Variant report

Variant	rs538416246
Chromosome Location	chr3:46734338-46734339
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	FOS	chr3:46734064-46734571	MCF10A-Er-Src	breast:	n/a	chr3:46734228-46734240 chr3:46734230-46734238 chr3:46734229-46734239
2	MYC	chr3:46734212-46734342	K562	blood:	n/a	n/a
3	POLR2A	chr3:46734022-46735332	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr3:46734109-46734443	H1-hESC	embryonic stem cell:	n/a	n/a
5	SMARCC1	chr3:46733793-46735141	Hela-S3	cervix:	n/a	chr3:46734229-46734238
6	FOS	chr3:46734053-46734493	MCF10A-Er-Src	breast:	n/a	chr3:46734228-46734240 chr3:46734230-46734238 chr3:46734229-46734239
7	NR2F2	chr3:46733902-46734622	MCF-7	breast:	n/a	n/a
8	NR2F2	chr3:46733962-46735115	MCF-7	breast:	n/a	n/a
9	MYC	chr3:46734033-46734424	MCF-7	breast:	n/a	n/a
10	MYC	chr3:46734059-46734762	MCF10A-Er-Src	breast:	n/a	chr3:46734535-46734545 chr3:46734616-46734625
11	POLR2A	chr3:46733934-46735221	Hela-S3	cervix:	n/a	n/a
12	MYC	chr3:46734107-46734461	MCF10A-Er-Src	breast:	n/a	n/a
13	NFIC	chr3:46733864-46735058	ECC-1	luminal epithelium:	n/a	n/a
14	ZKSCAN1	chr3:46733947-46734576	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:46734047-46735474	MCF10A-Er-Src	breast:	n/a	n/a
16	TEAD4	chr3:46734068-46734498	H1-hESC	embryonic stem cell:	n/a	n/a
17	FOS	chr3:46734050-46734461	MCF10A-Er-Src	breast:	n/a	chr3:46734228-46734240 chr3:46734230-46734238 chr3:46734229-46734239
18	POLR2A	chr3:46733799-46735185	Hela-S3	cervix:	n/a	n/a
19	NFYB	chr3:46734077-46734411	Hela-S3	cervix:	n/a	n/a
20	ESR1	chr3:46734144-46734435	T-47D	breast:	n/a	chr3:46734327-46734344 chr3:46734328-46734343
21	MAX	chr3:46734039-46735181	A549	lung:	n/a	chr3:46734870-46734879 chr3:46734535-46734545 chr3:46734616-46734625
22	POLR2A	chr3:46734052-46735472	MCF-7	breast:	n/a	n/a
23	STAT3	chr3:46734260-46734460	MCF10A-Er-Src	breast:	n/a	n/a
24	SIN3A	chr3:46734127-46735397	H1-hESC	embryonic stem cell:	n/a	chr3:46735021-46735034 chr3:46735021-46735032
25	TCF12	chr3:46733842-46735352	ECC-1	luminal epithelium:	n/a	chr3:46734673-46734683 chr3:46734291-46734299
26	MAFK	chr3:46734059-46734798	Hela-S3	cervix:	n/a	chr3:46734231-46734240
27	TCF12	chr3:46733901-46735010	ECC-1	luminal epithelium:	n/a	chr3:46734673-46734683 chr3:46734291-46734299
28	YY1	chr3:46734093-46734445	HCT-116	colon:	n/a	n/a
29	EP300	chr3:46733839-46735284	ECC-1	luminal epithelium:	n/a	n/a
30	CEBPB	chr3:46734030-46734446	Hela-S3	cervix:	n/a	n/a
31	NFIC	chr3:46733902-46735210	ECC-1	luminal epithelium:	n/a	n/a
32	MAFK	chr3:46734136-46734384	H1-hESC	embryonic stem cell:	n/a	chr3:46734231-46734240
33	POLR2A	chr3:46734265-46734353	A549	lung:	n/a	n/a
34	NFYA	chr3:46734103-46734420	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr3:46733865-46735240	ECC-1	luminal epithelium:	n/a	n/a
36	ELK1	chr3:46734138-46734819	Hela-S3	cervix:	n/a	n/a
37	MAX	chr3:46733849-46735719	ECC-1	luminal epithelium:	n/a	chr3:46734870-46734879 chr3:46734535-46734545 chr3:46734616-46734625 chr3:46735563-46735572
38	ESR1	chr3:46733973-46734577	ECC-1	luminal epithelium:	n/a	chr3:46734327-46734344 chr3:46734328-46734343
39	TCF7L2	chr3:46734237-46735035	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr3:46734260-46734410	Hela-S3	cervix:	n/a	n/a
41	TBP	chr3:46734095-46734945	Hela-S3	cervix:	n/a	n/a
42	USF2	chr3:46734333-46734669	H1-hESC	embryonic stem cell:	n/a	n/a
43	TEAD4	chr3:46733948-46735209	ECC-1	luminal epithelium:	n/a	n/a
44	CHD2	chr3:46733976-46735314	Hela-S3	cervix:	n/a	n/a
45	TAF1	chr3:46733984-46734647	ECC-1	luminal epithelium:	n/a	n/a
46	STAT3	chr3:46734111-46734349	MCF10A-Er-Src	breast:	n/a	chr3:46734187-46734199 chr3:46734183-46734195
47	RFX5	chr3:46734042-46735169	Hela-S3	cervix:	n/a	n/a
48	ZBTB7A	chr3:46733763-46736413	ECC-1	luminal epithelium:	n/a	chr3:46736311-46736318 chr3:46734540-46734549
49	MYC	chr3:46734136-46734353	MCF-7	breast:	n/a	n/a
50	TEAD4	chr3:46734079-46734488	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:87350782..87351467-chr3:46734125..46734941,2	Hela-S3	cervix:
2	chr3:46733801..46735413-chr3:46924430..46926212,2	MCF-7	breast:
3	chr3:46728002..46730865-chr3:46732714..46734493,2	K562	blood:
4	chr3:46722742..46724325-chr3:46733459..46735116,2	K562	blood:
5	chr3:46727378..46730139-chr3:46733383..46735627,3	MCF-7	breast:
6	chr3:46733350..46734890-chr3:46932280..46935238,2	MCF-7	breast:
7	chr3:46733050..46735013-chr3:46736523..46739104,3	K562	blood:
8	chr3:46589952..46592593-chr3:46732036..46734467,2	K562	blood:
9	chr3:46733404..46735141-chr3:46748725..46750536,2	MCF-7	breast:
10	chr1:145382730..145383465-chr3:46734207..46734831,2	Hela-S3	cervix:
11	chr3:46733775..46736386-chr3:46933231..46935509,2	MCF-7	breast:
12	chr18:9913950..9914878-chr3:46734098..46734723,2	Hela-S3	cervix:
13	chr3:46729365..46731831-chr3:46732714..46735067,2	K562	blood:

Variant related genes	Relation type
ALS2CL	TF binding region
ENSG00000270006	Chromatin interaction
ENSG00000178038	Chromatin interaction
ENSG00000160801	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000264306	Chromatin interaction
ENSG00000101558	Chromatin interaction
ENSG00000260456	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1804680	chr3:46704348-46869911	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv876742	chr3:46705369-46763839	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	nsv536555	chr3:46706571-46817963	Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv536556	chr3:46706571-46849443	Genic enhancers Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv536557	chr3:46706571-46853434	Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv10268	chr3:46707169-46736718	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	esv1797503	chr3:46708712-46760713	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
17	nsv876743	chr3:46716523-46753577	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
18	nsv876744	chr3:46716523-46763839	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
19	nsv460525	chr3:46728659-46790397	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
20	nsv590179	chr3:46728659-46790397	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
21	esv1847964	chr3:46729757-46753976	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
22	esv3438151	chr3:46734173-46736721	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46705400-46734400	Weak transcription	Ovary	ovary
2	chr3:46730200-46734400	Weak transcription	Aorta	Aorta
3	chr3:46732000-46734400	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr3:46732200-46734400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:46732200-46734600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:46732600-46734600	Enhancers	Spleen	Spleen
7	chr3:46733400-46734400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr3:46733400-46734400	Flanking Active TSS	Esophagus	oesophagus
9	chr3:46733400-46734400	Bivalent Enhancer	Fetal Thymus	thymus
10	chr3:46733400-46734400	Enhancers	Small Intestine	intestine
11	chr3:46733400-46734800	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr3:46733600-46734400	Flanking Active TSS	Lung	lung
13	chr3:46733600-46734600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:46733600-46735000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr3:46733600-46735000	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr3:46733800-46734400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:46733800-46734400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:46733800-46734800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr3:46733800-46735000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr3:46733800-46735000	Flanking Active TSS	Fetal Intestine Large	intestine
21	chr3:46733800-46735000	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr3:46734000-46734400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:46734000-46734400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr3:46734000-46734400	Bivalent Enhancer	Primary B cells from cord blood	blood
25	chr3:46734000-46734400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:46734000-46734400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr3:46734000-46734400	Bivalent Enhancer	Fetal Brain Female	brain
28	chr3:46734000-46734400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr3:46734000-46734400	Active TSS	Rectal Smooth Muscle	rectum
30	chr3:46734000-46734400	Enhancers	HSMMtube	muscle
31	chr3:46734000-46734400	Enhancers	NH-A	brain
32	chr3:46734000-46734600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
33	chr3:46734000-46734600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:46734000-46734600	Flanking Active TSS	Colonic Mucosa	Colon
35	chr3:46734000-46734600	Enhancers	Fetal Heart	heart
36	chr3:46734000-46734600	Flanking Active TSS	Left Ventricle	heart
37	chr3:46734000-46734600	Flanking Active TSS	Right Ventricle	heart
38	chr3:46734000-46734600	Flanking Active TSS	A549	lung
39	chr3:46734000-46734800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
40	chr3:46734000-46734800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr3:46734000-46734800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:46734000-46734800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:46734000-46734800	Flanking Active TSS	Pancreas	Pancrea
44	chr3:46734000-46734800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr3:46734000-46735000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr3:46734000-46735000	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr3:46734000-46735000	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr3:46734000-46735000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr3:46734000-46735600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:46734000-46735600	Active TSS	Breast Myoepithelial Primary Cells	Breast

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