Variant report

Variant	rs9257401
Chromosome Location	chr6:28916889-28916890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28908842..28913919-chr6:28914065..28917198,6	K562	blood:
2	chr6:28916396..28919032-chr6:28931395..28932899,2	K562	blood:
3	chr6:28889795..28892316-chr6:28916609..28919222,2	MCF-7	breast:
4	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
5	chr6:28916735..28919060-chr6:28983575..28986159,2	K562	blood:

Variant related genes	Relation type
ENSG00000263426	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000227214	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1005123	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1237485	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1476016	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1543796	0.88[ASN][1000 genomes]
rs1794587	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs184093	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2013848	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032500	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2071785	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071790	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs209122	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs209126	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs209128	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs209129	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs209137	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs209138	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs209148	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs209149	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs209152	0.80[ASN][1000 genomes]
rs209153	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs209160	0.81[ASN][1000 genomes]
rs209161	0.81[ASN][1000 genomes]
rs209163	0.81[ASN][1000 genomes]
rs209164	0.81[ASN][1000 genomes]
rs2157312	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2157313	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2179648	0.87[ASN][1000 genomes]
rs2187807	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2187808	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269555	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2394512	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2765229	0.89[ASN][1000 genomes]
rs3129792	0.92[ASN][1000 genomes]
rs3129793	0.90[ASN][1000 genomes]
rs3130841	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3130842	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3130886	0.93[ASN][1000 genomes]
rs3130889	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3130897	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3131070	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3131074	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3131077	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3131100	0.80[ASN][1000 genomes]
rs3131102	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3132386	0.81[AFR][1000 genomes]
rs3135303	0.81[ASN][1000 genomes]
rs3135315	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3135319	0.81[ASN][1000 genomes]
rs3135321	0.92[ASN][1000 genomes]
rs3135322	0.92[ASN][1000 genomes]
rs3135323	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3135324	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3135326	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3135327	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3135328	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs381808	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs393431	0.81[ASN][1000 genomes]
rs4427026	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713186	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713187	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713188	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713190	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713192	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4947339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456876	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456880	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6456883	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456891	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6900967	0.81[ASN][1000 genomes]
rs6901599	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6904975	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6906909	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6914955	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6916161	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6920392	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6931823	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763009	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7743189	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761547	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768299	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257403	0.85[ASN][1000 genomes]
rs9257404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257405	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9257408	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257421	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9257447	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9257449	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9257455	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9257461	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257464	0.85[EUR][1000 genomes]
rs9348816	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9393939	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468467	0.87[ASN][1000 genomes]
rs9468472	0.83[EUR][1000 genomes];0.85[ASN][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	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28912200-28921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28912400-28920800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:28912400-28921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:28912400-28921200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:28912400-28921200	Weak transcription	Right Atrium	heart
6	chr6:28914400-28917000	Enhancers	Hela-S3	cervix
7	chr6:28915400-28917000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:28915400-28917000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:28915400-28917000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:28915600-28921200	Weak transcription	Esophagus	oesophagus
11	chr6:28915800-28920600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:28916000-28917000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:28916000-28918400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:28916000-28918400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:28916000-28920800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:28916000-28921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:28916200-28920800	Weak transcription	NH-A	brain
18	chr6:28916200-28920800	Weak transcription	Osteobl	bone
19	chr6:28916200-28921200	Weak transcription	HMEC	breast
20	chr6:28916200-28921200	Weak transcription	NHEK	skin
21	chr6:28916400-28921200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:28916600-28918400	Weak transcription	A549	lung
23	chr6:28916600-28918400	Weak transcription	K562	blood
24	chr6:28916600-28920600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:28916800-28917000	Enhancers	HepG2	liver
26	chr6:28916800-28917200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:28916800-28917200	Active TSS	Rectal Smooth Muscle	rectum
28	chr6:28916800-28918400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:28916800-28921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links