Variant report

Variant	rs2071785
Chromosome Location	chr6:28912458-28912459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
3	chr6:28583985..28585633-chr6:28910730..28913227,2	K562	blood:
4	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
5	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
6	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000227214	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1002925	0.81[ASN][1000 genomes]
rs1005123	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1237485	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1476016	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1543796	0.87[ASN][1000 genomes]
rs1794587	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs184093	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2013848	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2032500	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2071790	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs209122	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs209126	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs209128	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs209129	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs209137	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs209138	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs209148	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs209149	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs209152	0.83[ASN][1000 genomes]
rs209153	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs209160	0.84[ASN][1000 genomes]
rs209161	0.84[ASN][1000 genomes]
rs209163	0.84[ASN][1000 genomes]
rs209164	0.83[ASN][1000 genomes]
rs209176	0.81[ASN][1000 genomes]
rs2157312	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2157313	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2179648	0.85[ASN][1000 genomes]
rs2187807	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187808	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269555	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2394512	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2765229	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3129792	0.91[ASN][1000 genomes]
rs3129793	0.89[ASN][1000 genomes]
rs3130841	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3130842	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3130886	0.92[ASN][1000 genomes]
rs3130889	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3130897	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3131070	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3131074	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3131077	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3131100	0.83[ASN][1000 genomes]
rs3131102	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3132386	0.81[ASN][1000 genomes]
rs3135303	0.84[ASN][1000 genomes]
rs3135315	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3135321	0.91[ASN][1000 genomes]
rs3135322	0.91[ASN][1000 genomes]
rs3135323	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3135324	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3135326	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3135327	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3135328	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs381808	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs393431	0.84[ASN][1000 genomes]
rs4427026	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713186	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713187	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713188	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713190	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713192	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4947339	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456876	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456880	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456883	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6456891	0.83[ASN][1000 genomes]
rs6901599	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6904975	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906909	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914955	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916161	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6920392	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6931823	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs763009	0.95[ASN][1000 genomes]
rs7743189	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7755875	0.81[ASN][1000 genomes]
rs7761547	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7768299	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9257401	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9257403	0.82[ASN][1000 genomes]
rs9257404	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9257405	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257408	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9257421	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257447	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257449	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257455	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9257461	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9257464	0.83[EUR][1000 genomes]
rs9348816	0.87[ASN][1000 genomes]
rs9393939	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468467	0.85[ASN][1000 genomes]
rs9468472	0.81[EUR][1000 genomes];0.83[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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28906600-28912600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28907400-28912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28907400-28913400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:28911000-28912600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:28911000-28912600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:28911000-28912600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:28911000-28912600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr6:28911000-28912600	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr6:28911000-28912600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:28911000-28912800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:28911200-28912600	Active TSS	Fetal Kidney	kidney
12	chr6:28912200-28912600	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr6:28912200-28912600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:28912200-28912600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:28912200-28912600	Active TSS	Monocytes-CD14+_RO01746	blood
16	chr6:28912200-28912800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:28912200-28913800	Weak transcription	Spleen	Spleen
18	chr6:28912200-28915000	Weak transcription	Stomach Mucosa	stomach
19	chr6:28912200-28915200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:28912200-28915600	Weak transcription	Pancreas	Pancrea
21	chr6:28912200-28921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:28912400-28912600	Weak transcription	Brain Substantia Nigra	brain
23	chr6:28912400-28912600	Enhancers	Stomach Smooth Muscle	stomach
24	chr6:28912400-28912800	Enhancers	Primary B cells from cord blood	blood
25	chr6:28912400-28912800	Enhancers	Hela-S3	cervix
26	chr6:28912400-28912800	Flanking Active TSS	HepG2	liver
27	chr6:28912400-28913000	Enhancers	Primary hematopoietic stem cells	blood
28	chr6:28912400-28913200	Enhancers	Primary B cells from peripheral blood	blood
29	chr6:28912400-28913200	Enhancers	GM12878-XiMat	blood
30	chr6:28912400-28913200	Flanking Active TSS	K562	blood
31	chr6:28912400-28913600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:28912400-28913800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:28912400-28914200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:28912400-28914200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:28912400-28914800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:28912400-28915000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:28912400-28915200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:28912400-28915200	Weak transcription	Colonic Mucosa	Colon
39	chr6:28912400-28915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:28912400-28915400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:28912400-28915400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:28912400-28915400	Weak transcription	Esophagus	oesophagus
43	chr6:28912400-28915400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:28912400-28915400	Weak transcription	A549	lung
45	chr6:28912400-28915400	Weak transcription	HUVEC	blood vessel
46	chr6:28912400-28915400	Weak transcription	NHEK	skin
47	chr6:28912400-28915600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:28912400-28915600	Weak transcription	HMEC	breast
49	chr6:28912400-28915800	Weak transcription	NH-A	brain
50	chr6:28912400-28915800	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links