Variant report

Variant	nsv520108
Chromosome Location	chr3:60059041-60062939
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:60052745..60054653-chr3:60055819..60059567,3	MCF-7	breast:

Extended variants
information (count: 200 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:200 , 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	rs2630207	chr3:60059041-60059042	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs73830679	chr3:60059045-60059046	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs141170307	chr3:60059058-60059059	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs540495019	chr3:60059062-60059063	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs116320406	chr3:60059071-60059072	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs142515625	chr3:60059091-60059092	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs550774729	chr3:60059101-60059102	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs569287796	chr3:60059115-60059116	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs62238445	chr3:60059135-60059136	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs576495597	chr3:60059147-60059148	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs537111851	chr3:60059159-60059160	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs75732877	chr3:60059184-60059185	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs185631044	chr3:60059193-60059194	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs115581895	chr3:60059196-60059197	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs534230926	chr3:60059203-60059204	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs140618971	chr3:60059211-60059212	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs570730369	chr3:60059221-60059222	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs202188405	chr3:60059228-60059229	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs77945535	chr3:60059229-60059230	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs548616055	chr3:60059242-60059243	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs77246665	chr3:60059290-60059291	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs575295792	chr3:60059319-60059320	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs542662536	chr3:60059321-60059322	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs138286643	chr3:60059395-60059396	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs534075755	chr3:60059396-60059397	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs572763985	chr3:60059397-60059398	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs188868119	chr3:60059398-60059399	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs76079511	chr3:60059470-60059471	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs540032330	chr3:60059481-60059482	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs141347538	chr3:60059558-60059559	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs544458645	chr3:60059571-60059572	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs145074952	chr3:60059582-60059583	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs2736821	chr3:60059610-60059611	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs78998186	chr3:60059618-60059619	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs548623126	chr3:60059623-60059624	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs566765355	chr3:60059634-60059635	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs527648236	chr3:60059651-60059652	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs192132641	chr3:60059667-60059668	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs540051623	chr3:60059690-60059691	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs558151090	chr3:60059709-60059710	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs570842075	chr3:60059734-60059735	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs538148389	chr3:60059756-60059757	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs548463194	chr3:60059797-60059798	Enhancers Flanking Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs138869602	chr3:60059824-60059825	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs77824914	chr3:60059864-60059865	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs537044269	chr3:60059868-60059869	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs371070637	chr3:60059885-60059886	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs184472703	chr3:60059932-60059933	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs141997528	chr3:60059942-60059943	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs188856572	chr3:60059950-60059951	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:97)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Cancer	18162546	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Urothelial cell carcinoma	18451213	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Colorectal cancer	16272173	CNVD
Mental retardation	17847001	CNVD
Neuroticism	17667963	CNVD
Squamous cell cancer	19047905	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Cancer	20164920	CNVD
Schizophrenia	23813976	CNVD
Autism	22102821	CNVD
Prostate cancer	19363497	CNVD
Malaria	21533027	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Colorectal cancer	21518781	CNVD
Esophageal cancer	21518781	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Glioblastoma multiforme	21569311	CNVD

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60048800-60059400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr3:60051600-60062000	Weak transcription	Aorta	Aorta
3	chr3:60051800-60063000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:60052000-60059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:60057000-60059200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:60057400-60059400	Weak transcription	Fetal Thymus	thymus
7	chr3:60057600-60059200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:60057800-60059400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:60057800-60060200	Weak transcription	Thymus	Thymus
10	chr3:60058000-60060800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:60058000-60061200	Genic enhancers	Dnd41	blood
12	chr3:60058400-60059200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:60058400-60061800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr3:60058800-60059400	Enhancers	Primary T cells from cord blood	blood
15	chr3:60058800-60059400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:60059000-60059200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr3:60059200-60059400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:60059200-60059800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:60059200-60060200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr3:60059200-60060400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:60059400-60059600	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr3:60059400-60059600	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr3:60059400-60059800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr3:60059400-60061600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr3:60059400-60061800	Enhancers	Fetal Thymus	thymus
26	chr3:60059400-60062200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr3:60059600-60059800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:60059600-60059800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr3:60059600-60060000	Enhancers	Fetal Heart	heart
30	chr3:60059600-60061400	Enhancers	Primary T cells from cord blood	blood
31	chr3:60059800-60061000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:60059800-60061200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr3:60059800-60061800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:60059800-60064800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:60060200-60060600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:60060200-60062000	Enhancers	Thymus	Thymus
37	chr3:60060400-60061000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:60060400-60061400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:60060600-60061400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr3:60060800-60061600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:60061000-60061200	Enhancers	Right Atrium	heart
42	chr3:60061000-60061800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:60061000-60064000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr3:60061200-60061600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:60061200-60061800	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:60061200-60061800	Transcr. at gene 5' and 3'	Dnd41	blood
47	chr3:60061400-60061800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:60061400-60061800	Enhancers	Brain Substantia Nigra	brain
49	chr3:60061400-60061800	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr3:60061400-60062400	Active TSS	Primary T helper naive cells from peripheral blood	blood

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