Variant report

Variant	rs1076701
Chromosome Location	chr6:53791688-53791689
allele	C/T
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	JUND	chr6:53791191-53791844	HCT-116	colon:	n/a	n/a
2	NFIC	chr6:53791078-53792454	ECC-1	luminal epithelium:	n/a	chr6:53792271-53792287 chr6:53792270-53792287
3	TEAD4	chr6:53791235-53792424	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr6:53791149-53792460	ECC-1	luminal epithelium:	n/a	chr6:53792118-53792125
5	JUND	chr6:53791330-53792345	HCT-116	colon:	n/a	n/a
6	EP300	chr6:53791203-53792612	ECC-1	luminal epithelium:	n/a	n/a
7	SIN3AK20	chr6:53791648-53792352	MCF-7	breast:	n/a	n/a
8	FOSL1	chr6:53791274-53792434	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:53791111..53793110-chr6:53802444..53804078,2	MCF-7	breast:
2	chr6:53656777..53661250-chr6:53790077..53794763,7	MCF-7	breast:
3	chr6:53669263..53671782-chr6:53791090..53793404,2	MCF-7	breast:

Variant related genes	Relation type
MLIP	TF binding region
ENSG00000236740	TF binding region
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10755766	0.81[AMR][1000 genomes]
rs1076702	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10948775	0.81[AMR][1000 genomes]
rs12526194	0.94[EUR][1000 genomes]
rs1883632	0.82[JPT][hapmap]
rs2073020	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2076495	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2294790	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2294791	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2494088	0.91[ASN][1000 genomes]
rs3777661	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4314499	0.84[AMR][1000 genomes]
rs6903399	0.90[AMR][1000 genomes]
rs6921605	0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs9349685	0.93[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9357776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357778	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9370233	0.94[CEU][hapmap]
rs9370241	0.82[EUR][1000 genomes]
rs9370244	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9370246	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382232	0.81[AMR][1000 genomes]
rs9382233	0.81[AMR][1000 genomes]
rs9382243	0.94[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[AMR][1000 genomes]
rs9382244	0.93[AMR][1000 genomes]
rs9382246	0.93[AMR][1000 genomes]
rs9382248	0.88[AMR][1000 genomes]
rs9382252	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9382253	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9382254	0.94[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9382256	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382257	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395876	0.81[AMR][1000 genomes]
rs9395878	0.94[CEU][hapmap];0.81[MEX][hapmap]
rs9395881	0.90[AMR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv3346482	chr6:53788493-53791691	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
2	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:53772000-53803000	Weak transcription	Lung	lung
6	chr6:53778000-53791800	Weak transcription	Small Intestine	intestine
7	chr6:53784600-53794200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:53784800-53794000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:53785600-53794400	Weak transcription	Thymus	Thymus
10	chr6:53786000-53791800	Weak transcription	Fetal Stomach	stomach
11	chr6:53786000-53794200	Weak transcription	Left Ventricle	heart
12	chr6:53786800-53794400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:53787800-53793600	Weak transcription	HepG2	liver
14	chr6:53787800-53794400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:53787800-53794400	Weak transcription	Pancreas	Pancrea
16	chr6:53787800-53794800	Weak transcription	Spleen	Spleen
17	chr6:53787800-53796000	Weak transcription	Primary T cells from cord blood	blood
18	chr6:53787800-53807800	Weak transcription	Aorta	Aorta
19	chr6:53787800-53810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:53788000-53794400	Weak transcription	Primary B cells from cord blood	blood
21	chr6:53789400-53792600	Enhancers	Stomach Mucosa	stomach
22	chr6:53789600-53792800	Enhancers	Dnd41	blood
23	chr6:53790400-53792200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:53790400-53793000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:53790600-53797200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:53790600-53798000	Weak transcription	Fetal Thymus	thymus
27	chr6:53790800-53792400	Enhancers	Fetal Heart	heart
28	chr6:53790800-53792400	Enhancers	Fetal Muscle Leg	muscle
29	chr6:53790800-53793000	Enhancers	HMEC	breast
30	chr6:53790800-53794800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:53790800-53795000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:53791000-53792200	Enhancers	Brain Hippocampus Middle	brain
33	chr6:53791000-53792400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:53791000-53793600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr6:53791000-53794200	Enhancers	NHEK	skin
36	chr6:53791000-53795600	Weak transcription	Brain Germinal Matrix	brain
37	chr6:53791000-53795800	Weak transcription	Brain Substantia Nigra	brain
38	chr6:53791000-53796200	Enhancers	HUVEC	blood vessel
39	chr6:53791200-53791800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:53791200-53791800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:53791200-53792000	Enhancers	Colonic Mucosa	Colon
42	chr6:53791200-53792000	Enhancers	NH-A	brain
43	chr6:53791200-53792200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:53791200-53792200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr6:53791200-53792200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr6:53791200-53792400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr6:53791200-53792400	Enhancers	Colon Smooth Muscle	Colon
48	chr6:53791200-53792400	Enhancers	HSMM	muscle
49	chr6:53791200-53792600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:53791200-53795000	Enhancers	Hela-S3	cervix

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