Variant report

Variant	nsv3292
Chromosome Location	chr20:11233247-11267986
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	chr20:11247995-11248306	HepG2	liver:	n/a	n/a
2	ARID3A	chr20:11254652-11255091	HepG2	liver:	n/a	n/a
3	ATF1	chr20:11258878-11259027	K562	blood:	n/a	n/a
4	ATF2	chr20:11242156-11242642	GM12878	blood:	n/a	n/a
5	ATF2	chr20:11251947-11252321	H1-hESC	embryonic stem cell:	n/a	n/a
6	ATF2	chr20:11242142-11242608	GM12878	blood:	n/a	n/a
7	ATF2	chr20:11247765-11248607	GM12878	blood:	n/a	n/a
8	ATF2	chr20:11247790-11248613	GM12878	blood:	n/a	n/a
9	ATF3	chr20:11247759-11248485	A549	lung:	n/a	chr20:11248127-11248141
10	ATF3	chr20:11247698-11248460	A549	lung:	n/a	chr20:11248127-11248141
11	BACH1	chr20:11252115-11252315	H1-hESC	embryonic stem cell:	n/a	n/a
12	BATF	chr20:11255459-11255682	GM12878	blood:	n/a	n/a
13	BATF	chr20:11236518-11236795	GM12878	blood:	n/a	chr20:11236676-11236687
14	BATF	chr20:11242144-11242512	GM12878	blood:	n/a	chr20:11242288-11242299 chr20:11242354-11242365
15	BATF	chr20:11247953-11248425	GM12878	blood:	n/a	chr20:11248163-11248173 chr20:11248162-11248173
16	BATF	chr20:11249297-11249629	GM12878	blood:	n/a	n/a
17	BATF	chr20:11247874-11248415	GM12878	blood:	n/a	chr20:11248163-11248173 chr20:11248162-11248173
18	BCL11A	chr20:11242189-11242618	GM12878	blood:	n/a	chr20:11242478-11242487
19	BCL11A	chr20:11242265-11242526	GM12878	blood:	n/a	chr20:11242478-11242487
20	BCL11A	chr20:11247869-11248477	GM12878	blood:	n/a	n/a
21	BCL11A	chr20:11247917-11248381	GM12878	blood:	n/a	n/a
22	BCL3	chr20:11247425-11248663	A549	lung:	n/a	n/a
23	BCL3	chr20:11242102-11242620	GM12878	blood:	n/a	chr20:11242478-11242487
24	BCL3	chr20:11247723-11248766	A549	lung:	n/a	n/a
25	BCL3	chr20:11247772-11248477	GM12878	blood:	n/a	n/a
26	BCLAF1	chr20:11247797-11248428	GM12878	blood:	n/a	n/a
27	BCLAF1	chr20:11247875-11248514	GM12878	blood:	n/a	n/a
28	BHLHE40	chr20:11242282-11242593	GM12878	blood:	n/a	n/a
29	BHLHE40	chr20:11247647-11248493	GM12878	blood:	n/a	n/a
30	BRCA1	chr20:11248087-11248201	GM12878	blood:	n/a	n/a
31	BRCA1	chr20:11254696-11255044	Hela-S3	cervix:	n/a	n/a
32	CBX3	chr20:11247765-11248450	HCT-116	colon:	n/a	n/a
33	CBX3	chr20:11247887-11248472	HCT-116	colon:	n/a	n/a
34	CEBPB	chr20:11254804-11255162	IMR90	lung:	n/a	chr20:11255092-11255103
35	CEBPB	chr20:11247426-11248569	A549	lung:	n/a	chr20:11247464-11247475
36	CEBPB	chr20:11254836-11255184	HepG2	liver:	n/a	chr20:11255092-11255103
37	CEBPB	chr20:11260258-11260381	H1-hESC	embryonic stem cell:	n/a	chr20:11260319-11260330
38	CEBPB	chr20:11243534-11243783	HepG2	liver:	n/a	chr20:11243672-11243683
39	CEBPB	chr20:11247943-11248425	A549	lung:	n/a	n/a
40	CEBPB	chr20:11254717-11255214	Hela-S3	cervix:	n/a	chr20:11255092-11255103
41	CEBPB	chr20:11260155-11260482	A549	lung:	n/a	chr20:11260319-11260330
42	CEBPB	chr20:11260149-11260486	IMR90	lung:	n/a	chr20:11260319-11260330
43	CEBPB	chr20:11247897-11248612	GM12878	blood:	n/a	n/a
44	CEBPB	chr20:11254638-11255156	A549	lung:	n/a	chr20:11255092-11255103
45	CEBPB	chr20:11254656-11255354	A549	lung:	n/a	chr20:11255092-11255103
46	CEBPB	chr20:11242218-11242989	IMR90	lung:	n/a	n/a
47	CEBPB	chr20:11242539-11242664	HepG2	liver:	n/a	n/a
48	CEBPB	chr20:11260154-11260501	HepG2	liver:	n/a	chr20:11260319-11260330
49	CHD1	chr20:11247815-11248178	GM12878	blood:	n/a	n/a
50	CHD2	chr20:11247748-11248452	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:10655327..10655986-chr20:11254319..11255290,2	MCF-7	breast:
2	chr20:10653814..10656504-chr20:11241150..11243933,2	MCF-7	breast:
3	chr20:11185575..11186124-chr20:11254374..11255017,2	MCF-7	breast:
4	chr20:10652090..10655937-chr20:11248830..11252112,5	MCF-7	breast:
5	chr20:11079357..11080270-chr20:11254391..11255324,2	MCF-7	breast:
6	chr20:10449236..10450857-chr20:11245415..11248103,2	MCF-7	breast:
7	chr20:10652886..10654670-chr20:11251547..11255008,4	MCF-7	breast:
8	chr20:10652412..10655636-chr20:11252781..11255204,3	MCF-7	breast:
9	chr20:11254480..11254986-chr20:11524838..11525340,2	MCF-7	breast:
10	chr20:10652267..10657207-chr20:11246238..11249424,5	MCF-7	breast:
11	chr20:10654964..10657120-chr20:11255406..11257324,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JAG1-3	chr20:11240592-11240639	NONHSAT078628
2	lnc-JAG1-3	chr20:11250907-11251326	ENSG00000230990
3	lnc-JAG1-3	chr20:11253982-11254031	NONHSAT078630
4	lnc-JAG1-3	chr20:11246764-11247091	ENSG00000230990
5	lnc-JAG1-3	chr20:11249398-11249530	ENSG00000230990
6	lnc-JAG1-3	chr20:11267310-11267427	ENSG00000230990
7	lnc-JAG1-3	chr20:11249398-11249483	ENSG00000230990
8	lnc-JAG1-3	chr20:11249398-11249530	NONHSAT078628
9	lnc-JAG1-3	chr20:11247307-11249530	NONHSAT078630
10	lnc-JAG1-3	chr20:11253982-11254017	NONHSAT078628
11	lnc-JAG1-3	chr20:11253982-11254031	ENSG00000230990
12	lnc-JAG1-3	chr20:11251853-11251931	ENSG00000230990

Variant related genes	Relation type
ENSG00000230990	TF binding region
ENSG00000270792	chromatin interactions
ENSG00000101384	chromatin interactions

Extended variants
information (count: 1526 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:1526 , 50 per page) page: 1 2 3 4 5 6 7 ... 31

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540774656	chr20:11233271-11233272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs34163988	chr20:11233299-11233300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs560738645	chr20:11233300-11233301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs186952236	chr20:11233334-11233335	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs550000913	chr20:11233367-11233368	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs569872234	chr20:11233401-11233402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs34413777	chr20:11233417-11233418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs531693616	chr20:11233426-11233427	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs1473703	chr20:11233456-11233457	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs376681453	chr20:11233497-11233498	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs528235964	chr20:11233552-11233553	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs571719294	chr20:11233653-11233654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs192509216	chr20:11233673-11233674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs141799231	chr20:11233675-11233676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs375252646	chr20:11233677-11233678	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs567815063	chr20:11233709-11233710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs375376968	chr20:11233730-11233731	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs536468706	chr20:11233739-11233740	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs556783043	chr20:11233751-11233752	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs548289475	chr20:11233854-11233855	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs114548228	chr20:11233908-11233909	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs185025984	chr20:11233933-11233934	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs6104731	chr20:11233941-11233942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs6033071	chr20:11233981-11233982	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs558125995	chr20:11233986-11233987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs571749464	chr20:11234077-11234078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs147209977	chr20:11234082-11234083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs560652605	chr20:11234084-11234085	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs529868954	chr20:11234120-11234121	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs188932847	chr20:11234141-11234142	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs563530556	chr20:11234173-11234174	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs532280710	chr20:11234214-11234215	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs140545856	chr20:11234215-11234216	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs6033072	chr20:11234216-11234217	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs527690974	chr20:11234225-11234226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs547884935	chr20:11234249-11234250	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs144389146	chr20:11234250-11234251	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs536787573	chr20:11234260-11234261	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs550085367	chr20:11234273-11234274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs570276918	chr20:11234274-11234275	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs538954982	chr20:11234291-11234292	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs147285509	chr20:11234364-11234365	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs2223857	chr20:11234406-11234407	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs534336725	chr20:11234417-11234418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs62191786	chr20:11234418-11234419	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs574431204	chr20:11234420-11234421	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs34510027	chr20:11234421-11234422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs181669646	chr20:11234478-11234479	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs543530480	chr20:11234480-11234481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs566932921	chr20:11234525-11234526	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:390 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11216200-11238800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:11227400-11235000	Weak transcription	Fetal Kidney	kidney
3	chr20:11234600-11236400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:11235000-11235200	ZNF genes & repeats	Fetal Kidney	kidney
5	chr20:11235200-11235600	Weak transcription	Fetal Kidney	kidney
6	chr20:11235600-11251200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr20:11238800-11239600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr20:11239600-11241200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:11240200-11241200	Enhancers	Stomach Mucosa	stomach
10	chr20:11241000-11241200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:11241000-11243000	Enhancers	HMEC	breast
12	chr20:11241000-11243000	Enhancers	NH-A	brain
13	chr20:11241200-11241800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:11241200-11243000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:11241200-11243200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr20:11241200-11247200	Weak transcription	Stomach Mucosa	stomach
17	chr20:11241400-11241600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:11241600-11243000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr20:11241600-11243000	Enhancers	A549	lung
20	chr20:11241600-11243200	Enhancers	Osteobl	bone
21	chr20:11241800-11242200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr20:11241800-11243000	Enhancers	HSMM	muscle
23	chr20:11241800-11243200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:11241800-11243200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr20:11242000-11242600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr20:11242000-11242600	Enhancers	Pancreas	Pancrea
27	chr20:11242000-11242600	Enhancers	GM12878-XiMat	blood
28	chr20:11242000-11242800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr20:11242000-11242800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr20:11242000-11242800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:11242000-11242800	Enhancers	NHLF	lung
32	chr20:11242000-11243000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr20:11242000-11243000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr20:11242000-11243000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr20:11242000-11243000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr20:11242000-11243000	Enhancers	NHDF-Ad	bronchial
37	chr20:11242000-11243600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr20:11242200-11242400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr20:11242200-11242400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr20:11242200-11242600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr20:11242200-11242600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr20:11242200-11242600	Enhancers	Esophagus	oesophagus
43	chr20:11242200-11242800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr20:11242200-11242800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr20:11242200-11243000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr20:11242400-11242600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr20:11242400-11242800	Enhancers	Brain Hippocampus Middle	brain
48	chr20:11242400-11242800	Enhancers	NHEK	skin
49	chr20:11242600-11242800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr20:11242600-11243000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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