Variant report

Variant	rs566520960
Chromosome Location	chr12:56583939-56583940
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:378)
CpG islands
(count:0)
Chromatin interactive
region (count:37)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:378 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr12:56583888-56584176	HepG2	liver:	n/a	n/a
2	ELK1	chr12:56583876-56584263	Hela-S3	cervix:	n/a	chr12:56584069-56584078 chr12:56584069-56584078
3	SIX5	chr12:56583579-56584832	A549	lung:	n/a	chr12:56583689-56583698
4	JUN	chr12:56583058-56584365	K562	blood:	n/a	n/a
5	MXI1	chr12:56583810-56584219	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr12:56583833-56583946	Spleen_OC	spleen:	n/a	n/a
7	POLR2A	chr12:56583047-56584255	NB4	blood:	n/a	n/a
8	TEAD4	chr12:56583853-56584226	H1-hESC	embryonic stem cell:	n/a	n/a
9	ETS1	chr12:56583767-56584255	GM12878	blood:	n/a	chr12:56584069-56584078 chr12:56584069-56584078 chr12:56584069-56584078 chr12:56584069-56584078 chr12:56584070-56584079 chr12:56583863-56583877 chr12:56584069-56584078 chr12:56584069-56584078 chr12:56584071-56584080
10	POLR2A	chr12:56582901-56584409	MCF-7	breast:	n/a	n/a
11	SMC3	chr12:56583884-56584211	K562	blood:	n/a	n/a
12	SP1	chr12:56583874-56584366	H1-hESC	embryonic stem cell:	n/a	n/a
13	BDP1	chr12:56583888-56584344	Hela-S3	cervix:	n/a	n/a
14	MAX	chr12:56583758-56584344	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAZ	chr12:56583127-56584202	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:56583785-56584194	A549	lung:	n/a	n/a
17	JUND	chr12:56583828-56584403	A549	lung:	n/a	n/a
18	ELF1	chr12:56583001-56584410	MCF-7	breast:	n/a	chr12:56583454-56583463 chr12:56583411-56583420 chr12:56583461-56583473 chr12:56584070-56584079 chr12:56584068-56584081
19	CTCF	chr12:56583214-56584193	K562	blood:	n/a	chr12:56583492-56583510 chr12:56583495-56583508
20	ZBTB33	chr12:56583763-56584344	A549	lung:	n/a	n/a
21	TAF1	chr12:56582972-56584331	K562	blood:	n/a	n/a
22	MXI1	chr12:56583918-56584283	K562	blood:	n/a	n/a
23	RFX5	chr12:56583798-56584300	K562	blood:	n/a	n/a
24	SIN3A	chr12:56582408-56584283	H1-hESC	embryonic stem cell:	n/a	n/a
25	ETS1	chr12:56583384-56584460	A549	lung:	n/a	chr12:56584069-56584078 chr12:56584069-56584078 chr12:56583412-56583423 chr12:56584069-56584078 chr12:56584069-56584078 chr12:56584070-56584079 chr12:56583863-56583877 chr12:56584069-56584078 chr12:56584069-56584078 chr12:56584071-56584080
26	CHD2	chr12:56583930-56584298	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr12:56583111-56584216	GM12878	blood:	n/a	n/a
28	POU2F2	chr12:56583800-56584329	GM12891	blood:	n/a	n/a
29	CREB1	chr12:56583721-56584363	H1-hESC	embryonic stem cell:	n/a	n/a
30	RCOR1	chr12:56583858-56584304	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:56583377-56584248	HUVEC	blood vessel:	n/a	n/a
32	ATF3	chr12:56583837-56584368	K562	blood:	n/a	n/a
33	MAX	chr12:56582658-56584985	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr12:56583040-56584266	GM19099	blood:	n/a	n/a
35	MAX	chr12:56583127-56584256	GM12878	blood:	n/a	n/a
36	TEAD4	chr12:56583751-56584430	HepG2	liver:	n/a	n/a
37	POLR2A	chr12:56583403-56584384	SK-N-MC	brain:	n/a	n/a
38	NFYB	chr12:56583869-56583962	Hela-S3	cervix:	n/a	n/a
39	MAX	chr12:56582920-56584302	HepG2	liver:	n/a	n/a
40	CTCF	chr12:56583718-56583956	GM12891	blood:	n/a	n/a
41	CTCF	chr12:56583788-56583959	GM19240	blood:	n/a	n/a
42	CUX1	chr12:56583915-56584216	K562	blood:	n/a	n/a
43	FOSL2	chr12:56583762-56584412	MCF-7	breast:	n/a	n/a
44	POLR2A	chr12:56583786-56584173	HepG2	liver:	n/a	n/a
45	POLR2A	chr12:56583361-56584245	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr12:56583424-56584129	U87	brain:	n/a	n/a
47	POLR2A	chr12:56583454-56584222	Hela-S3	cervix:	n/a	n/a
48	GABPA	chr12:56583817-56584198	HepG2	liver:	n/a	n/a
49	ELK1	chr12:56583138-56584291	GM12878	blood:	n/a	chr12:56584069-56584078 chr12:56584069-56584078
50	TEAD4	chr12:56583004-56584541	SK-N-SH	brain:	n/a	n/a

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56583397..56584102-chr19:48111105..48111640,2	NB4	blood:
2	chr12:56582602..56584136-chr12:56615794..56617313,2	K562	blood:
3	chr12:56583197..56585219-chr12:56650966..56653576,3	MCF-7	breast:
4	chr12:56434140..56437753-chr12:56579716..56586472,8	K562	blood:
5	chr12:56512777..56513734-chr12:56583353..56584069,3	MCF-7	breast:
6	chr12:56583715..56585705-chr12:56588416..56589988,2	K562	blood:
7	chr12:56511802..56513894-chr12:56582502..56584213,17	K562	blood:
8	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
9	chr12:56434274..56437218-chr12:56582509..56584521,4	MCF-7	breast:
10	chr12:56573305..56575645-chr12:56580157..56583977,4	MCF-7	breast:
11	chr12:56583529..56586106-chr12:57117314..57120068,2	MCF-7	breast:
12	chr12:56473548..56475475-chr12:56582788..56585025,2	K562	blood:
13	chr12:56581127..56584994-chr12:56605345..56610385,5	MCF-7	breast:
14	chr12:56583501..56584230-chr16:3333583..3334447,2	Hela-S3	cervix:
15	chr12:56507991..56525761-chr12:56579808..56586137,68	MCF-7	breast:
16	chr12:56543953..56550163-chr12:56578779..56585351,11	MCF-7	breast:
17	chr12:56582915..56585012-chr12:56659471..56660986,2	K562	blood:
18	chr12:56581557..56584767-chr12:56708519..56710789,3	K562	blood:
19	chr12:56582602..56584894-chr12:56615504..56618371,3	K562	blood:
20	chr12:56583235..56585154-chr12:56650552..56653890,4	MCF-7	breast:
21	chr12:56583524..56584056-chr14:51410711..51411291,2	Hela-S3	cervix:
22	chr12:56518236..56525779-chr12:56581707..56584752,14	MCF-7	breast:
23	chr12:56582670..56585645-chr12:56588160..56590728,3	MCF-7	breast:
24	chr12:56583418..56584005-chr12:56651692..56652463,2	MCF-7	breast:
25	chr12:56434529..56437485-chr12:56581091..56583996,4	K562	blood:
26	chr12:56582633..56585522-chr12:56623000..56624592,2	MCF-7	breast:
27	chr12:56579883..56589030-chr12:56613342..56620091,21	MCF-7	breast:
28	chr12:56568053..56570139-chr12:56582886..56584432,2	MCF-7	breast:
29	chr12:56508832..56515879-chr12:56578376..56587782,37	MCF-7	breast:
30	chr12:56582213..56584132-chr12:56708371..56710862,2	MCF-7	breast:
31	chr12:56583291..56584232-chr12:56617785..56618516,2	MCF-7	breast:
32	chr12:56576539..56578813-chr12:56582057..56584361,3	MCF-7	breast:
33	chr12:56473891..56477008-chr12:56583227..56585798,3	MCF-7	breast:
34	chr12:56471914..56476515-chr12:56581933..56586574,4	MCF-7	breast:
35	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:
36	chr12:56480948..56483944-chr12:56582412..56584224,2	MCF-7	breast:
37	chr12:56582392..56584464-chr12:56753681..56756139,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMARCC2-1	chr12:56583857-56584068	ENSG00000258199.1

No data

Variant related genes	Relation type
SMARCC2	TF binding region
RN7SL770P	TF binding region
ENSG00000266023	Chromatin interaction
ENSG00000006194	Chromatin interaction
ENSG00000063169	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000100504	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000257727	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	esv1792521	chr12:56575188-56587576	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	esv3389557	chr12:56581710-56584658	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv3492532	chr12:56582085-56584833	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	esv3492533	chr12:56582085-56584833	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv973989	chr12:56582243-56602996	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 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	chr12:56581400-56584600	Active TSS	Fetal Kidney	kidney
2	chr12:56581400-56584800	Active TSS	Colonic Mucosa	Colon
3	chr12:56581800-56584600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:56582000-56584600	Active TSS	GM12878-XiMat	blood
5	chr12:56582000-56584800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr12:56582000-56584800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:56582000-56584800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:56582000-56584800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr12:56582000-56584800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:56582000-56584800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr12:56582000-56585000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr12:56582200-56584200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:56582200-56584200	Active TSS	Aorta	Aorta
14	chr12:56582200-56584200	Active TSS	Lung	lung
15	chr12:56582200-56584200	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr12:56582200-56584400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:56582200-56584400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:56582200-56584400	Active TSS	Fetal Brain Male	brain
19	chr12:56582200-56584400	Active TSS	Fetal Brain Female	brain
20	chr12:56582200-56584400	Active TSS	A549	lung
21	chr12:56582200-56584400	Active TSS	NHDF-Ad	bronchial
22	chr12:56582200-56584600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:56582200-56584600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:56582200-56584600	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr12:56582200-56584600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:56582200-56584600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:56582200-56584600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr12:56582200-56584600	Active TSS	Thymus	Thymus
29	chr12:56582200-56584800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:56582200-56584800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:56582200-56584800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:56582200-56584800	Active TSS	Ovary	ovary
33	chr12:56582200-56585000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr12:56582200-56585000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr12:56582400-56584200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:56582400-56584200	Active TSS	Small Intestine	intestine
37	chr12:56582400-56584400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:56582400-56584400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:56582400-56584400	Active TSS	Esophagus	oesophagus
40	chr12:56582400-56584400	Active TSS	Rectal Smooth Muscle	rectum
41	chr12:56582400-56584600	Active TSS	H9 Cell Line	embryonic stem cell
42	chr12:56582400-56584600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr12:56582400-56584600	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr12:56582400-56584600	Active TSS	Brain Angular Gyrus	brain
45	chr12:56582400-56584600	Active TSS	Brain Cingulate Gyrus	brain
46	chr12:56582400-56584600	Active TSS	Colon Smooth Muscle	Colon
47	chr12:56582400-56584600	Active TSS	Fetal Intestine Large	intestine
48	chr12:56582400-56584600	Active TSS	Fetal Intestine Small	intestine
49	chr12:56582400-56584600	Active TSS	Pancreas	Pancrea
50	chr12:56582400-56584600	Active TSS	K562	blood

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