Variant report

Variant	nsv975641
Chromosome Location	chr12:103663103-103667663
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	BATF	chr12:103667459-103667741	GM12878	blood:	n/a	chr12:103667583-103667594
2	BATF	chr12:103666746-103667008	GM12878	blood:	n/a	chr12:103666916-103666927 chr12:103666917-103666927 chr12:103666896-103666907
3	BATF	chr12:103666787-103666990	GM12878	blood:	n/a	chr12:103666916-103666927 chr12:103666917-103666927 chr12:103666896-103666907
4	CHD2	chr12:103667496-103667760	GM12878	blood:	n/a	n/a
5	CREB1	chr12:103662708-103663324	GM12878	blood:	n/a	n/a
6	CUX1	chr12:103663210-103663303	GM12878	blood:	n/a	n/a
7	EP300	chr12:103666928-103666958	GM12878	blood:	n/a	n/a
8	EP300	chr12:103667506-103667835	GM12878	blood:	n/a	chr12:103667790-103667804
9	FOS	chr12:103667399-103667712	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr12:103666756-103667111	MCF10A-Er-Src	breast:	n/a	chr12:103666920-103666928 chr12:103666920-103666927 chr12:103666920-103666928
11	FOS	chr12:103666733-103667090	MCF10A-Er-Src	breast:	n/a	chr12:103666920-103666928 chr12:103666920-103666927 chr12:103666920-103666928
12	FOS	chr12:103663809-103663935	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr12:103666718-103667120	MCF10A-Er-Src	breast:	n/a	chr12:103666920-103666928 chr12:103666920-103666927 chr12:103666920-103666928
14	FOS	chr12:103663784-103663974	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr12:103667400-103667746	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr12:103667448-103667750	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr12:103666712-103667120	MCF10A-Er-Src	breast:	n/a	chr12:103666920-103666928 chr12:103666920-103666927 chr12:103666920-103666928
18	FOSL1	chr12:103666699-103667133	HCT-116	colon:	n/a	chr12:103666920-103666928 chr12:103666920-103666927 chr12:103666920-103666928
19	JUND	chr12:103666810-103666960	HepG2	liver:	n/a	chr12:103666920-103666928 chr12:103666894-103666905 chr12:103666918-103666929 chr12:103666920-103666927 chr12:103666920-103666928
20	MAFF	chr12:103667425-103667754	HepG2	liver:	n/a	chr12:103667585-103667603
21	MAFK	chr12:103667478-103667678	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAFK	chr12:103667528-103667746	HepG2	liver:	n/a	n/a
23	MAFK	chr12:103667435-103667769	HepG2	liver:	n/a	n/a
24	MXI1	chr12:103667258-103667821	GM12878	blood:	n/a	n/a
25	NFIC	chr12:103662619-103663271	GM12878	blood:	n/a	n/a
26	NFYB	chr12:103665717-103665909	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:103667520-103667794	H1-neurons	neurons:	n/a	n/a
28	REST	chr12:103667611-103667834	H1-hESC	embryonic stem cell:	n/a	chr12:103667730-103667750 chr12:103667735-103667744
29	RUNX3	chr12:103662565-103663248	GM12878	blood:	n/a	chr12:103662826-103662835 chr12:103662826-103662835
30	STAT3	chr12:103666827-103667027	MCF10A-Er-Src	breast:	n/a	n/a
31	ZNF263	chr12:103662946-103663268	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:103665222..103666141-chr7:19784414..19785287,2	MCF-7	breast:
2	chr12:103567206..103569823-chr12:103663759..103665929,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAH-2	chr12:103663585-103663631	NONHSAT030368
2	lnc-PAH-2	chr12:103663585-103663631	NONHSAT030365
3	lnc-PAH-2	chr12:103663598-103663631	NONHSAT030370
4	lnc-PAH-2	chr12:103663927-103664086	NONHSAT030370
5	lnc-PAH-2	chr12:103663585-103663631	NONHSAT030367
6	lnc-PAH-2	chr12:103667570-103667661	NR_103526
7	lnc-PAH-2	chr12:103663585-103663700	NONHSAT030369
8	lnc-PAH-2	chr12:103663585-103663631	NR_103526

Variant related genes	Relation type
C12orf42	TF binding region

Extended variants
information (count: 150 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:150 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs556562381	chr12:103663103-103663104	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs576026073	chr12:103663134-103663135	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs541775392	chr12:103663135-103663136	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs536103672	chr12:103663185-103663186	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs572175366	chr12:103663231-103663232	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs76336296	chr12:103663238-103663239	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs560069270	chr12:103663242-103663243	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs532469270	chr12:103663259-103663260	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs4764729	chr12:103663275-103663276	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs562548235	chr12:103663301-103663302	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs181961227	chr12:103663330-103663331	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs533913261	chr12:103663350-103663351	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs140803883	chr12:103663379-103663380	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs144766665	chr12:103663394-103663395	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs533843619	chr12:103663502-103663503	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs184784641	chr12:103663506-103663507	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs58616642	chr12:103663526-103663527	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs75524125	chr12:103663536-103663537	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs370811508	chr12:103663587-103663588	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
20	rs539256029	chr12:103663602-103663603	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
21	rs535475719	chr12:103663717-103663718	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs374768770	chr12:103663752-103663753	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs562989205	chr12:103663760-103663761	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs555315544	chr12:103663838-103663839	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs572236849	chr12:103663849-103663850	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs367841791	chr12:103663906-103663907	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs12828579	chr12:103663965-103663966	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs541148574	chr12:103663967-103663968	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs147918157	chr12:103663977-103663978	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs577819871	chr12:103663982-103663983	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs545933131	chr12:103663993-103663994	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs562780543	chr12:103664040-103664041	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs531601486	chr12:103664041-103664042	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs541866627	chr12:103664063-103664064	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs561644647	chr12:103664084-103664085	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs527423087	chr12:103664130-103664131	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs71440852	chr12:103664143-103664144	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs557542250	chr12:103664144-103664145	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs34449856	chr12:103664147-103664148	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs12829522	chr12:103664150-103664151	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs191231487	chr12:103664156-103664157	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs558371882	chr12:103664157-103664158	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs189380642	chr12:103664160-103664161	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs35248416	chr12:103664175-103664176	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs371860524	chr12:103664182-103664183	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs576016164	chr12:103664188-103664189	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs180992657	chr12:103664267-103664268	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs77147201	chr12:103664278-103664279	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs201243040	chr12:103664289-103664290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs199778012	chr12:103664304-103664305	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
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
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
T-cell prolymphocytic leukemia	19278963	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
Lung cancer	18438408	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Breast cancer	22032731	CNVD
Cancer	16751803	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Wilms tumour	21544195	CNVD
Ovarian cancer	21720365	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
lymphocytic leukemia	21291569	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16397240	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Sudden cardiac death	19188705	CNVD
Breast cancer	17133270	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Neurocytoma	17123091	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Breast cancer	21509527	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	16616336	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103662600-103663600	Enhancers	Primary T cells fromperipheralblood	blood
2	chr12:103662800-103666200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:103663000-103663800	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr12:103663000-103663800	Bivalent Enhancer	Dnd41	blood
5	chr12:103663200-103663600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:103663200-103663800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:103663200-103664000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr12:103663400-103664000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:103663600-103663800	Enhancers	Thymus	Thymus
10	chr12:103663600-103664200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:103663600-103664600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr12:103663800-103664200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr12:103663800-103664800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:103664000-103665000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:103664200-103667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:103664200-103671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:103664800-103665000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr12:103664800-103665000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr12:103665000-103665200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:103666200-103667800	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr12:103666600-103667000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:103667400-103667800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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