Variant report

Variant	rs149015999
Chromosome Location	chr12:56583679-56583680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:279)
CpG islands
(count:0)
Chromatin interactive
region (count:45)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:279 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIX5	chr12:56583579-56584832	A549	lung:	n/a	chr12:56583689-56583698
2	JUN	chr12:56583058-56584365	K562	blood:	n/a	n/a
3	TAF1	chr12:56582972-56583695	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr12:56583180-56583782	A549	lung:	n/a	chr12:56583493-56583512 chr12:56583604-56583618
5	POLR2A	chr12:56583047-56584255	NB4	blood:	n/a	n/a
6	POLR2A	chr12:56582901-56584409	MCF-7	breast:	n/a	n/a
7	MAZ	chr12:56583127-56584202	Hela-S3	cervix:	n/a	n/a
8	ELF1	chr12:56583001-56584410	MCF-7	breast:	n/a	chr12:56583454-56583463 chr12:56583411-56583420 chr12:56583461-56583473 chr12:56584070-56584079 chr12:56584068-56584081
9	CTCF	chr12:56583214-56584193	K562	blood:	n/a	chr12:56583492-56583510 chr12:56583495-56583508
10	TAF1	chr12:56582972-56584331	K562	blood:	n/a	n/a
11	YY1	chr12:56582672-56583689	K562	blood:	n/a	chr12:56583411-56583420 chr12:56583235-56583255 chr12:56583457-56583471 chr12:56583423-56583437 chr12:56583405-56583419 chr12:56583412-56583423
12	CTCF	chr12:56583560-56583710	A549	lung:	n/a	n/a
13	POLR2A	chr12:56583446-56583726	HepG2	liver:	n/a	n/a
14	E2F6	chr12:56583359-56583734	A549	lung:	n/a	chr12:56583544-56583555
15	SIN3A	chr12:56582408-56584283	H1-hESC	embryonic stem cell:	n/a	n/a
16	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
17	POLR2A	chr12:56583111-56584216	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:56583377-56584248	HUVEC	blood vessel:	n/a	n/a
19	MAX	chr12:56582658-56584985	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr12:56583040-56584266	GM19099	blood:	n/a	n/a
21	MAX	chr12:56583127-56584256	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:56583403-56584384	SK-N-MC	brain:	n/a	n/a
23	USF1	chr12:56583281-56583680	A549	lung:	n/a	chr12:56583405-56583421
24	MAX	chr12:56582920-56584302	HepG2	liver:	n/a	n/a
25	RAD21	chr12:56583241-56583777	H1-hESC	embryonic stem cell:	n/a	chr12:56583493-56583512 chr12:56583604-56583618
26	POLR2A	chr12:56583361-56584245	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:56583424-56584129	U87	brain:	n/a	n/a
28	POLR2A	chr12:56583454-56584222	Hela-S3	cervix:	n/a	n/a
29	ELK1	chr12:56583138-56584291	GM12878	blood:	n/a	chr12:56584069-56584078 chr12:56584069-56584078
30	TEAD4	chr12:56583004-56584541	SK-N-SH	brain:	n/a	n/a
31	GABPA	chr12:56583046-56584407	MCF-7	breast:	n/a	n/a
32	POLR2A	chr12:56583034-56584274	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr12:56583013-56583693	PANC-1	pancreas:	n/a	n/a
34	NFIC	chr12:56583367-56584412	GM12878	blood:	n/a	n/a
35	TAF1	chr12:56583013-56584299	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr12:56583476-56584161	HCT-116	colon:	n/a	n/a
37	FOXM1	chr12:56583229-56584381	GM12878	blood:	n/a	n/a
38	TBP	chr12:56583434-56584419	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr12:56583288-56583703	GM12891	blood:	n/a	chr12:56583492-56583510 chr12:56583495-56583508
40	MXI1	chr12:56583185-56584298	HepG2	liver:	n/a	n/a
41	POLR2A	chr12:56583043-56584244	Raji	blood:	n/a	n/a
42	SMC3	chr12:56583222-56583683	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr12:56583194-56583954	A549	lung:	n/a	chr12:56583492-56583510 chr12:56583495-56583508
44	TEAD4	chr12:56583083-56584504	ECC-1	luminal epithelium:	n/a	n/a
45	MAX	chr12:56582472-56584998	A549	lung:	n/a	n/a
46	POLR2A	chr12:56582964-56584375	HUVEC	blood vessel:	n/a	n/a
47	MYBL2	chr12:56583262-56584427	HepG2	liver:	n/a	n/a
48	CTCF	chr12:56583054-56584104	K562	blood:	n/a	chr12:56583492-56583510 chr12:56583495-56583508
49	SMARCB1	chr12:56583108-56584179	Hela-S3	cervix:	n/a	n/a
50	PML	chr12:56583061-56584370	GM12878	blood:	n/a	n/a

No data

(count:45 , 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	chr12:56511802..56513894-chr12:56582502..56584213,17	K562	blood:
7	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
8	chr12:56434274..56437218-chr12:56582509..56584521,4	MCF-7	breast:
9	chr12:56582327..56583849-chr12:56861847..56864785,2	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	chr12:56583290..56583861-chr12:56615727..56616256,2	K562	blood:
21	chr12:56583235..56585154-chr12:56650552..56653890,4	MCF-7	breast:
22	chr12:56583524..56584056-chr14:51410711..51411291,2	Hela-S3	cervix:
23	chr12:56518236..56525779-chr12:56581707..56584752,14	MCF-7	breast:
24	chr12:56582670..56585645-chr12:56588160..56590728,3	MCF-7	breast:
25	chr12:56580530..56583816-chr12:56859558..56862740,3	K562	blood:
26	chr12:56583418..56584005-chr12:56651692..56652463,2	MCF-7	breast:
27	chr12:56434529..56437485-chr12:56581091..56583996,4	K562	blood:
28	chr12:56512788..56513764-chr12:56582958..56583860,7	MCF-7	breast:
29	chr12:56582633..56585522-chr12:56623000..56624592,2	MCF-7	breast:
30	chr12:56579883..56589030-chr12:56613342..56620091,21	MCF-7	breast:
31	chr12:56583246..56583812-chr12:56617774..56618395,2	MCF-7	breast:
32	chr12:56568053..56570139-chr12:56582886..56584432,2	MCF-7	breast:
33	chr12:56508832..56515879-chr12:56578376..56587782,37	MCF-7	breast:
34	chr12:56582213..56584132-chr12:56708371..56710862,2	MCF-7	breast:
35	chr12:56583291..56584232-chr12:56617785..56618516,2	MCF-7	breast:
36	chr12:56551518..56552159-chr12:56582778..56583751,4	MCF-7	breast:
37	chr12:56583086..56583882-chr3:54156501..54157004,2	K562	blood:
38	chr12:56576539..56578813-chr12:56582057..56584361,3	MCF-7	breast:
39	chr12:56473891..56477008-chr12:56583227..56585798,3	MCF-7	breast:
40	chr12:56471914..56476515-chr12:56581933..56586574,4	MCF-7	breast:
41	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:
42	chr12:56480948..56483944-chr12:56582412..56584224,2	MCF-7	breast:
43	chr12:56582084..56583845-chr12:56753291..56755155,2	MCF-7	breast:
44	chr12:56582392..56584464-chr12:56753681..56756139,2	MCF-7	breast:
45	chr12:56583077..56583903-chr12:56651754..56652414,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMARCC2	TF binding region
ENSG00000196465	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000100504	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000266023	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000006194	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000157445	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000063169	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000139579	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	chr12:56582200-56583800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:56582200-56584200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:56582200-56584200	Active TSS	Aorta	Aorta
15	chr12:56582200-56584200	Active TSS	Lung	lung
16	chr12:56582200-56584200	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr12:56582200-56584400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:56582200-56584400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:56582200-56584400	Active TSS	Fetal Brain Male	brain
20	chr12:56582200-56584400	Active TSS	Fetal Brain Female	brain
21	chr12:56582200-56584400	Active TSS	A549	lung
22	chr12:56582200-56584400	Active TSS	NHDF-Ad	bronchial
23	chr12:56582200-56584600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:56582200-56584600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:56582200-56584600	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr12:56582200-56584600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:56582200-56584600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:56582200-56584600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr12:56582200-56584600	Active TSS	Thymus	Thymus
30	chr12:56582200-56584800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:56582200-56584800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:56582200-56584800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:56582200-56584800	Active TSS	Ovary	ovary
34	chr12:56582200-56585000	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr12:56582200-56585000	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr12:56582400-56584200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:56582400-56584200	Active TSS	Small Intestine	intestine
38	chr12:56582400-56584400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:56582400-56584400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:56582400-56584400	Active TSS	Esophagus	oesophagus
41	chr12:56582400-56584400	Active TSS	Rectal Smooth Muscle	rectum
42	chr12:56582400-56584600	Active TSS	H9 Cell Line	embryonic stem cell
43	chr12:56582400-56584600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr12:56582400-56584600	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr12:56582400-56584600	Active TSS	Brain Angular Gyrus	brain
46	chr12:56582400-56584600	Active TSS	Brain Cingulate Gyrus	brain
47	chr12:56582400-56584600	Active TSS	Colon Smooth Muscle	Colon
48	chr12:56582400-56584600	Active TSS	Fetal Intestine Large	intestine
49	chr12:56582400-56584600	Active TSS	Fetal Intestine Small	intestine
50	chr12:56582400-56584600	Active TSS	Pancreas	Pancrea

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