Variant report

Variant	rs1076702
Chromosome Location	chr6:53792059-53792060
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	MAX	chr6:53791813-53792491	HCT-116	colon:	n/a	chr6:53792056-53792065
2	EP300	chr6:53791952-53792317	SK-N-SH_RA	brain:	n/a	n/a
3	NR3C1	chr6:53791931-53792372	ECC-1	luminal epithelium:	n/a	n/a
4	USF1	chr6:53791983-53792403	ECC-1	luminal epithelium:	n/a	n/a
5	SIN3AK20	chr6:53791697-53792610	MCF-7	breast:	n/a	n/a
6	ZNF217	chr6:53791876-53792333	MCF-7	breast:	n/a	n/a
7	EP300	chr6:53791814-53792440	ECC-1	luminal epithelium:	n/a	n/a
8	HDAC2	chr6:53791864-53792425	MCF-7	breast:	n/a	n/a
9	MAX	chr6:53791934-53792382	ECC-1	luminal epithelium:	n/a	chr6:53792056-53792065
10	NFIC	chr6:53791078-53792454	ECC-1	luminal epithelium:	n/a	chr6:53792271-53792287 chr6:53792270-53792287
11	MAX	chr6:53791885-53792356	MCF-7	breast:	n/a	chr6:53792056-53792065
12	FOXM1	chr6:53791708-53792389	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr6:53791960-53792110	MCF-7	breast:	n/a	chr6:53792025-53792033
14	TCF7L2	chr6:53792028-53792283	MCF-7	breast:	n/a	n/a
15	TEAD4	chr6:53791235-53792424	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr6:53791980-53792130	HAc	cerebellar:	n/a	chr6:53792025-53792033
17	CTCF	chr6:53791960-53792110	HEEpiC	esophagus:	n/a	chr6:53792025-53792033
18	POLR2A	chr6:53791946-53792324	HCT-116	colon:	n/a	n/a
19	EP300	chr6:53791888-53792339	MCF-7	breast:	n/a	n/a
20	POLR2A	chr6:53792034-53792321	HCT-116	colon:	n/a	n/a
21	NFIC	chr6:53791817-53792420	ECC-1	luminal epithelium:	n/a	chr6:53792271-53792287 chr6:53792270-53792287
22	CEBPB	chr6:53792027-53792367	ECC-1	luminal epithelium:	n/a	n/a
23	NR3C1	chr6:53791968-53792257	ECC-1	luminal epithelium:	n/a	n/a
24	RAD21	chr6:53791873-53792404	ECC-1	luminal epithelium:	n/a	chr6:53792076-53792088
25	SP1	chr6:53791854-53792383	HCT-116	colon:	n/a	n/a
26	YY1	chr6:53791969-53792320	ECC-1	luminal epithelium:	n/a	n/a
27	TCF12	chr6:53791767-53792399	ECC-1	luminal epithelium:	n/a	chr6:53792118-53792125
28	HA-E2F1	chr6:53791887-53792350	MCF-7	breast:	n/a	chr6:53792124-53792131 chr6:53792124-53792131 chr6:53792120-53792132 chr6:53792124-53792131
29	FOXA1	chr6:53792018-53792178	ECC-1	luminal epithelium:	n/a	n/a
30	TEAD4	chr6:53791876-53792407	ECC-1	luminal epithelium:	n/a	n/a
31	TCF12	chr6:53791149-53792460	ECC-1	luminal epithelium:	n/a	chr6:53792118-53792125
32	EP300	chr6:53792013-53792346	SK-N-SH_RA	brain:	n/a	n/a
33	FOXM1	chr6:53791854-53792343	ECC-1	luminal epithelium:	n/a	n/a
34	STAT3	chr6:53791983-53792158	MCF10A-Er-Src	breast:	n/a	chr6:53792096-53792107 chr6:53792128-53792139
35	YY1	chr6:53791787-53792362	ECC-1	luminal epithelium:	n/a	n/a
36	JUND	chr6:53791330-53792345	HCT-116	colon:	n/a	n/a
37	EP300	chr6:53791203-53792612	ECC-1	luminal epithelium:	n/a	n/a
38	CBX3	chr6:53791804-53792345	HCT-116	colon:	n/a	n/a
39	SIN3AK20	chr6:53791648-53792352	MCF-7	breast:	n/a	n/a
40	GATA3	chr6:53791707-53792456	MCF-7	breast:	n/a	n/a
41	CTCF	chr6:53791920-53792070	HCPEpiC	choroid plexus:	n/a	chr6:53792025-53792033
42	HDAC2	chr6:53791935-53792421	MCF-7	breast:	n/a	n/a
43	ELF1	chr6:53791828-53792444	MCF-7	breast:	n/a	n/a
44	GATA3	chr6:53791903-53792413	MCF-7	breast:	n/a	n/a
45	MAX	chr6:53791829-53792392	ECC-1	luminal epithelium:	n/a	chr6:53792056-53792065
46	CEBPB	chr6:53791911-53792381	ECC-1	luminal epithelium:	n/a	n/a
47	MAX	chr6:53791819-53792428	MCF-7	breast:	n/a	chr6:53792056-53792065
48	E2F4	chr6:53792032-53792258	MCF10A-Er-Src	breast:	n/a	chr6:53792124-53792131 chr6:53792124-53792131 chr6:53792120-53792132 chr6:53792124-53792131
49	FOSL1	chr6:53791274-53792434	HCT-116	colon:	n/a	n/a
50	SP1	chr6:53791874-53792388	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
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10755766	0.80[AMR][1000 genomes]
rs1076701	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	0.80[AMR][1000 genomes]
rs12526194	0.95[EUR][1000 genomes]
rs2073020	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2076495	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2294790	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2294791	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3777661	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4314499	0.82[AMR][1000 genomes]
rs6903399	0.89[AMR][1000 genomes]
rs9349685	0.93[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357776	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9357778	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9370233	0.94[CEU][hapmap]
rs9370241	0.82[EUR][1000 genomes]
rs9370244	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9370246	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382232	0.80[AMR][1000 genomes]
rs9382233	0.80[AMR][1000 genomes]
rs9382243	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes]
rs9382244	0.92[AMR][1000 genomes]
rs9382246	0.92[AMR][1000 genomes]
rs9382248	0.87[AMR][1000 genomes]
rs9382252	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9382253	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382254	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382256	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382257	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9395876	0.80[AMR][1000 genomes]
rs9395878	0.94[CEU][hapmap]
rs9395881	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:66 , 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	chr6:53784600-53794200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:53784800-53794000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:53785600-53794400	Weak transcription	Thymus	Thymus
9	chr6:53786000-53794200	Weak transcription	Left Ventricle	heart
10	chr6:53786800-53794400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:53787800-53793600	Weak transcription	HepG2	liver
12	chr6:53787800-53794400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:53787800-53794400	Weak transcription	Pancreas	Pancrea
14	chr6:53787800-53794800	Weak transcription	Spleen	Spleen
15	chr6:53787800-53796000	Weak transcription	Primary T cells from cord blood	blood
16	chr6:53787800-53807800	Weak transcription	Aorta	Aorta
17	chr6:53787800-53810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:53788000-53794400	Weak transcription	Primary B cells from cord blood	blood
19	chr6:53789400-53792600	Enhancers	Stomach Mucosa	stomach
20	chr6:53789600-53792800	Enhancers	Dnd41	blood
21	chr6:53790400-53792200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr6:53790400-53793000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:53790600-53797200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:53790600-53798000	Weak transcription	Fetal Thymus	thymus
25	chr6:53790800-53792400	Enhancers	Fetal Heart	heart
26	chr6:53790800-53792400	Enhancers	Fetal Muscle Leg	muscle
27	chr6:53790800-53793000	Enhancers	HMEC	breast
28	chr6:53790800-53794800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:53790800-53795000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:53791000-53792200	Enhancers	Brain Hippocampus Middle	brain
31	chr6:53791000-53792400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:53791000-53793600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr6:53791000-53794200	Enhancers	NHEK	skin
34	chr6:53791000-53795600	Weak transcription	Brain Germinal Matrix	brain
35	chr6:53791000-53795800	Weak transcription	Brain Substantia Nigra	brain
36	chr6:53791000-53796200	Enhancers	HUVEC	blood vessel
37	chr6:53791200-53792200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:53791200-53792200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:53791200-53792200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr6:53791200-53792400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:53791200-53792400	Enhancers	Colon Smooth Muscle	Colon
42	chr6:53791200-53792400	Enhancers	HSMM	muscle
43	chr6:53791200-53792600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:53791200-53795000	Enhancers	Hela-S3	cervix
45	chr6:53791400-53792200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:53791400-53792200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr6:53791400-53792200	Enhancers	Brain Anterior Caudate	brain
48	chr6:53791400-53792200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:53791400-53792400	Enhancers	Fetal Kidney	kidney
50	chr6:53791400-53794200	Enhancers	Fetal Intestine Small	intestine

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