Variant report

Variant	rs4147082
Chromosome Location	chr6:2246379-2246380
allele	A/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	BHLHE40	chr6:2245104-2246828	HepG2	liver:	n/a	chr6:2245835-2245851 chr6:2246639-2246655
2	TEAD4	chr6:2246090-2246885	K562	blood:	n/a	chr6:2246724-2246733
3	POLR2A	chr6:2245470-2246866	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:2246289-2246778	ECC-1	luminal epithelium:	n/a	n/a
5	HNF4G	chr6:2245933-2246836	HepG2	liver:	n/a	chr6:2246182-2246194 chr6:2246187-2246209 chr6:2246395-2246410
6	POLR2A	chr6:2245173-2247056	HepG2	liver:	n/a	n/a
7	EP300	chr6:2245667-2246980	HepG2	liver:	n/a	n/a
8	FOXA1	chr6:2246356-2246814	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:2245124-2246952	Hela-S3	cervix:	n/a	n/a
10	TBP	chr6:2245589-2246895	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:2246369-2246781	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:2245451-2246417	SK-N-MC	brain:	n/a	n/a
13	MXI1	chr6:2245136-2247021	HepG2	liver:	n/a	n/a
14	MYC	chr6:2245324-2246722	K562	blood:	n/a	n/a
15	POLR2A	chr6:2246351-2246781	HCT-116	colon:	n/a	n/a
16	MAZ	chr6:2245246-2246669	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:2245134-2246849	GM12892	blood:	n/a	n/a
18	JUN	chr6:2244606-2247054	K562	blood:	n/a	chr6:2246619-2246627 chr6:2246618-2246628 chr6:2246618-2246628 chr6:2246321-2246331 chr6:2246994-2247005 chr6:2246618-2246628 chr6:2246618-2246628
19	MBD4	chr6:2245918-2246993	HepG2	liver:	n/a	n/a
20	TCF12	chr6:2245171-2246934	ECC-1	luminal epithelium:	n/a	chr6:2246635-2246645
21	TBP	chr6:2245635-2246383	K562	blood:	n/a	n/a
22	RCOR1	chr6:2246057-2246730	K562	blood:	n/a	n/a
23	TCF12	chr6:2246213-2246883	SK-N-SH	brain:	n/a	chr6:2246635-2246645
24	NFIC	chr6:2246253-2247064	ECC-1	luminal epithelium:	n/a	chr6:2246661-2246677 chr6:2246661-2246678
25	MAFF	chr6:2246315-2246882	HepG2	liver:	n/a	n/a
26	TFAP2A	chr6:2245289-2246776	Hela-S3	cervix:	n/a	chr6:2246002-2246016 chr6:2246000-2246015 chr6:2246628-2246640 chr6:2246002-2246016 chr6:2246618-2246627 chr6:2246002-2246016 chr6:2245840-2245852
27	MAX	chr6:2245124-2246838	K562	blood:	n/a	n/a
28	RELA	chr6:2245295-2246743	GM18951	blood:	n/a	n/a
29	MAX	chr6:2244555-2247000	HepG2	liver:	n/a	n/a
30	POLR2A	chr6:2245588-2247155	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:2245306-2246970	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:2245169-2246726	GM19193	blood:	n/a	n/a
33	POLR2A	chr6:2245213-2246768	GM18526	blood:	n/a	n/a
34	POLR2A	chr6:2245577-2246720	K562	blood:	n/a	n/a
35	ARID3A	chr6:2245615-2246925	HepG2	liver:	n/a	n/a
36	SIN3AK20	chr6:2246264-2246781	HepG2	liver:	n/a	n/a
37	POLR2A	chr6:2245168-2246730	GM12892	blood:	n/a	n/a
38	SIN3AK20	chr6:2245958-2247054	MCF-7	breast:	n/a	n/a
39	STAT5A	chr6:2246277-2246636	GM12878	blood:	n/a	n/a
40	CUX1	chr6:2246107-2246912	K562	blood:	n/a	chr6:2246738-2246747
41	HEY1	chr6:2245473-2246945	HepG2	liver:	n/a	chr6:2245888-2245903
42	SP1	chr6:2246314-2246946	HepG2	liver:	n/a	n/a
43	MYBL2	chr6:2244975-2247172	HepG2	liver:	n/a	n/a
44	TEAD4	chr6:2246004-2247005	HepG2	liver:	n/a	chr6:2246724-2246733
45	ZEB1	chr6:2244538-2247191	HepG2	liver:	n/a	chr6:2245548-2245557 chr6:2245548-2245560 chr6:2245266-2245278
46	MAX	chr6:2245012-2246867	MCF-7	breast:	n/a	n/a
47	POLR2A	chr6:2245288-2246642	GM15510	blood:	n/a	n/a
48	REST	chr6:2246326-2246922	HepG2	liver:	n/a	n/a
49	POLR2A	chr6:2245141-2246823	GM18505	blood:	n/a	n/a
50	NFIC	chr6:2246299-2247048	ECC-1	luminal epithelium:	n/a	chr6:2246661-2246677 chr6:2246661-2246678

No.	Distal block	Cell Line	Cell type
1	chr6:2244284..2246271-chr6:2246300..2249565,3	K562	blood:
2	chr3:52321502..52322345-chr6:2245845..2246762,2	Hela-S3	cervix:
3	chr6:1608353..1611335-chr6:2245492..2248463,2	MCF-7	breast:
4	chr6:2245961..2247714-chr7:148785779..148788707,2	MCF-7	breast:

Variant related genes	Relation type
GMDS	TF binding region
ENSG00000197362	Chromatin interaction
ENSG00000250903	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000112699	Chromatin interaction
ENSG00000054598	Chromatin interaction
ENSG00000168237	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10046434	0.96[ASN][1000 genomes]
rs12175387	0.91[ASN][1000 genomes]
rs13207508	0.96[ASN][1000 genomes]
rs3778566	0.87[ASN][1000 genomes]
rs3800191	0.96[ASN][1000 genomes]
rs61245983	0.96[ASN][1000 genomes]
rs61372774	0.99[ASN][1000 genomes]
rs6903122	0.84[ASN][1000 genomes]
rs6903476	0.87[ASN][1000 genomes]
rs72830193	0.96[ASN][1000 genomes]
rs9501818	0.87[ASN][1000 genomes]
rs9501819	0.96[ASN][1000 genomes]
rs9501822	0.86[ASN][1000 genomes]
rs9503125	0.87[ASN][1000 genomes]
rs9503127	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
10	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
17	nsv1026678	chr6:2230064-2261297	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a
18	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 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	chr6:2243200-2246800	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr6:2243200-2246800	Active TSS	Gastric	stomach
3	chr6:2244200-2246600	Active TSS	Sigmoid Colon	Sigmoid Colon
4	chr6:2244200-2246600	Active TSS	Stomach Mucosa	stomach
5	chr6:2244200-2247000	Active TSS	Colonic Mucosa	Colon
6	chr6:2244400-2246600	Active TSS	Small Intestine	intestine
7	chr6:2244400-2247000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:2244600-2246400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:2244600-2246600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:2244600-2246600	Active TSS	Fetal Kidney	kidney
11	chr6:2244600-2246600	Active TSS	NHDF-Ad	bronchial
12	chr6:2244600-2247200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:2244600-2247200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr6:2244800-2246400	Active TSS	Brain Cingulate Gyrus	brain
15	chr6:2244800-2246400	Bivalent/Poised TSS	HepG2	liver
16	chr6:2244800-2246600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:2244800-2246600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:2244800-2246600	Active TSS	Aorta	Aorta
19	chr6:2244800-2246800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:2244800-2246800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:2244800-2246800	Active TSS	Esophagus	oesophagus
22	chr6:2244800-2246800	Active TSS	Ovary	ovary
23	chr6:2244800-2247000	Active TSS	Pancreas	Pancrea
24	chr6:2245000-2246400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:2245000-2246400	Active TSS	Fetal Brain Male	brain
26	chr6:2245000-2246400	Active TSS	Osteobl	bone
27	chr6:2245000-2246600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:2245000-2246600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:2245000-2246600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:2245000-2246600	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr6:2245000-2246600	Active TSS	Left Ventricle	heart
32	chr6:2245000-2246600	Active TSS	Placenta Amnion	Placenta Amnion
33	chr6:2245000-2246600	Active TSS	Right Atrium	heart
34	chr6:2245000-2246600	Active TSS	A549	lung
35	chr6:2245000-2246600	Active TSS	HMEC	breast
36	chr6:2245000-2246600	Active TSS	HSMMtube	muscle
37	chr6:2245000-2246600	Active TSS	NHLF	lung
38	chr6:2245000-2246800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:2245000-2246800	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:2245000-2246800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:2245000-2246800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:2245000-2246800	Active TSS	Brain Angular Gyrus	brain
43	chr6:2245000-2246800	Active TSS	Fetal Intestine Large	intestine
44	chr6:2245200-2246400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr6:2245200-2246400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:2245200-2246400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:2245200-2246400	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr6:2245200-2246400	Active TSS	Muscle Satellite Cultured Cells	--
49	chr6:2245200-2246400	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr6:2245200-2246400	Active TSS	Fetal Thymus	thymus

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