Variant report

Variant	rs783396
Chromosome Location	chr6:106987370-106987371
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:106985730-106987594	GM12892	blood:	n/a	n/a
2	POLR2A	chr6:106987044-106988289	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:106987163-106987490	GM12892	blood:	n/a	n/a
4	MAFK	chr6:106987083-106987417	HepG2	liver:	n/a	n/a
5	MAFK	chr6:106987112-106987386	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:106987060-106987685	GM12878	blood:	n/a	n/a
7	MAFF	chr6:106987101-106987389	HepG2	liver:	n/a	chr6:106987227-106987245
8	MAFK	chr6:106987261-106987425	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPB	chr6:106987354-106987644	K562	blood:	n/a	chr6:106987527-106987538
10	POLR2A	chr6:106987012-106988253	GM12892	blood:	n/a	n/a
11	POLR2A	chr6:106984707-106987556	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106976336..106978142-chr6:106984891..106987411,2	K562	blood:
2	chr6:106939256..106941678-chr6:106985710..106988008,2	MCF-7	breast:

Variant related genes	Relation type
AIM1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1111830	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1613722	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1616375	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1676008	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1676010	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1676023	0.82[ASN][1000 genomes]
rs1676024	0.89[ASN][1000 genomes]
rs1676025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1676028	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1770718	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs1770719	0.89[ASN][1000 genomes]
rs1770721	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs1770722	1.00[CHB][hapmap]
rs1770723	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1770733	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1799693	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs2066201	0.89[ASN][1000 genomes]
rs2247335	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[ASN][1000 genomes]
rs2615209	0.82[ASN][1000 genomes]
rs3747789	1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4946762	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs6902745	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs6906338	1.00[CEU][hapmap]
rs783395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783403	0.85[CEU][hapmap]
rs783406	0.85[JPT][hapmap]
rs783414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs783416	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs783418	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9386565	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs9486400	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1017419	chr6:106984669-106997000	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Stroke	17434096	GWAS catalog

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-106991000	Weak transcription	Spleen	Spleen
3	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
4	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:106973600-106992800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:106976600-106991400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:106978800-106993800	Weak transcription	NHLF	lung
8	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
9	chr6:106981400-106988000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:106981600-106995600	Weak transcription	Colonic Mucosa	Colon
11	chr6:106981800-106987800	Weak transcription	Lung	lung
12	chr6:106982400-106987400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:106982400-106987600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:106982400-106987800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:106982800-106993200	Weak transcription	HUVEC	blood vessel
17	chr6:106983000-106987800	Weak transcription	Adipose Nuclei	Adipose
18	chr6:106983400-106989000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:106983400-106989800	Strong transcription	Dnd41	blood
20	chr6:106984000-106987800	Genic enhancers	Primary T cells from cord blood	blood
21	chr6:106984000-106989200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:106984400-106987800	Genic enhancers	Primary B cells from cord blood	blood
23	chr6:106984400-106990200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:106984600-106988600	Enhancers	Primary hematopoietic stem cells	blood
25	chr6:106984800-106989800	Strong transcription	NHEK	skin
26	chr6:106985000-106987800	Strong transcription	GM12878-XiMat	blood
27	chr6:106985000-106988000	Strong transcription	HMEC	breast
28	chr6:106985000-106988200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:106985000-106993800	Weak transcription	NH-A	brain
30	chr6:106985400-106988200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:106985600-106988000	Strong transcription	Esophagus	oesophagus
32	chr6:106985800-106988600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:106985800-106988800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
35	chr6:106986000-106988200	Enhancers	Placenta	Placenta
36	chr6:106986200-106987400	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr6:106986200-106992000	Strong transcription	Fetal Intestine Small	intestine
38	chr6:106986200-106993400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:106986200-106994000	Weak transcription	Stomach Mucosa	stomach
40	chr6:106986400-106987600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:106986400-106988000	Weak transcription	Liver	Liver
42	chr6:106986400-106989200	Weak transcription	Fetal Thymus	thymus
43	chr6:106986400-106993000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:106986400-106994600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:106986400-106995000	Weak transcription	Thymus	Thymus
46	chr6:106986600-106987600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:106986600-106987600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:106986600-106987800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:106986600-106989000	Weak transcription	Fetal Intestine Large	intestine
50	chr6:106986800-106987800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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