Variant report

Variant	nsv962638
Chromosome Location	chr20:52883415-52917517
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:107)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:107 , 50 per page) page: 1 2 3

No.	Distal block	Cell Line	Cell type
1	chr20:52765761..52766290-chr20:52913080..52913871,2	MCF-7	breast:
2	chr20:52823927..52826251-chr20:52889879..52892276,2	MCF-7	breast:
3	chr20:52891487..52895363-chr20:52902222..52905146,4	MCF-7	breast:
4	chr20:52841965..52845171-chr20:52882309..52885405,4	MCF-7	breast:
5	chr20:52209254..52210865-chr20:52881648..52883949,2	MCF-7	breast:
6	chr20:52883714..52887393-chr20:53262850..53265125,5	MCF-7	breast:
7	chr20:52916826..52918729-chr3:64490949..64493940,2	MCF-7	breast:
8	chr20:52887664..52890260-chr20:52906709..52909647,3	MCF-7	breast:
9	chr20:52901774..52903726-chr20:52915299..52918140,2	MCF-7	breast:
10	chr20:52884699..52888516-chr20:52964644..52967204,3	MCF-7	breast:
11	chr20:52887148..52889148-chr20:52903005..52905781,2	MCF-7	breast:
12	chr20:52892335..52894745-chr20:52921772..52923928,2	MCF-7	breast:
13	chr20:52898596..52901613-chr20:52930745..52932671,3	MCF-7	breast:
14	chr20:52823784..52826256-chr20:52906954..52909912,3	MCF-7	breast:
15	chr20:52845835..52847665-chr20:52881455..52883980,2	MCF-7	breast:
16	chr20:52911450..52915662-chr20:52921093..52925920,4	MCF-7	breast:
17	chr17:57919124..57923290-chr20:52886956..52890114,3	MCF-7	breast:
18	chr20:52908727..52910556-chr20:52917946..52923275,4	MCF-7	breast:
19	chr20:52885360..52886093-chr20:52967759..52968496,2	MCF-7	breast:
20	chr20:52887540..52889848-chr20:52915513..52918256,2	MCF-7	breast:
21	chr20:52886227..52888754-chr20:52977596..52979522,2	MCF-7	breast:
22	chr20:52720871..52722915-chr20:52882468..52884514,2	MCF-7	breast:
23	chr20:49347658..49349686-chr20:52884532..52886332,2	MCF-7	breast:
24	chr20:52882722..52884267-chr20:53265302..53267025,2	MCF-7	breast:
25	chr20:52740380..52740956-chr20:52885457..52886103,2	MCF-7	breast:
26	chr20:52739897..52740786-chr20:52885429..52886265,2	MCF-7	breast:
27	chr20:52897327..52899009-chr20:52901309..52903934,2	K562	blood:
28	chr20:52908114..52910241-chr20:52912363..52914987,2	MCF-7	breast:
29	chr20:52823411..52826205-chr20:52895497..52899712,3	MCF-7	breast:
30	chr20:52891210..52894147-chr20:52899496..52901678,2	MCF-7	breast:
31	chr20:52884063..52885700-chr20:53076206..53077738,2	MCF-7	breast:
32	chr20:52885262..52886034-chr20:53264976..53265669,2	MCF-7	breast:
33	chr20:52883800..52885374-chr20:52939481..52942023,2	MCF-7	breast:
34	chr20:52765381..52766270-chr20:52885301..52885922,2	MCF-7	breast:
35	chr20:52881899..52886453-chr20:53260602..53265051,8	MCF-7	breast:
36	chr20:52864152..52866358-chr20:52903811..52906264,2	MCF-7	breast:
37	chr11:67465569..67466368-chr20:52910827..52911623,2	MCF-7	breast:
38	chr20:52864263..52865094-chr20:52885677..52886537,2	MCF-7	breast:
39	chr20:52823141..52827110-chr20:52881540..52888271,10	MCF-7	breast:
40	chr20:52837175..52839951-chr20:52903324..52905854,2	MCF-7	breast:
41	chr20:52872714..52873402-chr20:52883465..52884136,2	MCF-7	breast:
42	chr20:52867284..52867978-chr20:52883331..52884092,2	MCF-7	breast:
43	chr19:35738580..35741475-chr20:52904507..52907195,2	MCF-7	breast:
44	chr20:52903809..52908618-chr20:52965034..52968390,4	MCF-7	breast:
45	chr20:52891107..52893591-chr20:52960404..52961944,2	MCF-7	breast:
46	chr20:52883328..52886194-chr20:52903780..52906080,2	MCF-7	breast:
47	chr20:52897965..52899622-chr20:52923358..52924887,2	MCF-7	breast:
48	chr20:52881900..52884717-chr20:52925408..52927187,2	MCF-7	breast:
49	chr20:52882962..52884659-chr20:53063631..53065695,2	MCF-7	breast:
50	chr20:52901774..52903726-chr20:52915299..52918140,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYP24A1-1	chr20:52904265-52904357	XLOC_013803

No data

Variant related genes	Relation type
ENSG00000226017	chromatin interactions
ENSG00000106415	chromatin interactions
ENSG00000105699	chromatin interactions
ENSG00000101144	chromatin interactions
ENSG00000101132	chromatin interactions
ENSG00000200156	chromatin interactions
ENSG00000167644	chromatin interactions
ENSG00000163635	chromatin interactions
ENSG00000182871	chromatin interactions
ENSG00000171940	chromatin interactions
ENSG00000124171	chromatin interactions
ENSG00000163634	chromatin interactions
ENSG00000206737	chromatin interactions

Extended variants
information (count: 1269 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:1269 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs533474947	chr20:52883425-52883426	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
2	rs550048533	chr20:52883436-52883437	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
3	rs180866668	chr20:52883450-52883451	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs186150190	chr20:52883482-52883483	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs568579967	chr20:52883572-52883573	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs370054239	chr20:52883579-52883580	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs7271035	chr20:52883584-52883585	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs568029675	chr20:52883588-52883589	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs191251343	chr20:52883590-52883591	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs553550662	chr20:52883618-52883619	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs144885441	chr20:52883628-52883629	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs7270940	chr20:52883682-52883683	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs556014988	chr20:52883715-52883716	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs575978093	chr20:52883745-52883746	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs183055437	chr20:52883762-52883763	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs562343686	chr20:52883799-52883800	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs185976122	chr20:52883807-52883808	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs190541422	chr20:52883818-52883819	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
19	rs56085842	chr20:52883840-52883841	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs2061721	chr20:52883857-52883858	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs79675083	chr20:52883882-52883883	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
22	rs548368547	chr20:52883907-52883908	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
23	rs550225835	chr20:52883942-52883943	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
24	rs148619254	chr20:52883951-52883952	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs529253225	chr20:52883965-52883966	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs371651744	chr20:52883983-52883984	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs548985004	chr20:52883991-52883992	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
28	rs567964337	chr20:52884037-52884038	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
29	rs117268191	chr20:52884039-52884040	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
30	rs6068848	chr20:52884046-52884047	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
31	rs183151060	chr20:52884047-52884048	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
32	rs187852318	chr20:52884048-52884049	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
33	rs539291504	chr20:52884061-52884062	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
34	rs556191907	chr20:52884067-52884068	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
35	rs576081831	chr20:52884072-52884073	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
36	rs377532616	chr20:52884097-52884098	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
37	rs6068849	chr20:52884145-52884146	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
38	rs535382751	chr20:52884177-52884178	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
39	rs193149041	chr20:52884195-52884196	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
40	rs141098305	chr20:52884214-52884215	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
41	rs572113058	chr20:52884225-52884226	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
42	rs59946156	chr20:52884245-52884246	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs564797398	chr20:52884250-52884251	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
44	rs143266599	chr20:52884342-52884343	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
45	rs543669752	chr20:52884360-52884361	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
46	rs146708327	chr20:52884363-52884364	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
47	rs10485793	chr20:52884386-52884387	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs529369308	chr20:52884413-52884414	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
49	rs545746565	chr20:52884414-52884415	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
50	rs559310068	chr20:52884438-52884439	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 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
Melanoma	17363583	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:164 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52872800-52883800	Weak transcription	Pancreas	Pancrea
2	chr20:52874200-52883600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr20:52874200-52884000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr20:52879800-52883800	Weak transcription	Osteobl	bone
5	chr20:52880600-52884000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr20:52880800-52883600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:52881000-52884000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr20:52881200-52884000	Weak transcription	Fetal Lung	lung
9	chr20:52881200-52885000	Weak transcription	Fetal Stomach	stomach
10	chr20:52882800-52883600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr20:52882800-52884200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:52883200-52885000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:52883400-52884400	Enhancers	Esophagus	oesophagus
14	chr20:52883400-52884800	Enhancers	HMEC	breast
15	chr20:52883400-52885200	Enhancers	Ovary	ovary
16	chr20:52883400-52885400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr20:52883400-52885600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr20:52883400-52885600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr20:52883400-52885600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:52883400-52885600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr20:52883400-52885800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr20:52883400-52885800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr20:52883400-52885800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr20:52883400-52885800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr20:52883400-52885800	Enhancers	Placenta	Placenta
26	chr20:52883400-52886600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr20:52883600-52884000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr20:52883600-52884200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr20:52883600-52884200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr20:52883600-52884400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr20:52883600-52884400	Enhancers	Hela-S3	cervix
32	chr20:52883600-52884600	Bivalent Enhancer	HepG2	liver
33	chr20:52883600-52884800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr20:52883600-52884800	Enhancers	Stomach Mucosa	stomach
35	chr20:52883600-52885000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr20:52883600-52885400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr20:52883600-52886000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:52883600-52886000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr20:52883600-52886200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr20:52883600-52886200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr20:52883800-52884000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr20:52883800-52884400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr20:52883800-52884400	Enhancers	Pancreas	Pancrea
44	chr20:52883800-52884400	Enhancers	Osteobl	bone
45	chr20:52883800-52884600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr20:52883800-52884600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:52883800-52884600	Enhancers	Aorta	Aorta
48	chr20:52883800-52884600	Enhancers	NH-A	brain
49	chr20:52883800-52884600	Enhancers	NHEK	skin
50	chr20:52883800-52884800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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