Variant report

Variant	nsv559053
Chromosome Location	chr12:59563004-59643856
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:59567188..59568180-chr12:59766489..59767406,3	MCF-7	breast:
2	chr12:59567506..59568224-chr12:59739584..59740478,2	MCF-7	breast:
3	chr12:59577181..59579768-chr12:59589219..59591001,2	MCF-7	breast:
4	chr12:59586597..59588701-chr12:59589774..59591287,2	MCF-7	breast:
5	chr12:59577181..59579768-chr12:59589219..59591001,2	MCF-7	breast:
6	chr12:59586597..59588701-chr12:59589774..59591287,2	MCF-7	breast:

Extended variants
information (count: 1295 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:1295 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1500036	chr12:59563004-59563005	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs148004404	chr12:59563037-59563038	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs534429985	chr12:59563043-59563044	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs555562383	chr12:59563090-59563091	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs376124802	chr12:59563106-59563107	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs141645981	chr12:59563117-59563118	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs10877221	chr12:59563122-59563123	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs150516147	chr12:59563123-59563124	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs138363649	chr12:59563130-59563131	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs545289993	chr12:59563166-59563167	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs183663979	chr12:59563182-59563183	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs3913372	chr12:59570578-59570579	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs143372727	chr12:59570581-59570582	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs547240658	chr12:59570605-59570606	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs35533850	chr12:59570611-59570612	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs141519120	chr12:59570638-59570639	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs558166830	chr12:59570642-59570643	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs188278032	chr12:59570716-59570717	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs192848192	chr12:59570720-59570721	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs183746531	chr12:59570756-59570757	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs527895838	chr12:59570814-59570815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs543196212	chr12:59570827-59570828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs117496929	chr12:59570868-59570869	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs117786313	chr12:59570871-59570872	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs372910015	chr12:59570889-59570890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs568049696	chr12:59570894-59570895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs375883071	chr12:59570898-59570899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs369948474	chr12:59570911-59570912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs150861336	chr12:59570955-59570956	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs187711982	chr12:59570988-59570989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs192626278	chr12:59571038-59571039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs117096974	chr12:59571054-59571055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs367901825	chr12:59571055-59571056	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs527289075	chr12:59571071-59571072	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs386763438	chr12:59571072-59571073	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs557239701	chr12:59571073-59571074	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs61147050	chr12:59571074-59571075	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs397756964	chr12:59571082-59571083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs200571319	chr12:59571083-59571084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs143900633	chr12:59571097-59571098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs558343154	chr12:59571117-59571118	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs147250454	chr12:59571135-59571136	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs540630309	chr12:59571152-59571153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs554450533	chr12:59571162-59571163	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs572823755	chr12:59571177-59571178	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs140673003	chr12:59571183-59571184	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs547327027	chr12:59572236-59572237	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs199605533	chr12:59572239-59572240	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs199644773	chr12:59572240-59572241	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs200621284	chr12:59572241-59572242	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

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
Non-syndromic sensorineural hearing loss	21293372	CNVD
Osteosarcoma	21215367	CNVD

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59560400-59563200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:59570400-59570800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:59570800-59571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:59572200-59572400	Enhancers	HMEC	breast
5	chr12:59572400-59573400	Weak transcription	HMEC	breast
6	chr12:59573000-59573800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr12:59573200-59573600	Enhancers	Hela-S3	cervix
8	chr12:59573400-59573800	Enhancers	HMEC	breast
9	chr12:59573800-59575000	Weak transcription	HMEC	breast
10	chr12:59573800-59575400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:59575000-59575400	Enhancers	HMEC	breast
12	chr12:59575200-59575400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:59576000-59576200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:59576400-59576600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr12:59578400-59579000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:59578400-59579000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:59578600-59580400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:59579000-59579200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:59579000-59579400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:59579200-59579400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:59579400-59579600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:59579400-59580600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:59579600-59580000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:59579600-59580800	Enhancers	Brain Germinal Matrix	brain
25	chr12:59579800-59580600	Enhancers	Primary hematopoietic stem cells	blood
26	chr12:59580000-59580400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:59580400-59580600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:59585200-59585400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:59585200-59585400	Enhancers	HMEC	breast
30	chr12:59585400-59587200	Weak transcription	HMEC	breast
31	chr12:59585600-59587200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:59586000-59586800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr12:59587200-59587800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:59587200-59587800	Enhancers	HMEC	breast
35	chr12:59603600-59603800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:59603800-59608400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:59608400-59608600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:59608600-59609000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:59609000-59609800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:59609600-59610400	Enhancers	H9 Cell Line	embryonic stem cell
41	chr12:59609800-59615400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:59610000-59610200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr12:59628200-59628600	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:59628600-59631800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:59631200-59632200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr12:59631600-59632000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:59631600-59632000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr12:59631600-59632200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:59631600-59632800	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:59631800-59632000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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