Variant report

Variant	nsv178887
Chromosome Location	chr20:52885413-52894836
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:50)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52889394..52890221-chr20:52936512..52937186,2	MCF-7	breast:
2	chr20:52892335..52894745-chr20:52921772..52923928,2	MCF-7	breast:
3	chr17:57919124..57923290-chr20:52886956..52890114,3	MCF-7	breast:
4	chr20:52891487..52895363-chr20:52902222..52905146,4	MCF-7	breast:
5	chr20:52739968..52740956-chr20:52885332..52886103,2	MCF-7	breast:
6	chr20:52823148..52829420-chr20:52882441..52888238,13	MCF-7	breast:
7	chr20:52883714..52887393-chr20:53262850..53265125,5	MCF-7	breast:
8	chr20:52846960..52850669-chr20:52882090..52885757,4	MCF-7	breast:
9	chr20:52881899..52886453-chr20:53260602..53265051,8	MCF-7	breast:
10	chr20:52883328..52886194-chr20:52903780..52906080,2	MCF-7	breast:
11	chr20:52885163..52887679-chr20:53176549..53178400,2	MCF-7	breast:
12	chr20:52886227..52888754-chr20:52977596..52979522,2	MCF-7	breast:
13	chr20:52832813..52835165-chr20:52884473..52886237,2	MCF-7	breast:
14	chr20:52894243..52896440-chr20:53078562..53080828,2	MCF-7	breast:
15	chr20:52891151..52893259-chr21:33433759..33435627,2	MCF-7	breast:
16	chr20:52835239..52838782-chr20:52890174..52893182,4	MCF-7	breast:
17	chr20:52885360..52886093-chr20:52967759..52968496,2	MCF-7	breast:
18	chr20:52864263..52865094-chr20:52885677..52886537,2	MCF-7	breast:
19	chr20:52836483..52840611-chr20:52882316..52886295,8	MCF-7	breast:
20	chr20:52891755..52894002-chr3:64171405..64173308,2	MCF-7	breast:
21	chr20:52740380..52740956-chr20:52885457..52886103,2	MCF-7	breast:
22	chr20:52887664..52890260-chr20:52906709..52909647,3	MCF-7	breast:
23	chr20:52891107..52893591-chr20:52960404..52961944,2	MCF-7	breast:
24	chr20:52884175..52887299-chr20:52959985..52962637,4	MCF-7	breast:
25	chr20:52843780..52845745-chr20:52884098..52886121,2	MCF-7	breast:
26	chr20:52887540..52889848-chr20:52915513..52918256,2	MCF-7	breast:
27	chr20:52885127..52886115-chr7:8008156..8008786,2	MCF-7	breast:
28	chr20:52823927..52826251-chr20:52889879..52892276,2	MCF-7	breast:
29	chr20:52884699..52888516-chr20:52964644..52967204,3	MCF-7	breast:
30	chr20:52891210..52894147-chr20:52899496..52901678,2	MCF-7	breast:
31	chr20:52885262..52886034-chr20:53264976..53265669,2	MCF-7	breast:
32	chr20:52881988..52885819-chr20:52932723..52935221,3	MCF-7	breast:
33	chr20:52832649..52834532-chr20:52889938..52891832,2	MCF-7	breast:
34	chr15:65596894..65598661-chr20:52883990..52886001,2	MCF-7	breast:
35	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
36	chr20:52884063..52885700-chr20:53076206..53077738,2	MCF-7	breast:
37	chr20:52887973..52889800-chr21:46823594..46826427,2	MCF-7	breast:
38	chr20:52889290..52890241-chr20:53263132..53264016,3	MCF-7	breast:
39	chr20:52836080..52837145-chr20:52888954..52890297,11	MCF-7	breast:
40	chr20:52892973..52894968-chr20:52956980..52958556,2	MCF-7	breast:
41	chr20:52891578..52893729-chr20:52943256..52945368,2	MCF-7	breast:
42	chr20:52837894..52838793-chr20:52889468..52890085,3	MCF-7	breast:
43	chr20:49347658..49349686-chr20:52884532..52886332,2	MCF-7	breast:
44	chr20:52823141..52827110-chr20:52881540..52888271,10	MCF-7	breast:
45	chr20:52887148..52889148-chr20:52903005..52905781,2	MCF-7	breast:
46	chr20:52884195..52887005-chr20:53073312..53075000,2	MCF-7	breast:
47	chr20:52739897..52740786-chr20:52885429..52886265,2	MCF-7	breast:
48	chr20:52765381..52766270-chr20:52885301..52885922,2	MCF-7	breast:
49	chr20:52885398..52886107-chr20:53073038..53073570,3	MCF-7	breast:
50	chr20:52885191..52887868-chr20:55839667..55841629,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226017	chromatin interactions
ENSG00000106415	chromatin interactions
ENSG00000101132	chromatin interactions
ENSG00000101144	chromatin interactions
ENSG00000182871	chromatin interactions
ENSG00000124171	chromatin interactions
ENSG00000200156	chromatin interactions

Extended variants
information (count: 339 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:339 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11490962	chr20:52885413-52885414	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
2	rs11490963	chr20:52885414-52885415	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
3	rs11476888	chr20:52885440-52885441	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs112379671	chr20:52885455-52885456	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs113251872	chr20:52885485-52885486	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs369576288	chr20:52885488-52885489	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs544387406	chr20:52885547-52885548	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs139099735	chr20:52885567-52885568	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs574128437	chr20:52885599-52885600	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs542829640	chr20:52885662-52885663	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs553022938	chr20:52885669-52885670	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs573005092	chr20:52885693-52885694	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs558107092	chr20:52885825-52885826	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs544961539	chr20:52885842-52885843	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs6013944	chr20:52885852-52885853	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs530983621	chr20:52885896-52885897	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs143111487	chr20:52885930-52885931	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs147397113	chr20:52885935-52885936	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
19	rs529062434	chr20:52885942-52885943	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs560282697	chr20:52885957-52885958	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
21	rs34188000	chr20:52886000-52886001	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
22	rs34582270	chr20:52886010-52886011	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs188664790	chr20:52886011-52886012	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs34197250	chr20:52886020-52886021	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs292136	chr20:52886050-52886051	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs529417702	chr20:52886094-52886095	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs551494930	chr20:52886149-52886150	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs74627576	chr20:52886256-52886257	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs577080443	chr20:52886322-52886323	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs537076412	chr20:52886348-52886349	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs116371780	chr20:52886363-52886364	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs292137	chr20:52886366-52886367	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs536401488	chr20:52886374-52886375	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs553160148	chr20:52886385-52886386	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs573145554	chr20:52886416-52886417	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs11477671	chr20:52886422-52886423	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs114930246	chr20:52886423-52886424	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs538756096	chr20:52886449-52886450	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs559039697	chr20:52886511-52886512	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs117291809	chr20:52886529-52886530	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs544607529	chr20:52886570-52886571	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs563405657	chr20:52886580-52886581	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs192035472	chr20:52886602-52886603	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs141776190	chr20:52886694-52886695	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs35541334	chr20:52886696-52886697	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs559577401	chr20:52886703-52886704	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs528341617	chr20:52886712-52886713	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs115453752	chr20:52886740-52886741	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs184488141	chr20:52886742-52886743	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs189321722	chr20:52886748-52886749	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

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

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52883400-52885600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr20:52883400-52885600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:52883400-52885600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr20:52883400-52885600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr20:52883400-52885800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:52883400-52885800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr20:52883400-52885800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr20:52883400-52885800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:52883400-52885800	Enhancers	Placenta	Placenta
10	chr20:52883400-52886600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr20:52883600-52886000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:52883600-52886000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr20:52883600-52886200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr20:52883600-52886200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr20:52883800-52886000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr20:52883800-52886000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr20:52884000-52886000	Enhancers	Fetal Lung	lung
18	chr20:52884000-52889400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr20:52884600-52889200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr20:52885000-52885800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr20:52885000-52885800	Enhancers	Fetal Brain Male	brain
22	chr20:52885000-52885800	Enhancers	Fetal Stomach	stomach
23	chr20:52885000-52889600	Weak transcription	Pancreas	Pancrea
24	chr20:52885200-52889600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr20:52885200-52889600	Weak transcription	Ovary	ovary
26	chr20:52885400-52885800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr20:52885600-52886000	Enhancers	HepG2	liver
28	chr20:52885600-52889000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr20:52885800-52889200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr20:52885800-52889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr20:52886000-52889200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr20:52886000-52889200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr20:52886200-52889200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr20:52886200-52889200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr20:52889000-52890000	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr20:52889200-52889800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr20:52889200-52889800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr20:52889200-52890000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr20:52889200-52890000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr20:52889200-52890000	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr20:52889200-52890000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr20:52889400-52889800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr20:52889600-52890000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr20:52889600-52890000	Enhancers	H9 Cell Line	embryonic stem cell
45	chr20:52889600-52890000	Enhancers	Ovary	ovary
46	chr20:52889600-52890000	Enhancers	Pancreas	Pancrea
47	chr20:52889600-52890200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr20:52889800-52890000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr20:52890000-52893200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr20:52891800-52892400	Enhancers	Duodenum Mucosa	Duodenum

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