Variant report

Variant	esv20514
Chromosome Location	chr3:60056545-60058100
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: 105 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:105 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2736816	chr3:60056547-60056548	Weak transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs2736817	chr3:60056550-60056551	Weak transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs549491332	chr3:60056555-60056556	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs548029598	chr3:60056598-60056599	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs35618987	chr3:60056600-60056601	Weak transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs566157618	chr3:60056620-60056621	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs2736818	chr3:60056623-60056624	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs140789801	chr3:60056628-60056629	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs570595143	chr3:60056637-60056638	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs2630195	chr3:60056648-60056649	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs542092071	chr3:60056655-60056656	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs113911681	chr3:60056672-60056673	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs556238975	chr3:60056713-60056714	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs144077623	chr3:60056732-60056733	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs574325228	chr3:60056737-60056738	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs17062068	chr3:60056740-60056741	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs112224873	chr3:60056741-60056742	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs17062072	chr3:60056757-60056758	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs79790917	chr3:60056786-60056787	Enhancers Genic enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs145837536	chr3:60056801-60056802	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs563930503	chr3:60056814-60056815	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs147780907	chr3:60056837-60056838	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs115856322	chr3:60056844-60056845	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs2630196	chr3:60056853-60056854	Enhancers Genic enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs529251568	chr3:60056898-60056899	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs116347348	chr3:60056902-60056903	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs181438852	chr3:60056929-60056930	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs183994532	chr3:60056952-60056953	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs116397389	chr3:60056969-60056970	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs4679509	chr3:60056989-60056990	Enhancers Genic enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs2630197	chr3:60057008-60057009	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs570258079	chr3:60057023-60057024	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs537939487	chr3:60057024-60057025	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs77499478	chr3:60057049-60057050	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs559134693	chr3:60057050-60057051	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs567988228	chr3:60057064-60057065	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs577310194	chr3:60057082-60057083	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs2630198	chr3:60057101-60057102	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs529121602	chr3:60057117-60057118	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs553475648	chr3:60057135-60057136	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs2630199	chr3:60057137-60057138	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs181160772	chr3:60057141-60057142	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs575045462	chr3:60057144-60057145	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs17062079	chr3:60057145-60057146	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs141102427	chr3:60057158-60057159	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs2630200	chr3:60057160-60057161	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs114929129	chr3:60057182-60057183	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs2630201	chr3:60057184-60057185	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs201059722	chr3:60057231-60057232	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs536715506	chr3:60057259-60057260	Weak transcription Enhancers 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:39 , 50 per page) page: 1

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	chr3:60051800-60058200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:60051800-60063000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:60052000-60058400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:60052000-60059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:60052200-60056600	Weak transcription	Fetal Thymus	thymus
8	chr3:60052200-60058000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:60055600-60056600	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr3:60055600-60056600	Genic enhancers	Dnd41	blood
11	chr3:60055600-60057600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:60055800-60056600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:60055800-60056600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr3:60055800-60058800	Genic enhancers	Primary T cells from cord blood	blood
15	chr3:60056000-60057800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:60056400-60056600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr3:60056400-60057200	Weak transcription	Thymus	Thymus
18	chr3:60056600-60056800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr3:60056600-60057000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:60056600-60057400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr3:60056600-60057400	Enhancers	Fetal Thymus	thymus
22	chr3:60056600-60057600	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:60056600-60057800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:60056600-60058000	Enhancers	Dnd41	blood
25	chr3:60056800-60058400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:60057000-60059200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:60057200-60057400	Enhancers	Thymus	Thymus
28	chr3:60057400-60057600	Weak transcription	Thymus	Thymus
29	chr3:60057400-60059400	Weak transcription	Fetal Thymus	thymus
30	chr3:60057600-60057800	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr3:60057600-60057800	Enhancers	Thymus	Thymus
32	chr3:60057600-60059200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr3:60057800-60058000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr3:60057800-60059400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr3:60057800-60060200	Weak transcription	Thymus	Thymus
36	chr3:60058000-60058400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr3:60058000-60058800	Weak transcription	Primary B cells from cord blood	blood
38	chr3:60058000-60060800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:60058000-60061200	Genic enhancers	Dnd41	blood

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