Variant report

Variant	rs3186631
Chromosome Location	chr6:82461520-82461521
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	POLR2A	chr6:82461300-82463563	MCF-7	breast:	n/a	n/a
2	MYC	chr6:82461406-82461605	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr6:82460382-82463969	Hela-S3	cervix:	n/a	n/a
4	ZNF143	chr6:82461086-82461592	Hela-S3	cervix:	n/a	n/a
5	MYC	chr6:82461207-82464338	NB4	blood:	n/a	chr6:82462514-82462524 chr6:82462658-82462668
6	REST	chr6:82460988-82464217	HL-60	blood:	n/a	chr6:82462072-82462085 chr6:82462064-82462077 chr6:82463202-82463215 chr6:82463791-82463804 chr6:82463563-82463573
7	CEBPD	chr6:82461460-82461790	HepG2	liver:	n/a	n/a
8	MXI1	chr6:82459848-82464048	IMR90	lung:	n/a	n/a
9	CTBP2	chr6:82461178-82463903	H1-hESC	embryonic stem cell:	n/a	n/a
10	HMGN3	chr6:82461397-82463303	K562	blood:	n/a	n/a
11	MYC	chr6:82461211-82461863	MCF-7	breast:	n/a	n/a
12	CTCF	chr6:82461514-82461629	GM19239	blood:	n/a	n/a
13	POLR2A	chr6:82459317-82463996	Hela-S3	cervix:	n/a	n/a
14	HDAC2	chr6:82460963-82464072	MCF-7	breast:	n/a	chr6:82461048-82461062
15	RAD21	chr6:82461289-82464026	H1-hESC	embryonic stem cell:	n/a	chr6:82463048-82463061 chr6:82463771-82463790 chr6:82462146-82462155
16	RAD21	chr6:82459346-82464069	Hela-S3	cervix:	n/a	chr6:82463048-82463061 chr6:82463771-82463790 chr6:82462146-82462155
17	SIN3AK20	chr6:82461147-82461691	PFSK-1	brain:	n/a	n/a
18	YY1	chr6:82461415-82461632	GM12878	blood:	n/a	n/a
19	ZKSCAN1	chr6:82460407-82461721	Hela-S3	cervix:	n/a	n/a
20	TBP	chr6:82461387-82461578	HepG2	liver:	n/a	n/a
21	ZNF263	chr6:82460578-82464055	HEK293-T-REx	kidney:	n/a	n/a
22	BHLHE40	chr6:82461208-82463938	HepG2	liver:	n/a	chr6:82462214-82462230
23	RAD21	chr6:82461370-82464145	HCT-116	colon:	n/a	chr6:82463048-82463061 chr6:82463771-82463790 chr6:82462146-82462155
24	MAX	chr6:82461069-82464143	HepG2	liver:	n/a	chr6:82462514-82462524 chr6:82462658-82462668
25	EP300	chr6:82461503-82461739	HepG2	liver:	n/a	n/a
26	MAX	chr6:82461161-82464139	HCT-116	colon:	n/a	chr6:82462514-82462524 chr6:82462658-82462668
27	CEBPB	chr6:82461453-82461821	HepG2	liver:	n/a	n/a
28	MAX	chr6:82461156-82464378	NB4	blood:	n/a	chr6:82462514-82462524 chr6:82462658-82462668
29	CEBPB	chr6:82461450-82462037	MCF-7	breast:	n/a	n/a
30	RFX5	chr6:82460460-82463940	Hela-S3	cervix:	n/a	n/a
31	CHD2	chr6:82461248-82463912	Hela-S3	cervix:	n/a	chr6:82463141-82463151
32	YY1	chr6:82461189-82462666	HepG2	liver:	n/a	chr6:82462496-82462510 chr6:82462493-82462502 chr6:82462496-82462505 chr6:82462264-82462275 chr6:82462052-82462063
33	KAP1	chr6:82460236-82461575	HEK293	kidney:	n/a	chr6:82460950-82460959
34	MAX	chr6:82461244-82464047	HCT-116	colon:	n/a	chr6:82462514-82462524 chr6:82462658-82462668
35	POLR2A	chr6:82460761-82463552	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr6:82461308-82463918	HepG2	liver:	n/a	n/a
37	CEBPB	chr6:82461440-82462274	H1-hESC	embryonic stem cell:	n/a	n/a
38	TCF7L2	chr6:82461263-82463907	HCT-116	colon:	n/a	n/a
39	MAX	chr6:82460472-82464134	Hela-S3	cervix:	n/a	chr6:82462514-82462524 chr6:82462658-82462668
40	CEBPB	chr6:82461478-82461886	HepG2	liver:	n/a	n/a
41	MXI1	chr6:82461131-82461680	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr6:82461307-82464038	HepG2	liver:	n/a	n/a
43	SIN3AK20	chr6:82460269-82464093	MCF-7	breast:	n/a	n/a
44	STAT1	chr6:82461498-82461532	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:82461287-82461718	H1-hESC	embryonic stem cell:	n/a	n/a
46	RCOR1	chr6:82460381-82463989	Hela-S3	cervix:	n/a	n/a
47	E2F4	chr6:82461482-82461682	MCF10A-Er-Src	breast:	n/a	n/a
48	SMC3	chr6:82460963-82464689	SK-N-SH	brain:	n/a	chr6:82462141-82462155 chr6:82462147-82462157
49	MAX	chr6:82461183-82462685	H1-hESC	embryonic stem cell:	n/a	chr6:82462514-82462524 chr6:82462658-82462668
50	CEBPB	chr6:82461296-82461899	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:82442487..82447325-chr6:82460557..82464499,4	MCF-7	breast:
2	chr6:82458586..82464036-chr6:82521971..82527096,10	MCF-7	breast:
3	chr6:82460615..82464438-chr6:82472382..82478506,11	MCF-7	breast:

Variant related genes	Relation type
FAM46A	TF binding region
ENSG00000219702	Chromatin interaction
ENSG00000206886	Chromatin interaction
ENSG00000232031	Chromatin interaction
ENSG00000224995	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1033825	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10484871	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13197254	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13212881	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13220502	0.84[EUR][1000 genomes]
rs16893407	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2295984	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2323515	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34409317	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3736841	0.82[EUR][1000 genomes]
rs67841418	0.88[EUR][1000 genomes]
rs67880674	0.88[EUR][1000 genomes]
rs72899455	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72899456	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7745467	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9449363	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3387792	chr6:82460658-82463206	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:82455200-82464000	Active TSS	Right Ventricle	heart
2	chr6:82456400-82464000	Active TSS	Right Atrium	heart
3	chr6:82458400-82464600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr6:82458600-82461600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:82458600-82461600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:82458600-82461600	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr6:82458600-82463800	Active TSS	Stomach Smooth Muscle	stomach
8	chr6:82458800-82461600	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:82458800-82463800	Active TSS	Brain Anterior Caudate	brain
10	chr6:82458800-82463800	Active TSS	Colon Smooth Muscle	Colon
11	chr6:82459000-82463400	Active TSS	Colonic Mucosa	Colon
12	chr6:82459000-82464400	Active TSS	Stomach Mucosa	stomach
13	chr6:82459200-82464600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr6:82459400-82463800	Active TSS	Lung	lung
15	chr6:82459600-82461800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:82459600-82463800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:82459600-82464000	Active TSS	Rectal Smooth Muscle	rectum
18	chr6:82459800-82462800	Bivalent/Poised TSS	Thymus	Thymus
19	chr6:82459800-82463800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:82459800-82463800	Active TSS	Aorta	Aorta
21	chr6:82459800-82463800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:82459800-82463800	Active TSS	Brain Substantia Nigra	brain
23	chr6:82459800-82464000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr6:82459800-82464200	Active TSS	Placenta Amnion	Placenta Amnion
25	chr6:82459800-82464200	Active TSS	HSMM	muscle
26	chr6:82459800-82464200	Active TSS	NHLF	lung
27	chr6:82460000-82462000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:82460000-82463400	Active TSS	Muscle Satellite Cultured Cells	--
29	chr6:82460000-82463400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:82460000-82463400	Active TSS	Placenta	Placenta
31	chr6:82460000-82463400	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr6:82460000-82463400	Active TSS	NH-A	brain
33	chr6:82460000-82463600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:82460000-82463600	Active TSS	Duodenum Mucosa	Duodenum
35	chr6:82460000-82463600	Active TSS	Fetal Intestine Small	intestine
36	chr6:82460000-82463800	Active TSS	Liver	Liver
37	chr6:82460000-82463800	Active TSS	Gastric	stomach
38	chr6:82460000-82463800	Active TSS	Ovary	ovary
39	chr6:82460000-82463800	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:82460000-82463800	Active TSS	NHDF-Ad	bronchial
41	chr6:82460000-82463800	Active TSS	Osteobl	bone
42	chr6:82460000-82464000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:82460000-82464000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr6:82460000-82464000	Active TSS	Left Ventricle	heart
45	chr6:82460000-82464000	Active TSS	HSMMtube	muscle
46	chr6:82460200-82461600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr6:82460200-82461600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:82460200-82461600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:82460200-82461600	Bivalent/Poised TSS	Fetal Kidney	kidney
50	chr6:82460200-82463800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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