Variant report

Variant	nsv973201
Chromosome Location	chr12:55974291-56000681
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	CEBPB	chr12:55982671-55982798	HepG2	liver:	n/a	chr12:55982688-55982699 chr12:55982676-55982687
2	CTCF	chr12:55975538-55975642	GM10248	blood:	n/a	n/a
3	CTCF	chr12:55999017-55999104	Kidney_OC	kidney:	n/a	n/a
4	FOXA1	chr12:55984062-55984437	HepG2	liver:	n/a	n/a
5	FOXA1	chr12:55985713-55986181	HepG2	liver:	n/a	n/a
6	FOXA2	chr12:55992065-55992508	A549	lung:	n/a	n/a
7	FOXA2	chr12:55983994-55984519	A549	lung:	n/a	n/a
8	FOXA2	chr12:55984053-55984326	A549	lung:	n/a	n/a
9	GABPA	chr12:55983814-55983956	HepG2	liver:	n/a	n/a
10	HEY1	chr12:55983990-55984154	K562	blood:	n/a	n/a
11	JUND	chr12:55977529-55977749	HepG2	liver:	n/a	chr12:55977694-55977705 chr12:55977696-55977708
12	MAFK	chr12:55978824-55979089	HepG2	liver:	n/a	n/a
13	MXI1	chr12:55976040-55976082	Hela-S3	cervix:	n/a	n/a
14	MYC	chr12:55976035-55976037	MCF-7	breast:	n/a	n/a
15	MYC	chr12:55975920-55976015	MCF-7	breast:	n/a	n/a
16	MYC	chr12:55975962-55976005	MCF-7	breast:	n/a	n/a
17	NFYA	chr12:55979521-55979721	GM12878	blood:	n/a	chr12:55979535-55979545
18	POLR2A	chr12:55999711-55999750	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:55983719-55984497	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:55975944-55975960	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:55983981-55984190	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:55975973-55976049	MCF-7	breast:	n/a	n/a
23	POLR2A	chr12:55976443-55976484	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr12:55974844-55974972	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr12:55975910-55976108	A549	lung:	n/a	n/a
26	POLR2A	chr12:55976110-55976119	A549	lung:	n/a	n/a
27	POLR2A	chr12:55975909-55975941	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:55975976-55976133	MCF-7	breast:	n/a	n/a
29	SIN3A	chr12:55974218-55974292	H1-hESC	embryonic stem cell:	n/a	n/a
30	SPI1	chr12:55983857-55983961	K562	blood:	n/a	n/a
31	STAT3	chr12:55976332-55976532	MCF10A-Er-Src	breast:	n/a	n/a
32	TAF1	chr12:55983916-55984248	H1-hESC	embryonic stem cell:	n/a	n/a
33	TCF7L2	chr12:55977071-55977676	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR6C70-1	chr12:55979199-55979255	ENSG00000258763.1

Variant related genes	Relation type
ENSG00000258763	TF binding region
OR6U2P	TF binding region

Extended variants
information (count: 178 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:178 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs562174377	chr12:55974316-55974317	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs10876818	chr12:55974324-55974325	Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs551832502	chr12:55974327-55974328	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs567155811	chr12:55974330-55974331	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs78269664	chr12:55974331-55974332	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs147483717	chr12:55974341-55974342	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs567732058	chr12:55974383-55974384	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs570459629	chr12:55974384-55974385	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs556579651	chr12:55974389-55974390	Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs148497007	chr12:55974402-55974403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs539718637	chr12:55974422-55974423	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs549572075	chr12:55974423-55974424	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs557723121	chr12:55974440-55974441	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs142784550	chr12:55974445-55974446	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs540022574	chr12:55974452-55974453	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs561567703	chr12:55974453-55974454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs573380355	chr12:55974460-55974461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs200872937	chr12:55974509-55974510	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs543938055	chr12:55974516-55974517	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs562137019	chr12:55974546-55974547	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs532718581	chr12:55974628-55974629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs7134292	chr12:55974629-55974630	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs560588890	chr12:55974663-55974664	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs7305194	chr12:55974682-55974683	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs17120045	chr12:55974690-55974691	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs567890254	chr12:55974777-55974778	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs151048299	chr12:55974798-55974799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs200935268	chr12:55974843-55974844	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs11322911	chr12:55974844-55974845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs398076656	chr12:55974846-55974847	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs199648690	chr12:55974847-55974848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs571773839	chr12:55974848-55974849	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs538617499	chr12:55974855-55974856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs74093257	chr12:55974876-55974877	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs193238702	chr12:55974911-55974912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs7308519	chr12:55974917-55974918	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs534122788	chr12:55974931-55974932	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs555128657	chr12:55974934-55974935	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs535347429	chr12:55974935-55974936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs573541433	chr12:55974946-55974947	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs11171579	chr12:55975016-55975017	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs562203030	chr12:55975035-55975036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs577682472	chr12:55975039-55975040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs575231035	chr12:55975043-55975044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs544649934	chr12:55975106-55975107	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs537858669	chr12:55975124-55975125	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs558198434	chr12:55975147-55975148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs11171580	chr12:55975171-55975172	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs140382065	chr12:55975174-55975175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs543344570	chr12:55975175-55975176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:74)

Disease	PMID	Source
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
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
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	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
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Bladder cancer	21909424	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	20531469	CNVD
Multiple myeloma	16616336	CNVD
Rhabdomyosarcoma	16790082	CNVD
Renal cell carcinoma	18765545	CNVD
Urothelial cell carcinoma	18451213	CNVD
Glioblastoma multiforme	21138945	CNVD
Glioblastoma multiforme	21569311	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Osteosarcoma	21215367	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:55974000-55974400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:55974400-55976000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:55976000-55976200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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