Variant report

Variant	esv13593
Chromosome Location	chr3:60050980-60057155
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:60052745..60054653-chr3:60055819..60059567,3	MCF-7	breast:
2	chr3:60052745..60054653-chr3:60055819..60059567,3	MCF-7	breast:
3	chr3:60044792..60047333-chr3:60050018..60052719,2	MCF-7	breast:

Extended variants
information (count: 376 )
Associated
traits (count: 98 )

Variant overlapped rSNPs/rCNVs (count:376 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs191926	chr3:60050984-60050985	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs116781507	chr3:60050988-60050989	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs555118067	chr3:60051009-60051010	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs138551444	chr3:60051012-60051013	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs562524637	chr3:60051015-60051016	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs534016757	chr3:60051050-60051051	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs191927	chr3:60051071-60051072	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs577162221	chr3:60051087-60051088	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs3856667	chr3:60051116-60051117	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs2630154	chr3:60051133-60051134	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs114742895	chr3:60051163-60051164	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs542051284	chr3:60051180-60051181	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs568959936	chr3:60051188-60051189	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs560289514	chr3:60051201-60051202	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs3856668	chr3:60051227-60051228	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs549065342	chr3:60051229-60051230	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs367969290	chr3:60051253-60051254	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs181487063	chr3:60051256-60051257	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs4024131	chr3:60051300-60051301	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs144051580	chr3:60051334-60051335	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs374918885	chr3:60051339-60051340	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs4124059	chr3:60051382-60051383	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs186606541	chr3:60051385-60051386	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs147305439	chr3:60051394-60051395	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs548434161	chr3:60051425-60051426	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs4124060	chr3:60051428-60051429	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs374560472	chr3:60051452-60051453	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs2220239	chr3:60051459-60051460	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs3856669	chr3:60051461-60051462	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs535296995	chr3:60051505-60051506	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs191337873	chr3:60051509-60051510	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs139847470	chr3:60051523-60051524	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs115884634	chr3:60051532-60051533	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs183257885	chr3:60051554-60051555	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs553719759	chr3:60051564-60051565	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs2736807	chr3:60051565-60051566	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs125634	chr3:60051588-60051589	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs566534282	chr3:60051606-60051607	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs557159612	chr3:60051629-60051630	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs572505503	chr3:60051643-60051644	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs183322	chr3:60051659-60051660	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs76702288	chr3:60051709-60051710	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs117668634	chr3:60051714-60051715	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs543904546	chr3:60051727-60051728	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs76479766	chr3:60051780-60051781	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs372953462	chr3:60051789-60051790	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs530064557	chr3:60051797-60051798	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs149807901	chr3:60051843-60051844	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs560400928	chr3:60051857-60051858	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs527451163	chr3:60051864-60051865	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:98)

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
Hepatocellular carcinoma	22267523	CNVD

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60042000-60051600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:60043000-60051400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:60045000-60054200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr3:60045800-60052400	Enhancers	Primary T cells from cord blood	blood
5	chr3:60046800-60051800	Enhancers	Thymus	Thymus
6	chr3:60047400-60052200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:60048200-60054000	Enhancers	Dnd41	blood
8	chr3:60048800-60059400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:60049000-60051800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:60049200-60052000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr3:60049400-60053200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:60049800-60052000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:60049800-60052200	Enhancers	Fetal Thymus	thymus
14	chr3:60050000-60051400	Enhancers	NH-A	brain
15	chr3:60050000-60052000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:60050200-60051200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:60050200-60051200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:60050200-60051200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:60050200-60051200	Enhancers	Stomach Mucosa	stomach
20	chr3:60050200-60051200	Enhancers	Osteobl	bone
21	chr3:60050200-60051400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:60050200-60051400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:60050200-60051600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:60050200-60051600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:60050200-60051600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:60050400-60051000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:60050400-60051200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:60050400-60051200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:60050400-60051200	Enhancers	Fetal Heart	heart
30	chr3:60050400-60051200	Enhancers	NHDF-Ad	bronchial
31	chr3:60050400-60051400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:60050400-60051600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:60050600-60051000	Enhancers	Brain Hippocampus Middle	brain
34	chr3:60050600-60051400	Enhancers	Primary hematopoietic stem cells	blood
35	chr3:60050600-60051600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr3:60050600-60051800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:60050800-60051200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:60050800-60051200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:60050800-60051200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr3:60050800-60051200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:60050800-60051600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr3:60050800-60051800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:60050800-60052400	Enhancers	Primary T cells fromperipheralblood	blood
44	chr3:60051000-60051400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:60051000-60051600	Enhancers	Aorta	Aorta
46	chr3:60051200-60052400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr3:60051400-60051600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:60051400-60051600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr3:60051600-60051800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:60051600-60052400	Enhancers	Primary T helper cells PMA-I stimulated	--

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