Variant report

Variant	rs754404
Chromosome Location	chr6:33664730-33664731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr6:33664642-33665471	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr6:33664299-33665069	K562	blood:	n/a	n/a
3	POLR2A	chr6:33664715-33665176	MCF-7	breast:	n/a	n/a
4	POLR2A	chr6:33664611-33664862	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:33664619-33665363	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr6:33664702-33665403	ECC-1	luminal epithelium:	n/a	n/a
7	TCF7L2	chr6:33664468-33665176	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr6:33662026-33666005	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:33664689-33665098	K562	blood:	n/a	n/a
10	POLR2A	chr6:33662113-33666054	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:33664658-33664962	HCT-116	colon:	n/a	n/a
12	POLR2A	chr6:33664629-33665144	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:33660869-33664890	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:33664664-33665260	U87	brain:	n/a	n/a
15	POLR2A	chr6:33664317-33665042	K562	blood:	n/a	n/a
16	POLR2A	chr6:33664319-33665499	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr6:33664558-33665339	ECC-1	luminal epithelium:	n/a	n/a
18	NFIC	chr6:33664630-33665340	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr6:33664606-33665482	PFSK-1	brain:	n/a	n/a
20	REST	chr6:33664690-33665343	PFSK-1	brain:	n/a	chr6:33664788-33664808 chr6:33664794-33664808
21	ZNF263	chr6:33664630-33665178	HEK293-T-REx	kidney:	n/a	n/a
22	POLR2A	chr6:33663652-33665062	K562	blood:	n/a	n/a
23	CTCF	chr6:33664720-33664870	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr6:33664663-33665043	U87	brain:	n/a	n/a
25	POLR2A	chr6:33662019-33665616	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr6:33657437-33666414	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr6:33664586-33664786	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr6:33664396-33665437	Hela-S3	cervix:	n/a	n/a
29	STAT5A	chr6:33664275-33664836	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:33658911-33667009	K562	blood:	n/a	n/a
31	POLR2A	chr6:33664532-33664959	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:33664350-33665081	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:33664006-33665410	PANC-1	pancreas:	n/a	n/a
34	NFIC	chr6:33664681-33665262	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr6:33664575-33664919	A549	lung:	n/a	n/a
36	POLR2A	chr6:33664723-33664847	HepG2	liver:	n/a	n/a
37	POLR2A	chr6:33664630-33665710	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr6:33662639-33664943	HCT-116	colon:	n/a	n/a
39	POLR2A	chr6:33664644-33665013	H1-hESC	embryonic stem cell:	n/a	n/a
40	FOS	chr6:33664692-33665332	HUVEC	blood vessel:	n/a	chr6:33664929-33664939 chr6:33664929-33664939 chr6:33665233-33665244 chr6:33664929-33664939
41	POLR2A	chr6:33664639-33664973	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr6:33657421-33665985	SK-N-MC	brain:	n/a	n/a
43	MTA3	chr6:33663891-33665249	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:33664710-33665270	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr6:33664709-33664863	HepG2	liver:	n/a	n/a
46	POLR2A	chr6:33664274-33665412	K562	blood:	n/a	n/a
47	POLR2A	chr6:33664664-33665213	U87	brain:	n/a	n/a
48	NFIC	chr6:33664677-33665436	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
2	chr6:33588962..33590940-chr6:33663858..33665363,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269490	TF binding region
MIR3934	TF binding region
ENSG00000137288	Chromatin interaction
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1014933	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10947430	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10947434	0.92[EUR][1000 genomes]
rs11759396	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555965	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2147656	0.90[EUR][1000 genomes]
rs2147657	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2229642	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274458	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2281829	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296736	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296738	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296739	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296741	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296742	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2966	0.93[EUR][1000 genomes]
rs3227	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3818521	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818523	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818524	0.91[EUR][1000 genomes]
rs3818525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818527	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3818529	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818530	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4711336	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711337	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711338	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711339	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711340	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4713655	0.84[EUR][1000 genomes]
rs4713658	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4713659	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713660	0.90[EUR][1000 genomes]
rs4713661	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713662	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713665	0.92[EUR][1000 genomes]
rs4713666	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713667	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713669	0.83[EUR][1000 genomes]
rs4713670	0.86[EUR][1000 genomes]
rs4713671	0.86[EUR][1000 genomes]
rs542441	0.90[ASN][1000 genomes]
rs626156	0.93[ASN][1000 genomes]
rs6457739	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6904816	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6916949	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6917140	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6928010	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6938056	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs749338	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs749847	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs753890	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs764752	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764754	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7739505	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7759668	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7770465	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs791903	0.84[EUR][1000 genomes]
rs9366828	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9368773	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9368776	0.89[EUR][1000 genomes]
rs9380375	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9394163	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs942640	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs942641	0.81[EUR][1000 genomes]
rs942643	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9469566	0.94[EUR][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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:33655600-33664800	Weak transcription	Aorta	Aorta
11	chr6:33656400-33666000	Genic enhancers	Spleen	Spleen
12	chr6:33658000-33667200	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr6:33658200-33666600	Genic enhancers	Fetal Muscle Leg	muscle
14	chr6:33658600-33666400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:33659000-33666600	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr6:33659200-33665200	Genic enhancers	HMEC	breast
17	chr6:33659200-33665400	Genic enhancers	NHDF-Ad	bronchial
18	chr6:33659200-33665800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:33659200-33666600	Enhancers	Right Atrium	heart
20	chr6:33659400-33665000	Genic enhancers	Duodenum Mucosa	Duodenum
21	chr6:33659400-33666400	Genic enhancers	Fetal Thymus	thymus
22	chr6:33659400-33668400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:33659600-33665600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:33659600-33666400	Enhancers	Primary hematopoietic stem cells	blood
25	chr6:33659600-33667000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:33659800-33664800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:33659800-33665600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:33659800-33666000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:33659800-33666600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:33659800-33666600	Genic enhancers	Fetal Stomach	stomach
31	chr6:33660000-33666200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr6:33660200-33665600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:33660200-33667200	Genic enhancers	Lung	lung
34	chr6:33660200-33667800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:33660200-33669400	Strong transcription	HepG2	liver
36	chr6:33660400-33665600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:33660400-33665800	Enhancers	HUVEC	blood vessel
38	chr6:33660400-33666600	Genic enhancers	Thymus	Thymus
39	chr6:33660600-33666200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:33660800-33665400	Enhancers	Fetal Brain Male	brain
41	chr6:33661000-33665200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr6:33661200-33664800	Enhancers	Brain Cingulate Gyrus	brain
43	chr6:33661200-33665200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:33661200-33665400	Genic enhancers	Muscle Satellite Cultured Cells	--
45	chr6:33661400-33665000	Enhancers	Brain Anterior Caudate	brain
46	chr6:33661400-33669200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:33661600-33665000	Enhancers	Fetal Heart	heart
48	chr6:33661600-33665400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:33661600-33665400	Genic enhancers	Gastric	stomach
50	chr6:33661600-33666200	Genic enhancers	Esophagus	oesophagus

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