Variant report

Variant	esv3435443
Chromosome Location	chr12:41206734-41222972
allele	n/a
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	ATF2	chr12:41213368-41213748	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr12:41213311-41213590	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr12:41212956-41213785	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr12:41219800-41219950	HRE	kidney:	n/a	chr12:41219858-41219868
5	FOXP2	chr12:41213151-41213659	SK-N-MC	brain:	n/a	n/a
6	GTF2F1	chr12:41213483-41213499	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUN	chr12:41214636-41214970	HepG2	liver:	n/a	chr12:41214795-41214804 chr12:41214791-41214804
8	JUND	chr12:41214609-41214987	HepG2	liver:	n/a	chr12:41214795-41214804
9	JUND	chr12:41213384-41213697	H1-hESC	embryonic stem cell:	n/a	n/a
10	KAP1	chr12:41213182-41213690	U2OS	brain:	n/a	n/a
11	KAP1	chr12:41213051-41213763	HEK293	kidney:	n/a	n/a
12	MAFF	chr12:41222022-41222339	HepG2	liver:	n/a	chr12:41222145-41222163
13	MAFF	chr12:41222042-41222251	K562	blood:	n/a	chr12:41222145-41222163
14	MAFK	chr12:41221987-41222290	HepG2	liver:	n/a	chr12:41222150-41222166 chr12:41222147-41222163 chr12:41222148-41222159 chr12:41222147-41222158 chr12:41222146-41222160 chr12:41222147-41222162 chr12:41222147-41222158 chr12:41222151-41222165 chr12:41222148-41222168
15	MAFK	chr12:41222103-41222254	H1-hESC	embryonic stem cell:	n/a	chr12:41222150-41222166 chr12:41222147-41222163 chr12:41222148-41222159 chr12:41222147-41222158 chr12:41222146-41222160 chr12:41222147-41222162 chr12:41222147-41222158 chr12:41222151-41222165 chr12:41222148-41222168
16	MAFK	chr12:41222129-41222292	K562	blood:	n/a	chr12:41222150-41222166 chr12:41222147-41222163 chr12:41222148-41222159 chr12:41222147-41222158 chr12:41222146-41222160 chr12:41222147-41222162 chr12:41222147-41222158 chr12:41222151-41222165 chr12:41222148-41222168
17	MAFK	chr12:41222037-41222307	IMR90	lung:	n/a	chr12:41222150-41222166 chr12:41222147-41222163 chr12:41222148-41222159 chr12:41222147-41222158 chr12:41222146-41222160 chr12:41222147-41222162 chr12:41222147-41222158 chr12:41222151-41222165 chr12:41222148-41222168
18	MAFK	chr12:41221988-41222328	HepG2	liver:	n/a	chr12:41222150-41222166 chr12:41222147-41222163 chr12:41222148-41222159 chr12:41222147-41222158 chr12:41222146-41222160 chr12:41222147-41222162 chr12:41222147-41222158 chr12:41222151-41222165 chr12:41222148-41222168
19	MAFK	chr12:41222030-41222193	Hela-S3	cervix:	n/a	chr12:41222150-41222166 chr12:41222147-41222163 chr12:41222148-41222159 chr12:41222147-41222158 chr12:41222146-41222160 chr12:41222147-41222162 chr12:41222147-41222158 chr12:41222151-41222165 chr12:41222148-41222168
20	MXI1	chr12:41218994-41219053	K562	blood:	n/a	n/a
21	NANOG	chr12:41213243-41213559	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:41213272-41213567	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr12:41213363-41213511	A549	lung:	n/a	n/a
24	POLR2A	chr12:41221582-41222264	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr12:41213376-41213674	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr12:41213261-41213535	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr12:41222399-41222478	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr12:41213628-41213718	A549	lung:	n/a	n/a
29	POLR2A	chr12:41213167-41213708	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr12:41221621-41222234	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr12:41213688-41213693	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr12:41208681-41208923	Hela-S3	cervix:	n/a	n/a
33	RAD21	chr12:41213216-41213588	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr12:41213156-41213591	H1-hESC	embryonic stem cell:	n/a	n/a
35	REST	chr12:41221245-41222456	H1-neurons	neurons:	n/a	chr12:41221944-41221957
36	SP1	chr12:41213196-41213698	H1-hESC	embryonic stem cell:	n/a	n/a
37	STAT3	chr12:41217922-41218089	MCF10A-Er-Src	breast:	n/a	n/a
38	TAF1	chr12:41213291-41213553	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF12	chr12:41213312-41213582	H1-hESC	embryonic stem cell:	n/a	n/a
40	TCF12	chr12:41213303-41213574	H1-hESC	embryonic stem cell:	n/a	n/a
41	TEAD4	chr12:41213244-41213632	H1-hESC	embryonic stem cell:	n/a	n/a
42	TEAD4	chr12:41213266-41213695	H1-hESC	embryonic stem cell:	n/a	n/a
43	ZNF143	chr12:41213348-41213613	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:41221639-41221689	AG09309	skin:	n/a
2	chr12:41221639-41221689	AG09309	skin:	n/a
3	chr12:41221855-41221905	SK-N-SH	brain:	n/a
4	chr12:41221855-41221905	NHDF-neo	bronchial:	n/a
5	chr12:41221639-41221689	HCF	heart:	n/a
6	chr12:41221855-41221905	A549	lung:	n/a
7	chr12:41221639-41221689	HCM	heart:	n/a
8	chr12:41221855-41221905	BJ	skin:	n/a
9	chr12:41221689-41221739	GM06990	blood:	n/a
10	chr12:41221639-41221689	CMK	blood:	n/a
11	chr12:41221689-41221739	PFSK-1	brain:	n/a
12	chr12:41221639-41221689	NH-A	brain:	n/a
13	chr12:41221639-41221689	MCF-7	breast:	n/a
14	chr12:41221855-41221905	PANC-1	pancreas:	n/a
15	chr12:41221855-41221905	HEK293	kidney:	embryo
16	chr12:41221689-41221739	GM12892	blood:	n/a
17	chr12:41221855-41221905	ECC-1	luminal epithelium:	n/a
18	chr12:41221689-41221739	AG04450	lung:	fetal
19	chr12:41221689-41221739	NB4	blood:	n/a
20	chr12:41221855-41221905	GM12891	blood:	n/a
21	chr12:41221855-41221905	PrEC	prostate:	n/a
22	chr12:41221639-41221689	HepG2	liver:	n/a
23	chr12:41221689-41221739	HL-60	blood:	n/a
24	chr12:41221689-41221739	SK-N-MC	brain:	n/a
25	chr12:41221639-41221689	AG04450	lung:	fetal
26	chr12:41221689-41221739	PANC-1	pancreas:	n/a
27	chr12:41221639-41221689	HIPEpiC	eye:	n/a
28	chr12:41221855-41221905	HNPCEpiC	eye:	n/a
29	chr12:41221855-41221905	HCF	heart:	n/a
30	chr12:41221689-41221739	LNCaP	prostate:	n/a
31	chr12:41221689-41221739	HIPEpiC	eye:	n/a
32	chr12:41221639-41221689	GM12892	blood:	n/a
33	chr12:41221689-41221739	HPAEpiC	pulmonary alveolar:	n/a
34	chr12:41221689-41221739	Jurkat	blood:	n/a
35	chr12:41221855-41221905	MCF-7	breast:	n/a
36	chr12:41221689-41221739	HMEC	breast:	n/a
37	chr12:41221639-41221689	AG09319	gingival:	n/a
38	chr12:41221689-41221739	NHBE	bronchial:	n/a
39	chr12:41221689-41221739	SK-N-SH	brain:	n/a
40	chr12:41221855-41221905	K562	blood:	n/a
41	chr12:41221855-41221905	SK-N-SH_RA	brain:	n/a
42	chr12:41221639-41221689	HRPEpiC	eye:	n/a
43	chr12:41221689-41221739	HEK293	kidney:	embryo
44	chr12:41221639-41221689	ovcar-3	ovarian:	n/a
45	chr12:41221639-41221689	GM12878	blood:	n/a
46	chr12:41221855-41221905	HCPEpiC	choroid plexus:	n/a
47	chr12:41221639-41221689	NT2-D1	testis:	n/a
48	chr12:41221855-41221905	NB4	blood:	n/a
49	chr12:41221855-41221905	SK-N-MC	brain:	n/a
50	chr12:41221855-41221905	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:41222882..41225557-chr7:143112465..143114503,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC19-5	chr12:41221897-41222103	NONHSAT027744

Variant related genes	Relation type
CNTN1	TF binding region
CNTN1	CpG island

Extended variants
information (count: 462 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:462 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200971729	chr12:41211414-41211415	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs184598703	chr12:41211432-41211433	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs141450707	chr12:41211468-41211469	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs188473940	chr12:41211491-41211492	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs372261630	chr12:41211508-41211509	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs536846250	chr12:41211516-41211517	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs116521802	chr12:41211548-41211549	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs573701963	chr12:41211587-41211588	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs151211647	chr12:41211682-41211683	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs12146736	chr12:41211733-41211734	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs11178530	chr12:41211874-41211875	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs150847377	chr12:41211891-41211892	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs577543948	chr12:41211928-41211929	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs139321365	chr12:41211932-41211933	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs58649501	chr12:41211981-41211982	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs575151164	chr12:41212005-41212006	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs542436679	chr12:41212016-41212017	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs570122042	chr12:41212086-41212087	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs74777273	chr12:41212099-41212100	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs528622692	chr12:41212117-41212118	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs114891440	chr12:41212190-41212191	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs375061617	chr12:41212222-41212223	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs530946312	chr12:41212242-41212243	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs565329983	chr12:41212289-41212290	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs532390296	chr12:41212326-41212327	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs550951915	chr12:41212400-41212401	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs552518150	chr12:41212435-41212436	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs58093662	chr12:41212564-41212565	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs536916570	chr12:41212566-41212567	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs558290615	chr12:41212575-41212576	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs1854482	chr12:41212586-41212587	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs145552677	chr12:41212621-41212622	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs34797157	chr12:41212635-41212636	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs183611900	chr12:41212649-41212650	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs552784348	chr12:41212668-41212669	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs577627130	chr12:41212762-41212763	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs1854481	chr12:41212772-41212773	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs556511689	chr12:41212778-41212779	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs575185376	chr12:41212828-41212829	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs147730597	chr12:41212837-41212838	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs1854480	chr12:41212858-41212859	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs535997314	chr12:41212883-41212884	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs572952438	chr12:41212940-41212941	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs140984918	chr12:41212982-41212983	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs554253758	chr12:41212990-41212991	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs565241104	chr12:41213031-41213032	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs565155427	chr12:41213035-41213036	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs144930856	chr12:41213114-41213115	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs188308480	chr12:41213117-41213118	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs73116774	chr12:41213119-41213120	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD

Chromatin state (count:142 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41211400-41213200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr12:41211400-41213600	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr12:41211400-41214200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr12:41211600-41214400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr12:41212000-41213000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr12:41212400-41214200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:41212600-41213800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:41212800-41213400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:41212800-41213400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:41212800-41213400	Enhancers	Aorta	Aorta
11	chr12:41212800-41213800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:41212800-41214000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr12:41212800-41214000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:41212800-41214000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:41212800-41214200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr12:41212800-41214200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr12:41212800-41214400	Enhancers	Fetal Stomach	stomach
18	chr12:41213000-41213200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:41213000-41213400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr12:41213000-41213400	Enhancers	Brain Germinal Matrix	brain
21	chr12:41213000-41213400	Enhancers	Spleen	Spleen
22	chr12:41213000-41213600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:41213000-41213800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:41213000-41213800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr12:41213000-41213800	Enhancers	Fetal Muscle Trunk	muscle
26	chr12:41213000-41214000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:41213000-41214000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:41213000-41214000	Enhancers	A549	lung
29	chr12:41213000-41214000	Enhancers	NHEK	skin
30	chr12:41213000-41214400	Enhancers	Fetal Muscle Leg	muscle
31	chr12:41213200-41213600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:41213200-41213600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:41213200-41213800	Enhancers	H9 Cell Line	embryonic stem cell
34	chr12:41213200-41213800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:41213200-41213800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:41213200-41213800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:41213400-41213800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr12:41213400-41213800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:41213600-41213800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr12:41213600-41215200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:41213800-41214000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr12:41213800-41214200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr12:41213800-41214400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:41213800-41214400	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr12:41213800-41214600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:41214000-41218800	Weak transcription	A549	lung
47	chr12:41214000-41223200	Weak transcription	NHEK	skin
48	chr12:41214200-41220200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:41214200-41221400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:41214200-41221600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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