Variant report

Variant	nsv965931
Chromosome Location	chr20:10855702-10860385
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:10856745..10858884-chr20:10861213..10863486,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JAG1-2	chr20:10858972-10859021	ENSG00000232900.1
2	lnc-JAG1-2	chr20:10855981-10856878	ENSG00000232900.1

Extended variants
information (count: 178 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:178 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs373915105	chr20:10855752-10855753	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs77816315	chr20:10855932-10855933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs536541611	chr20:10855968-10855969	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs550361524	chr20:10855975-10855976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs143951934	chr20:10855990-10855991	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs539145530	chr20:10856056-10856057	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs190370918	chr20:10856064-10856065	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs182560876	chr20:10856068-10856069	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs79209945	chr20:10856077-10856078	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs6134061	chr20:10856114-10856115	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs2223977	chr20:10856122-10856123	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs116572445	chr20:10856135-10856136	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs545337154	chr20:10856145-10856146	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs542515384	chr20:10856146-10856147	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs562704535	chr20:10856156-10856157	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs576126479	chr20:10856160-10856161	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs369512618	chr20:10856168-10856169	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs542510122	chr20:10856191-10856192	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs564861490	chr20:10856192-10856193	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs565198958	chr20:10856216-10856217	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs140683712	chr20:10856218-10856219	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs117916782	chr20:10856228-10856229	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs530332980	chr20:10856230-10856231	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs144420708	chr20:10856247-10856248	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs115954981	chr20:10856295-10856296	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs373068270	chr20:10856399-10856400	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs561055840	chr20:10856488-10856489	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs532631178	chr20:10856509-10856510	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs552716134	chr20:10856517-10856518	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs73604338	chr20:10856558-10856559	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs112566738	chr20:10856612-10856613	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs140777655	chr20:10856626-10856627	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs55723512	chr20:10856654-10856655	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs112349387	chr20:10856679-10856680	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs368219960	chr20:10856684-10856685	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs7345898	chr20:10856713-10856714	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs568415600	chr20:10856746-10856747	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs536567542	chr20:10856759-10856760	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs556147832	chr20:10856801-10856802	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs56674600	chr20:10856815-10856816	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs397960443	chr20:10856816-10856817	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs73086928	chr20:10856820-10856821	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs6032976	chr20:10856849-10856850	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs73604339	chr20:10856892-10856893	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs199897925	chr20:10857007-10857008	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs186682604	chr20:10857014-10857015	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs150103174	chr20:10857072-10857073	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs60698858	chr20:10857076-10857077	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs550907468	chr20:10857083-10857084	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs138411007	chr20:10857108-10857109	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Glaucoma	21310917	CNVD
Alagille syndrome	22470819	CNVD
Lung cancer	16773561	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21804112	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Myelofibrosis	22110671	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	20409316	CNVD
Congenital diaphragmatic hernia	21525063	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:10845600-10856200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:10846400-10856200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:10851000-10863600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr20:10856200-10856600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:10856200-10856800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:10856600-10857000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:10856800-10857200	Weak transcription	Adipose Nuclei	Adipose
8	chr20:10856800-10877800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:10857000-10858600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr20:10857000-10858600	Enhancers	NHDF-Ad	bronchial
11	chr20:10857000-10858800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr20:10857200-10857400	ZNF genes & repeats	NHLF	lung
13	chr20:10857200-10858000	Enhancers	Osteobl	bone
14	chr20:10857200-10858200	Enhancers	Liver	Liver
15	chr20:10857200-10858600	Enhancers	Adipose Nuclei	Adipose
16	chr20:10857400-10857600	Enhancers	NHLF	lung
17	chr20:10857600-10858000	Weak transcription	NHLF	lung
18	chr20:10858000-10858200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:10858000-10858400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr20:10858000-10858400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr20:10858000-10858400	Enhancers	Esophagus	oesophagus
22	chr20:10858000-10858400	Enhancers	Fetal Muscle Leg	muscle
23	chr20:10858000-10858400	Enhancers	Left Ventricle	heart
24	chr20:10858000-10858400	Enhancers	Ovary	ovary
25	chr20:10858000-10858400	Enhancers	NHLF	lung
26	chr20:10858800-10859000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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