Variant report

Variant	nsv1039996
Chromosome Location	chr12:59556074-59645306
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:59586597..59588701-chr12:59589774..59591287,2	MCF-7	breast:
2	chr12:59567188..59568180-chr12:59766489..59767406,3	MCF-7	breast:
3	chr12:59577181..59579768-chr12:59589219..59591001,2	MCF-7	breast:
4	chr12:59567506..59568224-chr12:59739584..59740478,2	MCF-7	breast:
5	chr12:59586597..59588701-chr12:59589774..59591287,2	MCF-7	breast:
6	chr12:59543592..59544432-chr12:59558545..59559537,3	MCF-7	breast:
7	chr12:59577181..59579768-chr12:59589219..59591001,2	MCF-7	breast:

Extended variants
information (count: 1566 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:1566 , 50 per page) page: 1 2 3 4 5 6 7 ... 32

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs574178001	chr12:59556102-59556103	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs537910474	chr12:59556134-59556135	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs556631912	chr12:59556147-59556148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs186072029	chr12:59556204-59556205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs35520378	chr12:59556221-59556222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs545447888	chr12:59556228-59556229	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs554093169	chr12:59556229-59556230	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs140383303	chr12:59556301-59556302	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs542843426	chr12:59556328-59556329	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs560874706	chr12:59556347-59556348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs559059757	chr12:59556353-59556354	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs11172923	chr12:59556368-59556369	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs543119205	chr12:59556398-59556399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs147357759	chr12:59556401-59556402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs78872151	chr12:59556404-59556405	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs142978949	chr12:59556439-59556440	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs566821385	chr12:59556465-59556466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs559972298	chr12:59556501-59556502	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs576828821	chr12:59556505-59556506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs1846621	chr12:59556520-59556521	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs10877217	chr12:59556551-59556552	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs549660493	chr12:59556553-59556554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs377579216	chr12:59556566-59556567	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs2201988	chr12:59556581-59556582	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs191413153	chr12:59556590-59556591	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs375161454	chr12:59556591-59556592	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs181327100	chr12:59556596-59556597	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs571804389	chr12:59556604-59556605	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs149821663	chr12:59556605-59556606	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs554258520	chr12:59556624-59556625	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs572476531	chr12:59556653-59556654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs528980075	chr12:59556695-59556696	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs542904827	chr12:59556710-59556711	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs78993341	chr12:59556798-59556799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs576132753	chr12:59556807-59556808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs543634446	chr12:59556833-59556834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs140623440	chr12:59556836-59556837	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs145673978	chr12:59556856-59556857	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs367833920	chr12:59556910-59556911	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs185510723	chr12:59556932-59556933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs146549963	chr12:59556964-59556965	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs562383872	chr12:59556992-59556993	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs568817314	chr12:59557002-59557003	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs149126093	chr12:59557030-59557031	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs190327557	chr12:59557060-59557061	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs2173644	chr12:59557132-59557133	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs2173643	chr12:59557145-59557146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs550390498	chr12:59557180-59557181	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs143627835	chr12:59557238-59557239	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs539091241	chr12:59557250-59557251	Weak transcription	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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59551000-59557600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:59557400-59559000	Enhancers	NH-A	brain
3	chr12:59557600-59559000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:59558200-59558600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr12:59558600-59558800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:59558600-59559000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:59558600-59559000	Enhancers	Osteobl	bone
8	chr12:59558800-59559000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:59558800-59559000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:59559000-59560600	Weak transcription	NH-A	brain
11	chr12:59559200-59561200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:59559600-59562000	Enhancers	Fetal Intestine Small	intestine
13	chr12:59559600-59562800	Enhancers	Fetal Intestine Large	intestine
14	chr12:59559800-59560800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr12:59560000-59560200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:59560000-59560600	Enhancers	Stomach Mucosa	stomach
17	chr12:59560200-59560400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:59560400-59563200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:59560600-59561000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:59560600-59561000	Enhancers	NH-A	brain
21	chr12:59561200-59561600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:59561600-59561800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:59561800-59562200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:59561800-59562800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr12:59561800-59562800	Enhancers	Fetal Brain Female	brain
26	chr12:59562200-59562800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:59562200-59563000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:59562400-59562800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:59562400-59562800	Enhancers	Brain Germinal Matrix	brain
30	chr12:59570400-59570800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:59570800-59571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:59572200-59572400	Enhancers	HMEC	breast
33	chr12:59572400-59573400	Weak transcription	HMEC	breast
34	chr12:59573000-59573800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr12:59573200-59573600	Enhancers	Hela-S3	cervix
36	chr12:59573400-59573800	Enhancers	HMEC	breast
37	chr12:59573800-59575000	Weak transcription	HMEC	breast
38	chr12:59573800-59575400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:59575000-59575400	Enhancers	HMEC	breast
40	chr12:59575200-59575400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:59576000-59576200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:59576400-59576600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr12:59578400-59579000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:59578400-59579000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:59578600-59580400	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr12:59579000-59579200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:59579000-59579400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:59579200-59579400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:59579400-59579600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:59579400-59580600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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