Variant report

Variant	esv3454650
Chromosome Location	chr20:52452857-52453526
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59939333..59940887-chr20:52450988..52453979,2	MCF-7	breast:
2	chr20:52452353..52453193-chr20:52556867..52557776,2	MCF-7	breast:
3	chr20:52445630..52448175-chr20:52453269..52455432,3	K562	blood:
4	chr17:56707356..56710177-chr20:52450614..52453612,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	chromatin interactions
ENSG00000136492	chromatin interactions

Extended variants
information (count: 45 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:45 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs181468757	chr20:52452858-52452859	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs147238031	chr20:52452889-52452890	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs567510827	chr20:52452921-52452922	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs186110682	chr20:52452935-52452936	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs372082388	chr20:52452940-52452941	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs549211393	chr20:52452951-52452952	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs150754179	chr20:52452973-52452974	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs12624899	chr20:52452977-52452978	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs571072917	chr20:52452989-52452990	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs6064010	chr20:52452991-52452992	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs556502107	chr20:52453012-52453013	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs142087013	chr20:52453018-52453019	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs138133836	chr20:52453020-52453021	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs144696295	chr20:52453025-52453026	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs140895869	chr20:52453053-52453054	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs144794866	chr20:52453060-52453061	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs78092621	chr20:52453063-52453064	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs145463390	chr20:52453064-52453065	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs550199819	chr20:52453080-52453081	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs3971345	chr20:52453083-52453084	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs201302944	chr20:52453084-52453085	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs570108540	chr20:52453110-52453111	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs373430269	chr20:52453125-52453126	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs183988634	chr20:52453153-52453154	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs116168491	chr20:52453155-52453156	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs377047862	chr20:52453161-52453162	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs140148884	chr20:52453204-52453205	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs4350815	chr20:52453216-52453217	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs549672535	chr20:52453229-52453230	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs574737546	chr20:52453254-52453255	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs145665348	chr20:52453255-52453256	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs371138644	chr20:52453284-52453285	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs4455223	chr20:52453330-52453331	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs576736646	chr20:52453358-52453359	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs543561071	chr20:52453363-52453364	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs112829954	chr20:52453419-52453420	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs73272079	chr20:52453428-52453429	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs202228291	chr20:52453448-52453449	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs562439811	chr20:52453458-52453459	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs150535971	chr20:52453470-52453471	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs145192787	chr20:52453490-52453491	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs187318704	chr20:52453493-52453494	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs541786421	chr20:52453502-52453503	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs561649452	chr20:52453507-52453508	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs149149957	chr20:52453508-52453509	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Gastric cancer	17908304	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Medulloblastoma	21979893	CNVD
Urothelial carcinoma	21177765	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Colorectal cancer	21645411	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	21693616	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
colon cancer	17210682	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	22028636	CNVD
Breast cancer	21264507	CNVD
Thyroid cancer	19087340	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Colorectal cancer	19359472	CNVD
Gastric cancer	17167181	CNVD
Myeloproliferative neoplasm	19047681	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Breast cancer	17603634	CNVD
Melanoma	18172304	CNVD
Breast cancer	16608533	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17133270	CNVD
Oral cancer	21386901	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Myelodysplastic syndrome	21251322	CNVD
Ductal carcinoma	22052326	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Colorectal cancer	16774939	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Gastric cancer	20585902	CNVD
Ductal carcinoma	18381933	CNVD
Cancer	21129771	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	20864512	CNVD
Ovarian cancer	22174824	CNVD
Lung cancer	16740712	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16620391	CNVD
Okamoto syndrome	17623483	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21785460	CNVD
Bladder cancer	21909424	CNVD
Biliary cancer	19435499	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Cervical cancer	16585170	CNVD
Ovarian cancer	20844748	CNVD
Hirschsprung''s Disease	21712996	CNVD
Breast cancer	21364760	CNVD
Breast cancer	20459607	CNVD
Gastric cancer	18160780	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52443400-52456000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52444000-52453200	Weak transcription	Small Intestine	intestine
4	chr20:52444800-52456000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:52446600-52455400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:52447000-52456000	Weak transcription	Placenta	Placenta
7	chr20:52447200-52453400	Weak transcription	Fetal Intestine Small	intestine
8	chr20:52447200-52453400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr20:52447400-52453600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr20:52447400-52456200	Weak transcription	HUVEC	blood vessel
11	chr20:52447400-52459400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr20:52447600-52453200	Weak transcription	Colonic Mucosa	Colon
13	chr20:52449200-52456000	Weak transcription	Lung	lung
14	chr20:52449200-52456200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:52449600-52457800	Enhancers	Primary B cells from cord blood	blood
16	chr20:52449800-52461000	Enhancers	Primary B cells from peripheral blood	blood
17	chr20:52450000-52453800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr20:52450000-52462000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr20:52450200-52453200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr20:52450200-52454000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr20:52450400-52457800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr20:52450400-52465200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr20:52450600-52465200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr20:52450800-52453600	Weak transcription	HepG2	liver
25	chr20:52450800-52456000	Weak transcription	Fetal Muscle Leg	muscle
26	chr20:52451000-52453600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr20:52451000-52453600	Weak transcription	A549	lung
28	chr20:52451000-52456000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr20:52451000-52456200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:52451000-52456200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:52451000-52457000	Weak transcription	NHDF-Ad	bronchial
32	chr20:52451000-52462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:52451200-52454000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr20:52451200-52457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr20:52451200-52457200	Weak transcription	NHEK	skin
36	chr20:52451200-52464000	Weak transcription	HSMM	muscle
37	chr20:52452200-52454400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr20:52452200-52456800	Enhancers	Fetal Intestine Large	intestine
39	chr20:52452400-52453400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr20:52452400-52453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr20:52452400-52454000	Enhancers	Duodenum Mucosa	Duodenum
42	chr20:52452400-52454800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr20:52452400-52455000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr20:52452400-52455000	Weak transcription	Dnd41	blood
45	chr20:52452400-52455000	Weak transcription	GM12878-XiMat	blood
46	chr20:52452400-52455200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr20:52452400-52455200	Weak transcription	Thymus	Thymus
48	chr20:52452400-52456000	Weak transcription	Spleen	Spleen
49	chr20:52452400-52463800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr20:52452400-52465200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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