Variant report

Variant	nsv586277
Chromosome Location	chr20:52654219-52660741
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56707748..56711068-chr20:52660176..52663748,3	MCF-7	breast:
2	chr19:11025812..11027987-chr20:52653374..52655752,2	MCF-7	breast:
3	chr20:52655188..52657937-chr20:55839006..55840900,2	MCF-7	breast:
4	chr20:52659902..52660887-chr20:52678920..52680381,7	MCF-7	breast:
5	chr20:52643210..52646138-chr20:52658422..52660423,2	K562	blood:
6	chr20:52647368..52649299-chr20:52654193..52656329,2	MCF-7	breast:
7	chr1:121484253..121484817-chr20:52659977..52660776,2	MCF-7	breast:
8	chr20:52659945..52660854-chr20:52815931..52816527,2	MCF-7	breast:
9	chr17:57917278..57919596-chr20:52653625..52656516,2	MCF-7	breast:
10	chr20:52557746..52563146-chr20:52657006..52659772,4	MCF-7	breast:
11	chr20:52626505..52628533-chr20:52652801..52654568,2	MCF-7	breast:
12	chr20:52621471..52622138-chr20:52658585..52659278,2	MCF-7	breast:
13	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
14	chr20:52642833..52647245-chr20:52651317..52656592,5	MCF-7	breast:
15	chr20:52637408..52640155-chr20:52655059..52656752,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000199004	chromatin interactions
ENSG00000212195	chromatin interactions
ENSG00000064787	chromatin interactions
ENSG00000101144	chromatin interactions

Extended variants
information (count: 273 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:273 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs290466	chr20:52654219-52654220	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs73914475	chr20:52654289-52654290	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs369075016	chr20:52654291-52654292	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs290467	chr20:52654353-52654354	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs55729911	chr20:52654412-52654413	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs556847337	chr20:52654433-52654434	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs183866347	chr20:52654434-52654435	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs60038700	chr20:52654451-52654452	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs376614905	chr20:52654452-52654453	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs76949978	chr20:52654461-52654462	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs368217194	chr20:52654468-52654469	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs149090514	chr20:52654485-52654486	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs537313768	chr20:52654501-52654502	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs143172586	chr20:52654543-52654544	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs290468	chr20:52654547-52654548	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs564956668	chr20:52654549-52654550	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs115747248	chr20:52654571-52654572	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs148272991	chr20:52654584-52654585	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs111428853	chr20:52654648-52654649	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs113162472	chr20:52654674-52654675	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs6068760	chr20:52654684-52654685	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs290469	chr20:52654711-52654712	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs556882198	chr20:52654767-52654768	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs532359775	chr20:52654773-52654774	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs552284079	chr20:52654844-52654845	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs569029157	chr20:52654912-52654913	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs1381983	chr20:52654972-52654973	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs537737412	chr20:52655010-52655011	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs189671118	chr20:52655043-52655044	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs567299556	chr20:52655159-52655160	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs181516110	chr20:52655262-52655263	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs553293790	chr20:52655274-52655275	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs1381984	chr20:52655304-52655305	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs6068761	chr20:52655307-52655308	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs575654377	chr20:52655318-52655319	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs377468873	chr20:52655369-52655370	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs538616358	chr20:52655378-52655379	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs114753405	chr20:52655425-52655426	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs142484025	chr20:52655455-52655456	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs146359514	chr20:52655456-52655457	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs374262542	chr20:52655476-52655477	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs561577475	chr20:52655496-52655497	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs138253101	chr20:52655537-52655538	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs149620337	chr20:52655556-52655557	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs368716549	chr20:52655632-52655633	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs372633164	chr20:52655677-52655678	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs113343500	chr20:52655703-52655704	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs562696902	chr20:52655719-52655720	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs148808373	chr20:52655735-52655736	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs548388450	chr20:52655750-52655751	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

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
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
Medulloblastoma	16783165	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
2	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52646000-52657000	Weak transcription	Gastric	stomach
5	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:52654800-52656400	Enhancers	K562	blood
7	chr20:52655200-52656400	Enhancers	Fetal Kidney	kidney
8	chr20:52655200-52657200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr20:52655200-52658200	Enhancers	Fetal Stomach	stomach
10	chr20:52656400-52656800	Weak transcription	Fetal Kidney	kidney
11	chr20:52656400-52656800	Weak transcription	K562	blood
12	chr20:52656800-52657200	Enhancers	Colon Smooth Muscle	Colon
13	chr20:52656800-52657400	Enhancers	Fetal Kidney	kidney
14	chr20:52656800-52657400	Enhancers	K562	blood
15	chr20:52657000-52657400	Enhancers	Gastric	stomach
16	chr20:52657000-52657800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr20:52657000-52657800	Enhancers	HSMMtube	muscle
18	chr20:52657200-52657600	Enhancers	NHDF-Ad	bronchial
19	chr20:52657400-52658600	Weak transcription	K562	blood
20	chr20:52657600-52659400	Weak transcription	NHDF-Ad	bronchial
21	chr20:52657800-52659600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:52657800-52664800	Weak transcription	HSMMtube	muscle
23	chr20:52658200-52659400	Weak transcription	Fetal Stomach	stomach
24	chr20:52658600-52660000	Enhancers	K562	blood
25	chr20:52659400-52660400	Enhancers	Fetal Stomach	stomach
26	chr20:52659400-52661000	Enhancers	NHDF-Ad	bronchial
27	chr20:52659600-52659800	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr20:52659600-52660600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr20:52659600-52661000	Enhancers	GM12878-XiMat	blood
30	chr20:52659600-52661800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr20:52659800-52660600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr20:52660000-52660400	Enhancers	Fetal Brain Male	brain
33	chr20:52660000-52660600	Enhancers	Fetal Lung	lung
34	chr20:52660000-52660800	Flanking Active TSS	K562	blood
35	chr20:52660000-52661000	Enhancers	NHLF	lung
36	chr20:52660000-52661200	Enhancers	Osteobl	bone
37	chr20:52660200-52660400	Enhancers	Right Atrium	heart
38	chr20:52660200-52660600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:52660200-52661600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr20:52660200-52661600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr20:52660400-52661000	Enhancers	HMEC	breast
42	chr20:52660400-52664200	Weak transcription	Right Atrium	heart
43	chr20:52660600-52660800	Enhancers	Duodenum Smooth Muscle	Duodenum

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