Variant report

Variant	nsv1058035
Chromosome Location	chr20:13217890-13249342
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr20:13242668-13243057	HepG2	liver:	n/a	n/a
2	ARID3A	chr20:13224184-13225291	HepG2	liver:	n/a	n/a
3	ARID3A	chr20:13225796-13226403	HepG2	liver:	n/a	n/a
4	ATF2	chr20:13227864-13228573	GM12878	blood:	n/a	n/a
5	ATF3	chr20:13224327-13224907	A549	lung:	n/a	n/a
6	BATF	chr20:13241273-13241512	GM12878	blood:	n/a	n/a
7	BATF	chr20:13227971-13228436	GM12878	blood:	n/a	chr20:13228049-13228062 chr20:13228309-13228318
8	BCL11A	chr20:13228024-13228227	GM12878	blood:	n/a	n/a
9	BCL11A	chr20:13227920-13228337	GM12878	blood:	n/a	n/a
10	BCL3	chr20:13224249-13224988	A549	lung:	n/a	n/a
11	BCLAF1	chr20:13227948-13228349	GM12878	blood:	n/a	n/a
12	BCLAF1	chr20:13227848-13228366	GM12878	blood:	n/a	n/a
13	BHLHE40	chr20:13228283-13228432	HepG2	liver:	n/a	n/a
14	BHLHE40	chr20:13224471-13225052	HepG2	liver:	n/a	n/a
15	BHLHE40	chr20:13225966-13226376	HepG2	liver:	n/a	n/a
16	BRCA1	chr20:13226049-13226099	HepG2	liver:	n/a	n/a
17	BRCA1	chr20:13242643-13242959	HepG2	liver:	n/a	n/a
18	CEBPB	chr20:13226009-13226301	MCF-7	breast:	n/a	chr20:13226151-13226162
19	CEBPB	chr20:13241257-13241595	HepG2	liver:	n/a	n/a
20	CEBPB	chr20:13225895-13226307	HepG2	liver:	n/a	chr20:13226151-13226162
21	CEBPB	chr20:13225906-13226448	HepG2	liver:	n/a	chr20:13226151-13226162
22	CEBPB	chr20:13246753-13246763	K562	blood:	n/a	n/a
23	CEBPB	chr20:13243486-13243741	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr20:13226009-13226293	HepG2	liver:	n/a	chr20:13226151-13226162
25	CEBPB	chr20:13224206-13224843	A549	lung:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
26	CEBPB	chr20:13232220-13232400	HepG2	liver:	n/a	n/a
27	CEBPB	chr20:13224370-13224938	HepG2	liver:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
28	CEBPB	chr20:13224425-13224784	HepG2	liver:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
29	CEBPB	chr20:13224439-13224930	HepG2	liver:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
30	CEBPB	chr20:13226062-13226309	A549	lung:	n/a	chr20:13226151-13226162
31	CEBPB	chr20:13225957-13226410	HepG2	liver:	n/a	chr20:13226151-13226162
32	CEBPB	chr20:13224364-13224858	A549	lung:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
33	CEBPB	chr20:13224375-13224834	MCF-7	breast:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
34	CEBPB	chr20:13224365-13224817	MCF-7	breast:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
35	CEBPB	chr20:13232176-13232509	HepG2	liver:	n/a	n/a
36	CEBPB	chr20:13221222-13221522	HepG2	liver:	n/a	chr20:13221361-13221372
37	CEBPB	chr20:13224155-13225034	A549	lung:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
38	CEBPB	chr20:13224389-13225013	HepG2	liver:	n/a	chr20:13224569-13224581 chr20:13224646-13224663
39	CEBPD	chr20:13224469-13224812	HepG2	liver:	n/a	n/a
40	CEBPD	chr20:13225904-13226338	HepG2	liver:	n/a	n/a
41	CEBPD	chr20:13225956-13226272	HepG2	liver:	n/a	n/a
42	CHD2	chr20:13224434-13224919	HepG2	liver:	n/a	n/a
43	CHD2	chr20:13227947-13228291	GM12878	blood:	n/a	n/a
44	CHD2	chr20:13226009-13226221	HepG2	liver:	n/a	n/a
45	CHD2	chr20:13242501-13243041	HepG2	liver:	n/a	n/a
46	CREB1	chr20:13224291-13225051	HepG2	liver:	n/a	n/a
47	CTCF	chr20:13242007-13242039	Lung_OC	lung:	n/a	n/a
48	CTCF	chr20:13242880-13243030	WI-38	lung:	n/a	chr20:13242893-13242902 chr20:13242890-13242900 chr20:13242887-13242905
49	CTCF	chr20:13242840-13242990	GM12864	blood:	n/a	chr20:13242893-13242902 chr20:13242890-13242900 chr20:13242887-13242905
50	CTCF	chr20:13242860-13243010	HCM	heart:	n/a	chr20:13242893-13242902 chr20:13242890-13242900 chr20:13242887-13242905

No.	Distal block	Cell Line	Cell type
1	chr20:12950635..12951321-chr20:13242468..13243223,2	MCF-7	breast:
2	chr20:13217886..13220237-chr20:13220614..13223071,3	MCF-7	breast:
3	chr20:13222224..13226467-chr20:13226832..13229125,4	MCF-7	breast:
4	chr20:13225351..13227078-chr20:13232726..13234413,2	MCF-7	breast:
5	chr20:13099864..13101163-chr20:13242113..13243382,13	MCF-7	breast:
6	chr20:13099834..13100573-chr20:13242429..13243331,4	MCF-7	breast:
7	chr20:13217886..13220237-chr20:13220614..13223071,3	MCF-7	breast:
8	chr20:13186346..13187286-chr20:13242328..13243323,3	MCF-7	breast:
9	chr20:13224428..13227075-chr20:13229216..13232192,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TASP1-2	chr20:13218067-13218756	NONHSAT078683
2	lnc-TASP1-1	chr20:13225889-13226016	ENSG00000225956.1
3	lnc-TASP1-1	chr20:13224711-13225028	ENSG00000225956.1
4	lnc-SPTLC3-5	chr20:13219374-13219813	NONHSAT078685
5	lnc-TASP1-2	chr20:13218733-13218756	NONHSAT078684
6	lnc-SPTLC3-5	chr20:13229880-13230196	NONHSAT078685
7	lnc-TASP1-2	chr20:13219658-13220301	NONHSAT078684
8	lnc-TASP1-2	chr20:13220100-13220334	NONHSAT078683
9	lnc-TASP1-2	chr20:13219631-13219751	NONHSAT078683

Variant related genes	Relation type
ENSG00000225956	TF binding region
ISM1-AS1	TF binding region
ENSG00000225956	chromatin interactions

Extended variants
information (count: 1230 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:1230 , 50 per page) page: 1 2 3 4 5 6 7 ... 25

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs190859738	chr20:13217896-13217897	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs6109771	chr20:13217929-13217930	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs6109772	chr20:13217937-13217938	Weak transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs6105053	chr20:13217974-13217975	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs535775576	chr20:13217989-13217990	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs149016160	chr20:13218032-13218033	Enhancers Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs115411466	chr20:13218067-13218068	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs537797253	chr20:13218071-13218072	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs557592511	chr20:13218087-13218088	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs567896780	chr20:13218092-13218093	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs145904745	chr20:13218097-13218098	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs553560089	chr20:13218122-13218123	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs140385889	chr20:13218140-13218141	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs370634764	chr20:13218141-13218142	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs138190125	chr20:13218154-13218155	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs562004473	chr20:13218168-13218169	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs6105054	chr20:13218169-13218170	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs575237065	chr20:13218222-13218223	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs182441381	chr20:13218237-13218238	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs533775929	chr20:13218249-13218250	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs533500805	chr20:13218282-13218283	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs1060580	chr20:13218326-13218327	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs560340506	chr20:13218327-13218328	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs1060579	chr20:13218333-13218334	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs549305427	chr20:13218378-13218379	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs569147705	chr20:13218382-13218383	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs537859506	chr20:13218385-13218386	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs551392911	chr20:13218417-13218418	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs571136500	chr20:13218465-13218466	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs186630268	chr20:13218521-13218522	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs142769922	chr20:13218527-13218528	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs145035009	chr20:13218538-13218539	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs191984378	chr20:13218572-13218573	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs535607508	chr20:13218612-13218613	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs555661899	chr20:13218622-13218623	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs117635951	chr20:13218627-13218628	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs201735750	chr20:13218636-13218637	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs544561898	chr20:13218720-13218721	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs182916112	chr20:13218733-13218734	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs546900361	chr20:13218742-13218743	Enhancers Weak transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs567021200	chr20:13218766-13218767	Enhancers Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs188421661	chr20:13218767-13218768	Enhancers Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs555337118	chr20:13218770-13218771	Enhancers Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs397751447	chr20:13218773-13218774	Enhancers Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs397763312	chr20:13218774-13218775	Enhancers Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs371994663	chr20:13218830-13218831	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs575078590	chr20:13218969-13218970	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs377274223	chr20:13218972-13218973	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs560528442	chr20:13219058-13219059	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs529125617	chr20:13219070-13219071	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

Disease	PMID	Source
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
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	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
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Myelofibrosis	22110671	CNVD
Kabuki syndrome	21720541	CNVD
Glioblastoma multiforme	22286061	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Neurocytoma	17123091	CNVD
Autism	22102821	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:412 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13203600-13229800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr20:13212600-13226600	Weak transcription	Dnd41	blood
3	chr20:13212800-13218000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr20:13212800-13218400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr20:13212800-13224000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:13212800-13224200	Weak transcription	NHEK	skin
7	chr20:13213000-13218400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr20:13213000-13219000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr20:13215600-13220400	Enhancers	Liver	Liver
10	chr20:13215800-13220200	Weak transcription	Aorta	Aorta
11	chr20:13216000-13218800	Weak transcription	HepG2	liver
12	chr20:13216000-13219000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr20:13216200-13218000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr20:13216400-13225400	Weak transcription	Placenta	Placenta
15	chr20:13216600-13218200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr20:13217400-13218600	Enhancers	Pancreas	Pancrea
17	chr20:13218000-13218400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr20:13218000-13218600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr20:13218000-13218600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:13218000-13219200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr20:13218000-13219400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr20:13218200-13218600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:13218200-13218800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr20:13218200-13218800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr20:13218200-13219200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:13218400-13218600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr20:13218400-13218800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr20:13218400-13219000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr20:13218400-13219000	Enhancers	Osteobl	bone
30	chr20:13218400-13219200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:13218400-13219200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr20:13218600-13219400	Weak transcription	Pancreas	Pancrea
33	chr20:13218800-13219200	Enhancers	HepG2	liver
34	chr20:13218800-13243200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr20:13219000-13220400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr20:13219000-13223800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr20:13219000-13227200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr20:13219200-13223000	Weak transcription	HepG2	liver
39	chr20:13219200-13223800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr20:13219200-13223800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr20:13219200-13224000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr20:13219200-13224000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr20:13219400-13219800	Enhancers	Pancreas	Pancrea
44	chr20:13219400-13223800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr20:13219800-13223800	Weak transcription	Pancreas	Pancrea
46	chr20:13220200-13220400	ZNF genes & repeats	Aorta	Aorta
47	chr20:13220400-13221000	Weak transcription	Aorta	Aorta
48	chr20:13220400-13223000	Weak transcription	Liver	Liver
49	chr20:13220400-13223200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr20:13221600-13221800	Enhancers	Thymus	Thymus

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