Variant report

Variant	rs12019047
Chromosome Location	chr16:12707590-12707591
allele	C/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	ATF3	chr16:12707553-12707788	K562	blood:	n/a	n/a
2	FOXA1	chr16:12706252-12708264	HepG2	liver:	n/a	n/a
3	RCOR1	chr16:12706536-12707757	K562	blood:	n/a	n/a
4	GATA2	chr16:12707370-12707841	K562	blood:	n/a	n/a
5	FOXM1	chr16:12707561-12707911	MCF-7	breast:	n/a	n/a
6	POLR2A	chr16:12707587-12708221	HepG2	liver:	n/a	n/a
7	EP300	chr16:12707422-12707899	K562	blood:	n/a	n/a
8	CEBPB	chr16:12707347-12708054	HCT-116	colon:	n/a	n/a
9	EP300	chr16:12706229-12708381	HepG2	liver:	n/a	n/a
10	GATA3	chr16:12707236-12708046	SK-N-SH	brain:	n/a	n/a
11	HNF4A	chr16:12707096-12707814	HepG2	liver:	n/a	chr16:12707395-12707409 chr16:12707395-12707409 chr16:12707396-12707409 chr16:12707395-12707408 chr16:12707395-12707409 chr16:12707396-12707408 chr16:12707394-12707409 chr16:12707393-12707411 chr16:12707396-12707408
12	USF1	chr16:12707569-12707876	K562	blood:	n/a	chr16:12707657-12707668 chr16:12707685-12707696
13	GATA3	chr16:12707078-12707949	MCF-7	breast:	n/a	n/a
14	JUN	chr16:12706488-12708204	HepG2	liver:	n/a	n/a
15	HNF4A	chr16:12707034-12707896	HepG2	liver:	n/a	chr16:12707395-12707409 chr16:12707395-12707409 chr16:12707396-12707409 chr16:12707395-12707408 chr16:12707395-12707409 chr16:12707396-12707408 chr16:12707394-12707409 chr16:12707393-12707411 chr16:12707396-12707408
16	PAX5	chr16:12707204-12707924	GM12878	blood:	n/a	n/a
17	EP300	chr16:12706434-12708296	HepG2	liver:	n/a	n/a
18	REST	chr16:12707020-12708185	A549	lung:	n/a	n/a
19	PML	chr16:12707235-12708035	GM12878	blood:	n/a	n/a
20	FOXM1	chr16:12707151-12707979	GM12878	blood:	n/a	n/a
21	MAX	chr16:12706139-12708451	A549	lung:	n/a	n/a
22	MAX	chr16:12707108-12708209	HepG2	liver:	n/a	n/a
23	EP300	chr16:12707039-12707944	GM12878	blood:	n/a	n/a
24	PBX3	chr16:12707553-12707946	SK-N-SH	brain:	n/a	n/a
25	TCF7L2	chr16:12707216-12707892	HCT-116	colon:	n/a	chr16:12707399-12707409 chr16:12707399-12707406 chr16:12707398-12707407 chr16:12707395-12707411 chr16:12707399-12707408 chr16:12707395-12707411
26	FOSL2	chr16:12707442-12707970	MCF-7	breast:	n/a	n/a
27	JUND	chr16:12707211-12708380	HCT-116	colon:	n/a	chr16:12707672-12707683 chr16:12707700-12707711
28	SRF	chr16:12707393-12708130	HCT-116	colon:	n/a	n/a
29	BCL3	chr16:12707411-12707905	GM12878	blood:	n/a	n/a
30	FOS	chr16:12707500-12708007	MCF10A-Er-Src	breast:	n/a	chr16:12707700-12707711 chr16:12707672-12707683
31	ATF3	chr16:12707254-12707910	A549	lung:	n/a	n/a
32	FOS	chr16:12707516-12707869	MCF10A-Er-Src	breast:	n/a	chr16:12707700-12707711 chr16:12707672-12707683
33	TBL1XR1	chr16:12707579-12707762	K562	blood:	n/a	n/a
34	GATA3	chr16:12707255-12708078	MCF-7	breast:	n/a	n/a
35	EP300	chr16:12706287-12708137	HepG2	liver:	n/a	n/a
36	MAX	chr16:12707403-12708024	HCT-116	colon:	n/a	n/a
37	USF1	chr16:12707537-12707811	HepG2	liver:	n/a	chr16:12707657-12707668 chr16:12707685-12707696
38	USF2	chr16:12707527-12707870	GM12878	blood:	n/a	chr16:12707685-12707696 chr16:12707657-12707668
39	HNF4A	chr16:12706874-12707896	HepG2	liver:	n/a	chr16:12707395-12707409 chr16:12707395-12707409 chr16:12707396-12707409 chr16:12707395-12707408 chr16:12707395-12707409 chr16:12707396-12707408 chr16:12707394-12707409 chr16:12707393-12707411 chr16:12707396-12707408
40	POLR2A	chr16:12707471-12707860	K562	blood:	n/a	n/a
41	SMC3	chr16:12706452-12708092	HepG2	liver:	n/a	n/a
42	CUX1	chr16:12707256-12707779	K562	blood:	n/a	n/a
43	HEY1	chr16:12706306-12708350	HepG2	liver:	n/a	n/a
44	JUND	chr16:12707241-12707952	HepG2	liver:	n/a	chr16:12707672-12707683 chr16:12707700-12707711
45	FOXA1	chr16:12706997-12707917	HepG2	liver:	n/a	n/a
46	BATF	chr16:12707465-12707911	GM12878	blood:	n/a	chr16:12707702-12707713
47	JUND	chr16:12707543-12707926	A549	lung:	n/a	chr16:12707672-12707683 chr16:12707700-12707711
48	JUND	chr16:12707369-12708153	SK-N-SH	brain:	n/a	chr16:12707672-12707683 chr16:12707700-12707711
49	HDAC2	chr16:12707562-12707825	K562	blood:	n/a	n/a
50	SP1	chr16:12707182-12707855	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:12705362..12710268-chr16:12710311..12712475,5	K562	blood:
2	chr16:12705693..12708514-chr16:12893374..12897390,4	K562	blood:
3	chr16:12707551..12710268-chr16:12710403..12713580,3	K562	blood:

Variant related genes	Relation type
ENSG00000259899	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10500385	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28446620	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55678008	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55714446	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56004828	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68121083	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7186689	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7198969	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7199918	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72777091	0.80[EUR][1000 genomes]
rs8063508	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9925735	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9936556	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic 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 miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv437802	chr16:12667076-12708294	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv571469	chr16:12670401-12715480	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1804537	chr16:12671491-12708186	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv18351	chr16:12674207-12734557	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2757629	chr16:12676745-12712199	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2758631	chr16:12676745-12712199	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv1812058	chr16:12680270-12712059	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv9351	chr16:12681377-12708042	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1051014	chr16:12683657-12722792	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv2760435	chr16:12690859-12707737	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1048793	chr16:12690859-12707737	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1037906	chr16:12690859-12708208	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv1045233	chr16:12690859-12708294	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv1041721	chr16:12690859-12708403	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	esv1811848	chr16:12691643-12708186	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	esv1808513	chr16:12691653-12711233	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	esv1813801	chr16:12691653-12711233	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv905351	chr16:12697211-12721188	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv471083	chr16:12704140-12714394	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv457422	chr16:12705930-12711025	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv571478	chr16:12705930-12711025	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	esv1819970	chr16:12705930-12712304	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12703800-12708000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr16:12704000-12708800	Enhancers	Placenta	Placenta
3	chr16:12704200-12708400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:12704600-12708200	Enhancers	NHEK	skin
5	chr16:12704800-12709400	Enhancers	Fetal Intestine Large	intestine
6	chr16:12705000-12707800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr16:12705000-12709000	Enhancers	Fetal Intestine Small	intestine
8	chr16:12706000-12708800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr16:12706200-12708000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:12706400-12708200	Enhancers	NH-A	brain
11	chr16:12706400-12708400	Flanking Active TSS	HepG2	liver
12	chr16:12706400-12708400	Enhancers	HMEC	breast
13	chr16:12706400-12709000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr16:12706400-12709000	Enhancers	Fetal Thymus	thymus
15	chr16:12706600-12707600	Enhancers	Dnd41	blood
16	chr16:12706600-12708200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr16:12706600-12708200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr16:12706600-12708600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr16:12706600-12708600	Enhancers	Thymus	Thymus
20	chr16:12706600-12708600	Enhancers	GM12878-XiMat	blood
21	chr16:12706600-12708800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:12706800-12707600	Flanking Active TSS	K562	blood
23	chr16:12706800-12708800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr16:12707000-12708000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr16:12707000-12708400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr16:12707200-12707600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:12707200-12707600	Active TSS	A549	lung
28	chr16:12707200-12707800	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr16:12707200-12708000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr16:12707200-12708000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr16:12707200-12708200	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr16:12707200-12708400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr16:12707200-12708400	Enhancers	Liver	Liver
34	chr16:12707200-12708400	Bivalent Enhancer	Hela-S3	cervix
35	chr16:12707200-12709000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr16:12707400-12707800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr16:12707400-12708000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr16:12707400-12708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr16:12707400-12708800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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