Variant report

Variant	rs3130018
Chromosome Location	chr6:33290402-33290403
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	chr6:33290327-33291793	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYBL2	chr6:33290208-33291764	HepG2	liver:	n/a	n/a
3	CHD1	chr6:33289848-33291651	GM12878	blood:	n/a	n/a
4	GABPA	chr6:33290385-33291565	SK-N-SH	brain:	n/a	chr6:33290598-33290607
5	BRCA1	chr6:33290151-33291295	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr6:33290037-33291337	MCF10A-Er-Src	breast:	n/a	n/a
7	SRF	chr6:33290349-33291178	ECC-1	luminal epithelium:	n/a	chr6:33291096-33291106 chr6:33290832-33290842
8	POLR2A	chr6:33289855-33292052	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:33290005-33291461	K562	blood:	n/a	n/a
10	PML	chr6:33290400-33291421	K562	blood:	n/a	n/a
11	ELK1	chr6:33290300-33291438	K562	blood:	n/a	chr6:33290739-33290748 chr6:33290739-33290748
12	ELF1	chr6:33290340-33291573	MCF-7	breast:	n/a	chr6:33290809-33290821
13	E2F6	chr6:33289999-33291673	H1-hESC	embryonic stem cell:	n/a	chr6:33291304-33291313 chr6:33290472-33290482 chr6:33290471-33290482 chr6:33290469-33290481 chr6:33290598-33290607 chr6:33290474-33290481 chr6:33290470-33290481 chr6:33290473-33290481 chr6:33291018-33291027 chr6:33290473-33290481
14	ZBTB7A	chr6:33290274-33291657	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr6:33290061-33291609	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:33290254-33291278	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr6:33290349-33291591	SK-N-SH_RA	brain:	n/a	chr6:33290932-33290942 chr6:33290778-33290800 chr6:33290935-33290943 chr6:33290932-33290942 chr6:33290778-33290788 chr6:33290598-33290607 chr6:33290932-33290954 chr6:33290601-33290610
18	YY1	chr6:33290376-33291428	HCT-116	colon:	n/a	chr6:33290932-33290942 chr6:33290778-33290800 chr6:33290935-33290943 chr6:33290932-33290942 chr6:33290778-33290788 chr6:33290598-33290607 chr6:33290932-33290954 chr6:33290601-33290610
19	E2F4	chr6:33290356-33291520	MCF10A-Er-Src	breast:	n/a	chr6:33291304-33291313 chr6:33290472-33290482 chr6:33290471-33290482 chr6:33290469-33290481 chr6:33290598-33290607 chr6:33290474-33290481 chr6:33290470-33290481 chr6:33290473-33290481 chr6:33291018-33291027 chr6:33290473-33290481
20	PML	chr6:33289741-33291509	GM12878	blood:	n/a	n/a
21	RELA	chr6:33289851-33291448	GM12891	blood:	n/a	chr6:33291132-33291141 chr6:33291132-33291141
22	MYBL2	chr6:33290393-33291686	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:33289816-33290458	GM12892	blood:	n/a	n/a
24	ZBTB7A	chr6:33290305-33291681	K562	blood:	n/a	n/a
25	POLR2A	chr6:33290002-33291438	GM10847	blood:	n/a	n/a
26	MTA3	chr6:33289315-33292314	GM12878	blood:	n/a	n/a
27	ETS1	chr6:33290400-33291211	A549	lung:	n/a	chr6:33290598-33290609 chr6:33290736-33290749 chr6:33290739-33290748 chr6:33290601-33290612 chr6:33290740-33290750 chr6:33290739-33290748 chr6:33290484-33290495 chr6:33290739-33290748 chr6:33290739-33290748 chr6:33290736-33290751 chr6:33290739-33290748 chr6:33290739-33290748 chr6:33291025-33291039 chr6:33290735-33290751 chr6:33290739-33290748 chr6:33290466-33290477
28	MYC	chr6:33290297-33291545	K562	blood:	n/a	chr6:33290602-33290612 chr6:33290501-33290511
29	ELF1	chr6:33290332-33291570	GM12878	blood:	n/a	chr6:33290809-33290821
30	SIN3AK20	chr6:33290204-33291560	SK-N-SH	brain:	n/a	n/a
31	MXI1	chr6:33289631-33292178	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr6:33289323-33291688	K562	blood:	n/a	n/a
33	POLR2A	chr6:33290388-33291362	U87	brain:	n/a	n/a
34	HCFC1	chr6:33290373-33291487	K562	blood:	n/a	n/a
35	TAF1	chr6:33290326-33291165	SK-N-SH	brain:	n/a	n/a
36	GABPA	chr6:33290348-33291153	HepG2	liver:	n/a	chr6:33290598-33290607
37	GABPA	chr6:33290221-33291800	MCF-7	breast:	n/a	chr6:33290598-33290607
38	JUND	chr6:33290292-33291535	K562	blood:	n/a	chr6:33291020-33291029 chr6:33290833-33290842
39	POU2F2	chr6:33290002-33291438	GM12878	blood:	n/a	chr6:33290502-33290514
40	EP300	chr6:33290394-33291590	ECC-1	luminal epithelium:	n/a	chr6:33290498-33290514 chr6:33291181-33291195 chr6:33290740-33290747
41	POLR2A	chr6:33289903-33291247	Hela-S3	cervix:	n/a	n/a
42	MAX	chr6:33290345-33291716	H1-hESC	embryonic stem cell:	n/a	chr6:33290602-33290612 chr6:33290501-33290511
43	REST	chr6:33290392-33291755	K562	blood:	n/a	chr6:33291345-33291355 chr6:33291319-33291328 chr6:33290498-33290508
44	YY1	chr6:33290351-33291722	SK-N-SH	brain:	n/a	chr6:33290932-33290942 chr6:33290778-33290800 chr6:33290935-33290943 chr6:33290932-33290942 chr6:33290778-33290788 chr6:33290598-33290607 chr6:33290932-33290954 chr6:33290601-33290610
45	HMGN3	chr6:33290395-33290461	K562	blood:	n/a	n/a
46	YY1	chr6:33290318-33291765	HepG2	liver:	n/a	chr6:33290932-33290942 chr6:33290778-33290800 chr6:33290935-33290943 chr6:33290932-33290942 chr6:33290778-33290788 chr6:33290598-33290607 chr6:33290932-33290954 chr6:33290601-33290610
47	POLR2A	chr6:33290396-33291492	GM12878	blood:	n/a	n/a
48	TAF1	chr6:33290300-33291415	K562	blood:	n/a	n/a
49	MXI1	chr6:33289533-33291731	IMR90	lung:	n/a	n/a
50	POLR2A	chr6:33288128-33290518	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33290371-33290421	BJ	skin:	n/a
2	chr6:33290371-33290421	Caco-2	colon:	n/a
3	chr6:33290371-33290421	Hepatocyte	liver:	n/a
4	chr6:33290371-33290421	HRPEpiC	eye:	n/a
5	chr6:33290371-33290421	AG04449	skin:	fetal
6	chr6:33290379-33290429	GM06990	blood:	n/a
7	chr6:33290379-33290429	CMK	blood:	n/a
8	chr6:33290379-33290429	PANC-1	pancreas:	n/a
9	chr6:33290371-33290421	HAEpiC	amniotic membrane:	n/a
10	chr6:33290371-33290421	CMK	blood:	n/a
11	chr6:33290379-33290429	HCF	heart:	n/a
12	chr6:33290371-33290421	BE2_C	brain:	n/a
13	chr6:33290371-33290421	ECC-1	luminal epithelium:	n/a
14	chr6:33290371-33290421	H1-hESC	embryonic stem cell:	embryo
15	chr6:33290379-33290429	K562	blood:	n/a
16	chr6:33290371-33290421	Jurkat	blood:	n/a
17	chr6:33290379-33290429	Jurkat	blood:	n/a
18	chr6:33290371-33290421	NHDF-neo	bronchial:	n/a
19	chr6:33290371-33290421	IMR90	lung:	fetal
20	chr6:33290379-33290429	ovcar-3	ovarian:	n/a
21	chr6:33290371-33290421	K562	blood:	n/a
22	chr6:33290371-33290421	GM19239	blood:	n/a
23	chr6:33290379-33290429	NHBE	bronchial:	n/a
24	chr6:33290371-33290421	HRCEpiC	kidney:	n/a
25	chr6:33290379-33290429	HEEpiC	esophagus:	n/a
26	chr6:33290371-33290421	SK-N-SH	brain:	n/a
27	chr6:33290371-33290421	HEK293	kidney:	embryo
28	chr6:33290379-33290429	NH-A	brain:	n/a
29	chr6:33290371-33290421	AoSMC	blood vessel:	n/a
30	chr6:33290379-33290429	IMR90	lung:	fetal
31	chr6:33290371-33290421	SAEC	small airway:	n/a
32	chr6:33290379-33290429	GM12878	blood:	n/a
33	chr6:33290379-33290429	HL-60	blood:	n/a
34	chr6:33290379-33290429	ProgFib	skin:	n/a
35	chr6:33290371-33290421	A549	lung:	n/a
36	chr6:33290379-33290429	GM12891	blood:	n/a
37	chr6:33290379-33290429	PrEC	prostate:	n/a
38	chr6:33290371-33290421	AG09319	gingival:	n/a
39	chr6:33290379-33290429	AoSMC	blood vessel:	n/a
40	chr6:33290379-33290429	T-47D	breast:	n/a
41	chr6:33290379-33290429	H1-hESC	embryonic stem cell:	embryo
42	chr6:33290371-33290421	HEEpiC	esophagus:	n/a
43	chr6:33290379-33290429	NHDF-neo	bronchial:	n/a
44	chr6:33290379-33290429	HCPEpiC	choroid plexus:	n/a
45	chr6:33290379-33290429	AG09309	skin:	n/a
46	chr6:33290379-33290429	AG04450	lung:	fetal
47	chr6:33290371-33290421	GM12878	blood:	n/a
48	chr6:33290371-33290421	GM06990	blood:	n/a
49	chr6:33290371-33290421	PFSK-1	brain:	n/a
50	chr6:33290379-33290429	GM12892	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33247934..33250111-chr6:33290391..33292325,2	MCF-7	breast:
2	chr6:32937579..32939434-chr6:33288341..33290768,2	MCF-7	breast:
3	chr6:33259755..33275794-chr6:33276314..33291745,68	MCF-7	breast:
4	chr1:113161307..113161980-chr6:33290215..33290894,2	Hela-S3	cervix:
5	chr6:32938603..32941969-chr6:33287550..33290595,4	K562	blood:
6	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
7	chr6:33166722..33169414-chr6:33289909..33292602,2	K562	blood:
8	chr22:50353923..50354850-chr6:33290121..33290790,2	HCT-116	colon:
9	chr6:33285348..33292496-chr6:33357328..33361566,13	K562	blood:
10	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
11	chr6:32938603..32941969-chr6:33287550..33290595,3	K562	blood:
12	chr6:33283943..33291558-chr6:33357867..33362243,10	MCF-7	breast:

Variant related genes	Relation type
DAXX	TF binding region
ZBTB22	TF binding region
ZBTB22	CpG island
DAXX	CpG island
ENSG00000112514	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000198355	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000263756	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1014779	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1061783	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1800838	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2013891	0.82[EUR][1000 genomes]
rs2071888	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071889	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2395379	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2894334	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3106190	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3106195	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130016	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130099	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130100	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130101	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130102	0.80[EUR][1000 genomes]
rs3130262	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3130263	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130264	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130265	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3130266	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130267	0.87[EUR][1000 genomes]
rs3130269	0.87[EUR][1000 genomes]
rs3130270	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3130271	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3135405	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135407	0.90[EUR][1000 genomes]
rs3135408	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3135409	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs446735	0.81[EUR][1000 genomes]
rs456261	0.84[EUR][1000 genomes]
rs463260	0.81[EUR][1000 genomes]
rs464865	0.81[EUR][1000 genomes]
rs469064	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9277968	0.85[EUR][1000 genomes];0.81[ASN][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	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
3	esv10737	chr6:33289511-33296285	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33289000-33291400	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr6:33289200-33290600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:33289200-33290800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
4	chr6:33289200-33291600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:33289200-33292000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:33289400-33290600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:33289400-33290600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:33289400-33291600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:33289400-33291600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:33289400-33291600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:33289400-33292000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:33289400-33292000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:33289600-33290600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:33289600-33290800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr6:33289600-33291200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:33289600-33291400	Active TSS	HSMM	muscle
17	chr6:33289600-33291600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:33289600-33291600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:33289600-33291600	Active TSS	Fetal Kidney	kidney
20	chr6:33289600-33292400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr6:33289800-33291200	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr6:33289800-33291200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:33289800-33291200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:33289800-33291200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:33289800-33291400	Active TSS	H1 Cell Line	embryonic stem cell
26	chr6:33289800-33291400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:33289800-33291400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:33289800-33291400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:33289800-33291400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:33289800-33291400	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr6:33289800-33291400	Active TSS	Stomach Mucosa	stomach
32	chr6:33289800-33291400	Active TSS	NHDF-Ad	bronchial
33	chr6:33289800-33291600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:33289800-33291600	Active TSS	Fetal Intestine Small	intestine
35	chr6:33289800-33291600	Active TSS	Gastric	stomach
36	chr6:33289800-33291600	Active TSS	GM12878-XiMat	blood
37	chr6:33289800-33291800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr6:33289800-33291800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:33289800-33291800	Active TSS	Small Intestine	intestine
40	chr6:33289800-33292000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr6:33289800-33292000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:33289800-33292000	Active TSS	A549	lung
43	chr6:33290000-33291000	Active TSS	Primary T cells fromperipheralblood	blood
44	chr6:33290000-33291000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:33290000-33291000	Active TSS	NHLF	lung
46	chr6:33290000-33291200	Active TSS	Primary B cells from peripheral blood	blood
47	chr6:33290000-33291200	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr6:33290000-33291200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:33290000-33291200	Active TSS	Fetal Thymus	thymus
50	chr6:33290000-33291200	Active TSS	HSMMtube	muscle

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