	skin
21	chr6:54721200-54722800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:54721200-54724000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:54721200-54724400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:54721200-54724400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:54721200-54724600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:54721200-54727000	Weak transcription	Fetal Kidney	kidney
27	chr6:54721200-54727000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:54721200-54730000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links