Variant report

Variant	rs9296862
Chromosome Location	chr6:57051017-57051018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:57048931..57051887-chr6:57068074..57070259,2	K562	blood:
2	chr6:57041061..57044747-chr6:57049624..57053338,3	MCF-7	breast:
3	chr6:57005624..57007757-chr6:57049962..57051684,2	K562	blood:
4	chr6:57005006..57007757-chr6:57049256..57051462,2	K562	blood:
5	chr6:57049527..57051552-chr6:57182303..57183889,2	K562	blood:
6	chr6:57049566..57051204-chr6:57085235..57086771,2	MCF-7	breast:
7	chr6:57012321..57014450-chr6:57048955..57051340,2	K562	blood:
8	chr6:57049527..57052019-chr6:57181022..57183889,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112210	Chromatin interaction
ENSG00000146143	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1002996	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1040461	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1556245	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs16888316	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3757296	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6459179	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6907653	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6932278	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7749960	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7771328	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9296861	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9349845	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9357940	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9357941	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs9367706	1.00[CEU][hapmap]
rs9367710	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs9367711	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9367713	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9370562	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9370563	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9370567	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs9382684	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs9382686	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9396260	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9396261	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9396263	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs9464418	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs9464419	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9475768	0.87[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs9475781	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9475782	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9475788	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9475789	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57038000-57054200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:57038000-57056000	Weak transcription	Spleen	Spleen
3	chr6:57038000-57081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:57038200-57051200	Weak transcription	Small Intestine	intestine
5	chr6:57038200-57063800	Weak transcription	Esophagus	oesophagus
6	chr6:57038200-57063800	Weak transcription	Gastric	stomach
7	chr6:57038400-57056200	Weak transcription	Brain Germinal Matrix	brain
8	chr6:57038400-57072800	Weak transcription	Pancreas	Pancrea
9	chr6:57038400-57079600	Weak transcription	Fetal Brain Female	brain
10	chr6:57038600-57064000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:57038800-57056400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:57038800-57060400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:57039000-57056400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:57039000-57086000	Weak transcription	Thymus	Thymus
15	chr6:57039200-57054200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:57039200-57056200	Weak transcription	Fetal Intestine Small	intestine
17	chr6:57039400-57052000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:57039400-57052200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:57039400-57056200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:57039600-57064000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:57042200-57064000	Weak transcription	Colonic Mucosa	Colon
22	chr6:57042800-57060400	Weak transcription	Right Ventricle	heart
23	chr6:57043800-57063800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:57044000-57056200	Strong transcription	A549	lung
25	chr6:57044000-57057600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:57044400-57054200	Strong transcription	NHDF-Ad	bronchial
27	chr6:57044400-57059000	Strong transcription	Osteobl	bone
28	chr6:57044600-57054400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:57045400-57052600	Strong transcription	NH-A	brain
30	chr6:57045400-57055600	Weak transcription	Fetal Heart	heart
31	chr6:57045600-57059400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:57046000-57052400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:57046800-57058800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:57048000-57051200	Strong transcription	Placenta	Placenta
35	chr6:57048000-57053000	Strong transcription	NHLF	lung
36	chr6:57048000-57056200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:57048000-57059000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:57048200-57053800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:57048200-57056000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:57048200-57056200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:57048200-57064200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:57048200-57072200	Weak transcription	Fetal Brain Male	brain
43	chr6:57048400-57052400	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:57048400-57054000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:57048400-57054800	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr6:57048400-57057600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:57048400-57059800	Weak transcription	Primary B cells from cord blood	blood
48	chr6:57048400-57067200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:57048400-57067200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:57048800-57051200	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links