Variant report

Variant	rs62412646
Chromosome Location	chr6:54711321-54711322
allele	A/G
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	chr6:54711212-54711677	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:54711091-54711664	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr6:54711126-54711720	MCF-7	breast:	n/a	n/a
4	POLR2A	chr6:54710974-54713675	Hela-S3	cervix:	n/a	n/a
5	CHD2	chr6:54711112-54713044	Hela-S3	cervix:	n/a	chr6:54711229-54711239
6	POLR2A	chr6:54710993-54712194	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr6:54710926-54712518	HCT-116	colon:	n/a	n/a
8	STAT3	chr6:54711222-54711657	MCF10A-Er-Src	breast:	n/a	chr6:54711525-54711537 chr6:54711520-54711532
9	MYC	chr6:54711187-54711477	H1-hESC	embryonic stem cell:	n/a	chr6:54711427-54711437
10	POLR2A	chr6:54711101-54712033	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3AK20	chr6:54710924-54711875	MCF-7	breast:	n/a	n/a
12	STAT1	chr6:54711042-54713361	Hela-S3	cervix:	n/a	chr6:54712038-54712045 chr6:54712078-54712087 chr6:54712079-54712088 chr6:54711525-54711537 chr6:54712079-54712087 chr6:54713023-54713037 chr6:54712073-54712093 chr6:54711520-54711532 chr6:54711993-54712005 chr6:54712073-54712093 chr6:54713026-54713034 chr6:54712077-54712088 chr6:54713165-54713173
13	ZNF143	chr6:54711161-54712141	H1-hESC	embryonic stem cell:	n/a	chr6:54711986-54712004 chr6:54711517-54711535 chr6:54711259-54711268 chr6:54711521-54711539 chr6:54711736-54711746
14	E2F4	chr6:54711195-54712148	MCF10A-Er-Src	breast:	n/a	chr6:54711423-54711435 chr6:54711595-54711604 chr6:54711529-54711544 chr6:54711736-54711745 chr6:54711459-54711468
15	SMARCC1	chr6:54711045-54713431	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr6:54711168-54711646	MCF10A-Er-Src	breast:	n/a	chr6:54711525-54711537 chr6:54711520-54711532
17	TAF7	chr6:54711315-54711727	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr6:54710957-54713446	Hela-S3	cervix:	n/a	chr6:54711427-54711437
19	TCF12	chr6:54710972-54712270	ECC-1	luminal epithelium:	n/a	n/a
20	SMARCB1	chr6:54710981-54712318	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr6:54711104-54711756	ECC-1	luminal epithelium:	n/a	n/a
22	MXI1	chr6:54711289-54711489	H1-hESC	embryonic stem cell:	n/a	n/a
23	HDAC2	chr6:54711036-54712299	MCF-7	breast:	n/a	chr6:54711294-54711308
24	CTBP2	chr6:54711055-54712274	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr6:54710988-54712411	Hela-S3	cervix:	n/a	chr6:54711672-54711686
26	SIN3AK20	chr6:54710850-54713528	MCF-7	breast:	n/a	n/a
27	MYC	chr6:54711251-54711518	MCF10A-Er-Src	breast:	n/a	chr6:54711427-54711437
28	REST	chr6:54711052-54711667	MCF-7	breast:	n/a	chr6:54711484-54711504 chr6:54711209-54711218
29	MXI1	chr6:54711059-54713305	Hela-S3	cervix:	n/a	n/a
30	YY1	chr6:54710903-54711377	H1-hESC	embryonic stem cell:	n/a	n/a
31	EP300	chr6:54711198-54711680	T-47D	breast:	n/a	chr6:54711595-54711604 chr6:54711578-54711587 chr6:54711581-54711597 chr6:54711583-54711599
32	RCOR1	chr6:54711049-54712070	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr6:54711240-54711390	HRE	kidney:	n/a	n/a
34	TAF1	chr6:54710999-54712164	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr6:54711064-54713478	MCF10A-Er-Src	breast:	n/a	n/a
36	KAP1	chr6:54710888-54712803	HEK293	kidney:	n/a	n/a
37	ZKSCAN1	chr6:54711156-54711917	Hela-S3	cervix:	n/a	n/a
38	TAF1	chr6:54711003-54712273	MCF-7	breast:	n/a	n/a
39	POLR2A	chr6:54710891-54712384	MCF-7	breast:	n/a	n/a
40	FOS	chr6:54711293-54711534	MCF10A-Er-Src	breast:	n/a	n/a
41	NFIC	chr6:54711188-54711735	ECC-1	luminal epithelium:	n/a	n/a
42	FOS	chr6:54711313-54711590	MCF10A-Er-Src	breast:	n/a	n/a
43	CEBPB	chr6:54711262-54711473	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr6:54711151-54712976	Hela-S3	cervix:	n/a	n/a
45	TAF7	chr6:54711130-54711414	H1-hESC	embryonic stem cell:	n/a	n/a
46	ZNF263	chr6:54710951-54712438	HEK293-T-REx	kidney:	n/a	n/a
47	ELF1	chr6:54711156-54712150	MCF-7	breast:	n/a	chr6:54711954-54711965
48	POLR2A	chr6:54711082-54711775	HCT-116	colon:	n/a	n/a
49	MAX	chr6:54711052-54712166	H1-hESC	embryonic stem cell:	n/a	chr6:54711427-54711437
50	MAZ	chr6:54711007-54712408	Hela-S3	cervix:	n/a	chr6:54711427-54711437

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:54711276-54711326	CMK	blood:	n/a
2	chr6:54711276-54711326	NHDF-neo	bronchial:	n/a
3	chr6:54711276-54711326	Jurkat	blood:	n/a
4	chr6:54711276-54711326	HPAEpiC	pulmonary alveolar:	n/a
5	chr6:54711276-54711326	MCF-7	breast:	n/a
6	chr6:54711276-54711326	IMR90	lung:	fetal
7	chr6:54711276-54711326	AG10803	skin:	n/a
8	chr6:54711276-54711326	PrEC	prostate:	n/a
9	chr6:54711276-54711326	GM19239	blood:	n/a
10	chr6:54711276-54711326	HCM	heart:	n/a
11	chr6:54711276-54711326	HRPEpiC	eye:	n/a
12	chr6:54711276-54711326	NH-A	brain:	n/a
13	chr6:54711276-54711326	ProgFib	skin:	n/a
14	chr6:54711276-54711326	HIPEpiC	eye:	n/a
15	chr6:54711276-54711326	AG09309	skin:	n/a
16	chr6:54711276-54711326	SK-N-SH	brain:	n/a
17	chr6:54711276-54711326	SK-N-SH_RA	brain:	n/a
18	chr6:54711276-54711326	HUVEC	blood vessel:	n/a
19	chr6:54711276-54711326	HCPEpiC	choroid plexus:	n/a
20	chr6:54711276-54711326	BJ	skin:	n/a
21	chr6:54711276-54711326	MCF10A-Er-Src	breast:	n/a
22	chr6:54711276-54711326	ovcar-3	ovarian:	n/a
23	chr6:54711276-54711326	AG04449	skin:	fetal
24	chr6:54711276-54711326	HEEpiC	esophagus:	n/a
25	chr6:54711276-54711326	SAEC	small airway:	n/a
26	chr6:54711276-54711326	HCT-116	colon:	n/a
27	chr6:54711276-54711326	HNPCEpiC	eye:	n/a
28	chr6:54711276-54711326	HL-60	blood:	n/a
29	chr6:54711276-54711326	HAEpiC	amniotic membrane:	n/a
30	chr6:54711276-54711326	GM12878	blood:	n/a
31	chr6:54711276-54711326	AG04450	lung:	fetal
32	chr6:54711276-54711326	LNCaP	prostate:	n/a
33	chr6:54711276-54711326	T-47D	breast:	n/a
34	chr6:54711276-54711326	GM12892	blood:	n/a
35	chr6:54711276-54711326	K562	blood:	n/a
36	chr6:54711276-54711326	HRCEpiC	kidney:	n/a
37	chr6:54711276-54711326	ECC-1	luminal epithelium:	n/a
38	chr6:54711276-54711326	AG09319	gingival:	n/a
39	chr6:54711276-54711326	GM06990	blood:	n/a
40	chr6:54711276-54711326	HMEC	breast:	n/a
41	chr6:54711276-54711326	PFSK-1	brain:	n/a
42	chr6:54711276-54711326	PANC-1	pancreas:	n/a
43	chr6:54711276-54711326	NB4	blood:	n/a
44	chr6:54711276-54711326	A549	lung:	n/a
45	chr6:54711276-54711326	Hela-S3	cervix:	n/a
46	chr6:54711276-54711326	HRE	kidney:	n/a
47	chr6:54711276-54711326	SKMC	muscle:	n/a
48	chr6:54711276-54711326	HepG2	liver:	n/a
49	chr6:54711276-54711326	NHBE	bronchial:	n/a
50	chr6:54711276-54711326	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:54556132..54558033-chr6:54708676..54711461,2	MCF-7	breast:
2	chr6:16129307..16129833-chr6:54711262..54711766,2	Hela-S3	cervix:
3	chr14:65876592..65878564-chr6:54710365..54711981,2	MCF-7	breast:
4	chr6:54633061..54636995-chr6:54710354..54713223,5	MCF-7	breast:

Variant related genes	Relation type
FAM83B	TF binding region
FAM83B	CpG island
ENSG00000007944	Chromatin interaction
ENSG00000033170	Chromatin interaction
ENSG00000220635	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12664791	0.96[EUR][1000 genomes]
rs17682328	0.92[EUR][1000 genomes]
rs17682340	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17749547	0.92[EUR][1000 genomes]
rs62412606	0.96[EUR][1000 genomes]
rs62412628	0.96[EUR][1000 genomes]
rs62412629	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62412630	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62412631	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62412632	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412635	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412645	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412648	0.96[EUR][1000 genomes]
rs62412649	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357819	0.92[EUR][1000 genomes]
rs9396000	0.92[EUR][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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
3	chr6:54709800-54713400	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr6:54710200-54711600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:54710400-54713200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:54710600-54713800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:54710800-54711400	Flanking Active TSS	Placenta	Placenta
8	chr6:54710800-54711400	Active TSS	Rectal Smooth Muscle	rectum
9	chr6:54710800-54712200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:54710800-54712200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
11	chr6:54710800-54712400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr6:54710800-54712400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr6:54710800-54712400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:54710800-54712600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:54710800-54712600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:54710800-54712800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:54710800-54713000	Active TSS	Fetal Intestine Small	intestine
18	chr6:54710800-54713000	Active TSS	Right Atrium	heart
19	chr6:54710800-54713600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr6:54710800-54714400	Active TSS	Colonic Mucosa	Colon
21	chr6:54711000-54711400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:54711000-54711400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:54711000-54711400	Bivalent Enhancer	Brain Substantia Nigra	brain
24	chr6:54711000-54711400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
25	chr6:54711000-54711600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:54711000-54711600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:54711000-54711600	Enhancers	Spleen	Spleen
28	chr6:54711000-54711800	Active TSS	Stomach Mucosa	stomach
29	chr6:54711000-54711800	Bivalent/Poised TSS	NHLF	lung
30	chr6:54711000-54712000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:54711000-54712000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:54711000-54712000	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:54711000-54712000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:54711000-54712000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:54711000-54712000	Bivalent/Poised TSS	A549	lung
36	chr6:54711000-54712000	Active TSS	NH-A	brain
37	chr6:54711000-54712000	Bivalent/Poised TSS	Osteobl	bone
38	chr6:54711000-54712200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:54711000-54712200	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr6:54711000-54712200	Active TSS	Fetal Heart	heart
41	chr6:54711000-54712200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
42	chr6:54711000-54712200	Bivalent/Poised TSS	Psoas Muscle	Psoas
43	chr6:54711000-54712200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
44	chr6:54711000-54712200	Bivalent/Poised TSS	Thymus	Thymus
45	chr6:54711000-54712200	Active TSS	Hela-S3	cervix
46	chr6:54711000-54712400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:54711000-54712400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
48	chr6:54711000-54712400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:54711000-54712400	Active TSS	Pancreas	Pancrea
50	chr6:54711000-54712400	Active TSS	Small Intestine	intestine

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