Variant report

Variant	esv16545
Chromosome Location	chr12:59925488-59945796
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	BCL3	chr12:59928657-59928995	GM12878	blood:	n/a	n/a
2	BCL3	chr12:59928231-59928552	GM12878	blood:	n/a	n/a
3	BCL3	chr12:59928674-59929037	GM12878	blood:	n/a	n/a
4	BRCA1	chr12:59940309-59940328	GM12878	blood:	n/a	n/a
5	CEBPB	chr12:59928811-59928850	A549	lung:	n/a	n/a
6	FOXA1	chr12:59942809-59943016	T-47D	breast:	n/a	n/a
7	FOXA1	chr12:59942803-59943136	HepG2	liver:	n/a	n/a
8	NFATC1	chr12:59943727-59944028	GM12878	blood:	n/a	n/a
9	PBX3	chr12:59930497-59930722	GM12878	blood:	n/a	n/a
10	PBX3	chr12:59943765-59943962	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:59944465-59944495	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr12:59944605-59944684	MCF10A-Er-Src	breast:	n/a	n/a
13	TCF3	chr12:59943733-59944009	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59919709..59922642-chr12:59929595..59932355,2	MCF-7	breast:
2	chr12:59941726..59943985-chr12:59989663..59991635,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266724	TF binding region
ENSG00000265430	TF binding region
ENSG00000118596	chromatin interactions
ENSG00000265430	chromatin interactions
ENSG00000266724	chromatin interactions

Extended variants
information (count: 236 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:236 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs191078811	chr12:59929613-59929614	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs182152743	chr12:59929618-59929619	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs557441446	chr12:59929620-59929621	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs577478599	chr12:59929627-59929628	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs534967968	chr12:59929632-59929633	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs572873596	chr12:59929711-59929712	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs553176430	chr12:59929724-59929725	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs574687040	chr12:59929746-59929747	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs187677293	chr12:59929787-59929788	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs144450559	chr12:59929804-59929805	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs546204223	chr12:59929815-59929816	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs564289915	chr12:59929825-59929826	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs146599923	chr12:59929859-59929860	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs141314180	chr12:59929869-59929870	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs555743826	chr12:59929871-59929872	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs529109298	chr12:59929899-59929900	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs112309190	chr12:59929964-59929965	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs568955864	chr12:59929973-59929974	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs117996606	chr12:59930011-59930012	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs151266460	chr12:59930018-59930019	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs140446815	chr12:59930029-59930030	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs402342	chr12:59930050-59930051	Inactive region	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs371295317	chr12:59930065-59930066	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs568376844	chr12:59930069-59930070	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs535656758	chr12:59930126-59930127	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs375050815	chr12:59930141-59930142	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs557245434	chr12:59930146-59930147	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs113587340	chr12:59930165-59930166	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs138674468	chr12:59930208-59930209	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs558163496	chr12:59930255-59930256	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs573273387	chr12:59930268-59930269	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs115291932	chr12:59930280-59930281	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs77393259	chr12:59930281-59930282	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs561964039	chr12:59930283-59930284	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs529172145	chr12:59930303-59930304	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs11524053	chr12:59930320-59930321	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs544407822	chr12:59930350-59930351	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs192877097	chr12:59930359-59930360	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs533075997	chr12:59930368-59930369	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs142871855	chr12:59930382-59930383	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs537863116	chr12:59930385-59930386	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs566169704	chr12:59930405-59930406	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs183156693	chr12:59930427-59930428	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs368039341	chr12:59930434-59930435	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs188639568	chr12:59930444-59930445	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs568436509	chr12:59930453-59930454	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs535715587	chr12:59930472-59930473	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs559503568	chr12:59930535-59930536	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs76496485	chr12:59930546-59930547	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs375590142	chr12:59930552-59930553	Inactive region	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
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
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	18632612	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Urothelial cell carcinoma	18451213	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Leukemia	18628472	CNVD
Glioblastoma multiforme	22291905	CNVD
Glioblastoma multiforme	19435819	CNVD
Myelofibrosis	22110671	CNVD
Phyllodes tumor	17334353	CNVD
Glaucoma	21310917	CNVD
Breast cancer	16272173	CNVD
Mental retardation	19951919	CNVD
Glaucoma	21447600	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Developmental delay	21267005	CNVD
12q14 microdeletion syndrome	21267005	CNVD
Developmental delay	19277063	CNVD
Dwarfism	19277063	CNVD
Fibroblasts	20926602	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Glioblastoma multiforme	20080666	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	17133270	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Glioblastoma	17090523	CNVD
Multiple myeloma	16616336	CNVD
Lung cancer	16773561	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59942000-59943600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:59942200-59943800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:59942400-59943200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr12:59942400-59943200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr12:59942600-59943000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:59942600-59943200	Enhancers	Stomach Mucosa	stomach
7	chr12:59942600-59943400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr12:59942600-59943600	Enhancers	Esophagus	oesophagus
9	chr12:59942600-59944000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:59943000-59943200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:59943200-59943400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr12:59943200-59943600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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