Variant report

Variant	esv3402398
Chromosome Location	chr12:50270935-50273433
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50272122..50274588-chr12:50280399..50282303,2	MCF-7	breast:
2	chr12:50261492..50264871-chr12:50267070..50272951,8	MCF-7	breast:
3	chr12:50269088..50271373-chr12:50274652..50276581,2	MCF-7	breast:
4	chr12:50270045..50272990-chr12:50279975..50282889,2	MCF-7	breast:

Extended variants
information (count: 283 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:283 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs535472973	chr12:50270950-50270951	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs554149085	chr12:50270957-50270958	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs111250015	chr12:50270987-50270988	Enhancers Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs1893493	chr12:50271001-50271002	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs572212461	chr12:50271019-50271020	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs1248264	chr12:50271045-50271046	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs138764686	chr12:50271123-50271124	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs141815105	chr12:50271129-50271130	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs543586095	chr12:50271142-50271143	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs563462238	chr12:50271150-50271151	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs145480140	chr12:50271204-50271205	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs548217345	chr12:50271259-50271260	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs576617363	chr12:50271284-50271285	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs190575724	chr12:50271292-50271293	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs561704296	chr12:50271313-50271314	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs1248263	chr12:50271372-50271373	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs547456178	chr12:50271383-50271384	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs370908720	chr12:50271404-50271405	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs571038501	chr12:50271427-50271428	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs373587621	chr12:50271469-50271470	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs183503786	chr12:50271470-50271471	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs370145318	chr12:50271472-50271473	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs550329179	chr12:50271475-50271476	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs376600580	chr12:50271480-50271481	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs570302557	chr12:50271483-50271484	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs536149806	chr12:50271493-50271494	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs117619228	chr12:50271495-50271496	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs149597364	chr12:50271496-50271497	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs73116304	chr12:50271497-50271498	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs112275151	chr12:50271498-50271499	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs557600672	chr12:50271518-50271519	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs577643747	chr12:50271519-50271520	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs543298675	chr12:50271529-50271530	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs116578244	chr12:50271550-50271551	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs573603836	chr12:50271553-50271554	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs114084422	chr12:50271565-50271566	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs547436769	chr12:50271598-50271599	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs200581902	chr12:50271610-50271611	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs370056972	chr12:50271611-50271612	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs561765906	chr12:50271616-50271617	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs73293433	chr12:50271617-50271618	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs545609916	chr12:50271649-50271650	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs199758812	chr12:50271656-50271657	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs547372966	chr12:50271663-50271664	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs576642109	chr12:50271667-50271668	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs564453575	chr12:50271671-50271672	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs545299448	chr12:50271676-50271677	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs533464072	chr12:50271685-50271686	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs35203048	chr12:50271694-50271695	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs111203851	chr12:50271716-50271717	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:69)

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
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
low-grade B-cell lymphoma tumor	18367492	CNVD
Adenoid cystic carcinoma	18332873	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
Multiple myeloma	16616336	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Intracranial ependymoma	16609018	CNVD
Cancer	17160897	CNVD
Melanoma	20877625	CNVD
Cancer	20164919	CNVD

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50263800-50271800	Weak transcription	Pancreas	Pancrea
2	chr12:50264600-50271600	Weak transcription	Fetal Brain Male	brain
3	chr12:50266200-50275400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:50266800-50271400	Weak transcription	Fetal Brain Female	brain
5	chr12:50267000-50275800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:50267000-50297000	Weak transcription	Right Atrium	heart
7	chr12:50268200-50276400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:50268600-50271400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:50268800-50271600	Weak transcription	Fetal Kidney	kidney
10	chr12:50269000-50274800	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr12:50269200-50271400	Weak transcription	Brain Anterior Caudate	brain
12	chr12:50269200-50271400	Weak transcription	K562	blood
13	chr12:50269200-50271600	Weak transcription	Brain Substantia Nigra	brain
14	chr12:50269200-50273200	Strong transcription	Brain Angular Gyrus	brain
15	chr12:50269200-50274600	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:50269400-50275400	Weak transcription	Fetal Stomach	stomach
17	chr12:50269800-50272000	Strong transcription	Brain Hippocampus Middle	brain
18	chr12:50270000-50276400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50270400-50271200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:50270800-50271000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:50270800-50271400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:50270800-50271800	Strong transcription	Brain Germinal Matrix	brain
23	chr12:50271200-50274600	Strong transcription	Brain Cingulate Gyrus	brain
24	chr12:50271400-50271600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
25	chr12:50271400-50272200	Strong transcription	Fetal Brain Female	brain
26	chr12:50271400-50272200	ZNF genes & repeats	K562	blood
27	chr12:50271400-50274600	Strong transcription	Brain Anterior Caudate	brain
28	chr12:50271600-50271800	ZNF genes & repeats	Fetal Brain Male	brain
29	chr12:50271600-50271800	ZNF genes & repeats	Fetal Kidney	kidney
30	chr12:50271600-50274800	Strong transcription	Brain Substantia Nigra	brain
31	chr12:50271800-50272000	Enhancers	Pancreas	Pancrea
32	chr12:50271800-50273200	Strong transcription	Fetal Brain Male	brain
33	chr12:50271800-50273200	Weak transcription	Fetal Kidney	kidney
34	chr12:50271800-50274400	Weak transcription	Brain Germinal Matrix	brain
35	chr12:50272000-50273000	Weak transcription	Pancreas	Pancrea
36	chr12:50272000-50274400	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:50272200-50273000	Weak transcription	Fetal Brain Female	brain
38	chr12:50272800-50273400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:50273000-50273400	Enhancers	Pancreas	Pancrea
40	chr12:50273000-50276400	Strong transcription	Fetal Brain Female	brain
41	chr12:50273200-50273600	ZNF genes & repeats	Brain Angular Gyrus	brain
42	chr12:50273200-50274600	ZNF genes & repeats	Fetal Kidney	kidney
43	chr12:50273200-50274600	Active TSS	Fetal Lung	lung
44	chr12:50273200-50275000	ZNF genes & repeats	Fetal Brain Male	brain
45	chr12:50273400-50273800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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