Variant report

Variant	nsv458869
Chromosome Location	chr20:11271614-11306751
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	chr20:11297445-11297537	HepG2	liver:	n/a	n/a
2	BHLHE40	chr20:11283610-11283643	GM12878	blood:	n/a	n/a
3	BRCA1	chr20:11284530-11284593	GM12878	blood:	n/a	n/a
4	CEBPB	chr20:11300723-11301050	HepG2	liver:	n/a	chr20:11300848-11300859 chr20:11300878-11300889 chr20:11300878-11300891
5	CEBPB	chr20:11277674-11277996	IMR90	lung:	n/a	chr20:11277819-11277830
6	CEBPB	chr20:11290283-11290514	HepG2	liver:	n/a	chr20:11290368-11290379
7	CEBPB	chr20:11300793-11301061	IMR90	lung:	n/a	chr20:11300848-11300859 chr20:11300878-11300889 chr20:11300878-11300891
8	CEBPB	chr20:11277637-11277983	H1-hESC	embryonic stem cell:	n/a	chr20:11277819-11277830
9	CEBPB	chr20:11303505-11303650	HepG2	liver:	n/a	chr20:11303607-11303618
10	CEBPB	chr20:11277674-11277963	Hela-S3	cervix:	n/a	chr20:11277819-11277830
11	CEBPB	chr20:11277690-11277980	A549	lung:	n/a	chr20:11277819-11277830
12	CEBPB	chr20:11300825-11301026	A549	lung:	n/a	chr20:11300848-11300859 chr20:11300878-11300889 chr20:11300878-11300891
13	CEBPB	chr20:11277646-11277994	HepG2	liver:	n/a	chr20:11277819-11277830
14	CEBPB	chr20:11300746-11301033	K562	blood:	n/a	chr20:11300848-11300859 chr20:11300878-11300889 chr20:11300878-11300891
15	CEBPB	chr20:11290327-11290338	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr20:11272164-11272204	GM12878	blood:	n/a	n/a
17	CTCF	chr20:11272654-11272843	GM12878	blood:	n/a	n/a
18	E2F4	chr20:11275979-11276171	MCF10A-Er-Src	breast:	n/a	n/a
19	E2F6	chr20:11286095-11286711	H1-hESC	embryonic stem cell:	n/a	n/a
20	EBF1	chr20:11292867-11292895	GM12878	blood:	n/a	n/a
21	EBF1	chr20:11285484-11286387	GM12878	blood:	n/a	n/a
22	FAM48A	chr20:11277406-11277623	GM12878	blood:	n/a	n/a
23	FOS	chr20:11305709-11305910	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr20:11283166-11283365	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr20:11305801-11305943	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr20:11283232-11283359	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr20:11305687-11306015	MCF10A-Er-Src	breast:	n/a	n/a
28	FOXA1	chr20:11297168-11297530	HepG2	liver:	n/a	n/a
29	FOXA1	chr20:11297232-11297570	HepG2	liver:	n/a	n/a
30	FOXA1	chr20:11297176-11297536	HepG2	liver:	n/a	n/a
31	FOXA1	chr20:11297225-11297648	HepG2	liver:	n/a	n/a
32	FOXA2	chr20:11297303-11297508	HepG2	liver:	n/a	n/a
33	GATA3	chr20:11285341-11285656	SH-SY5Y	brain:	n/a	n/a
34	GTF2F1	chr20:11286156-11286352	H1-hESC	embryonic stem cell:	n/a	n/a
35	IKZF1	chr20:11283391-11283591	GM12878	blood:	n/a	n/a
36	IKZF1	chr20:11285997-11286415	GM12878	blood:	n/a	n/a
37	JUN	chr20:11300823-11300971	HepG2	liver:	n/a	chr20:11300879-11300892
38	JUN	chr20:11289694-11289699	H1-hESC	embryonic stem cell:	n/a	n/a
39	JUND	chr20:11300850-11300932	HepG2	liver:	n/a	n/a
40	JUND	chr20:11304336-11304392	HepG2	liver:	n/a	n/a
41	JUND	chr20:11277663-11277857	H1-hESC	embryonic stem cell:	n/a	n/a
42	KAP1	chr20:11287554-11287873	HEK293	kidney:	n/a	n/a
43	MAFF	chr20:11296937-11297247	HepG2	liver:	n/a	chr20:11297072-11297090
44	MAFK	chr20:11283046-11283352	IMR90	lung:	n/a	n/a
45	MAFK	chr20:11289727-11289882	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAFK	chr20:11296921-11297257	HepG2	liver:	n/a	chr20:11297074-11297089
47	MAFK	chr20:11296961-11297214	IMR90	lung:	n/a	chr20:11297074-11297089
48	MAFK	chr20:11280503-11280510	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAFK	chr20:11296923-11297259	HepG2	liver:	n/a	chr20:11297074-11297089
50	MAX	chr20:11286119-11286460	H1-hESC	embryonic stem cell:	n/a	chr20:11286351-11286361

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JAG1-3	chr20:11282088-11282173	ENSG00000230990
2	lnc-JAG1-3	chr20:11275284-11275382	ENSG00000230990

Variant related genes	Relation type
ENSG00000230990	TF binding region

Extended variants
information (count: 1302 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:1302 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1997877	chr20:11271614-11271615	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs1997876	chr20:11271664-11271665	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs545201599	chr20:11271674-11271675	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs201715545	chr20:11271710-11271711	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs36019498	chr20:11271750-11271751	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs148907999	chr20:11271825-11271826	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs558723703	chr20:11271827-11271828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs563759367	chr20:11271847-11271848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs575934284	chr20:11271849-11271850	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs532501504	chr20:11271862-11271863	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs369357660	chr20:11271879-11271880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs566157736	chr20:11271904-11271905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs143584375	chr20:11271925-11271926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs548878819	chr20:11271934-11271935	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs568817607	chr20:11271940-11271941	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs537036712	chr20:11271961-11271962	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs557005955	chr20:11271967-11271968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs6134175	chr20:11271975-11271976	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs148042669	chr20:11271977-11271978	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs140984104	chr20:11271980-11271981	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs62191820	chr20:11271993-11271994	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs541666281	chr20:11272064-11272065	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs189590159	chr20:11272079-11272080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs559725647	chr20:11272099-11272100	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs2024622	chr20:11272101-11272102	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs375053585	chr20:11272108-11272109	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs563553717	chr20:11272177-11272178	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs532602569	chr20:11272187-11272188	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs12481363	chr20:11272208-11272209	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs145739941	chr20:11272248-11272249	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs181771637	chr20:11272254-11272255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs528693827	chr20:11272281-11272282	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs138308324	chr20:11272328-11272329	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs568730373	chr20:11272349-11272350	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs537746169	chr20:11272370-11272371	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs550523906	chr20:11272383-11272384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs77245005	chr20:11272384-11272385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs186355762	chr20:11272421-11272422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs143950635	chr20:11272446-11272447	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs34290882	chr20:11272450-11272451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs543317317	chr20:11272521-11272522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs140583234	chr20:11272522-11272523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs200430007	chr20:11272537-11272538	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs150615954	chr20:11272538-11272539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs549423815	chr20:11272539-11272540	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs555143334	chr20:11272609-11272610	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs74652223	chr20:11272637-11272638	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs544113488	chr20:11272705-11272706	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs60081001	chr20:11272722-11272723	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs577145939	chr20:11272762-11272763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

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
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11270600-11276800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:11274600-11278000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:11276800-11277600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:11277000-11278200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr20:11277000-11278200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:11277000-11278200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr20:11277000-11278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr20:11277000-11278200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:11277000-11278200	Enhancers	HMEC	breast
10	chr20:11277000-11278200	Enhancers	NHEK	skin
11	chr20:11277000-11278400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr20:11277200-11278200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr20:11277400-11278000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr20:11277400-11278000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr20:11277400-11278000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr20:11277400-11278200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr20:11277600-11278200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr20:11277600-11278200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr20:11277600-11278200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr20:11277600-11282400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:11277800-11278200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr20:11277800-11278200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr20:11277800-11278200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr20:11278000-11278200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr20:11278200-11278400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr20:11278200-11282000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr20:11278200-11282400	Weak transcription	HMEC	breast
28	chr20:11278200-11282400	Weak transcription	NHEK	skin
29	chr20:11278200-11282600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr20:11278400-11282000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr20:11279600-11279800	ZNF genes & repeats	Pancreas	Pancrea
32	chr20:11282000-11283600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:11282000-11283600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr20:11282400-11282800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:11282400-11282800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr20:11282400-11282800	Enhancers	Esophagus	oesophagus
37	chr20:11282400-11283600	Enhancers	HMEC	breast
38	chr20:11282400-11283800	Enhancers	NHEK	skin
39	chr20:11282600-11283600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr20:11282600-11283600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr20:11282800-11284400	Weak transcription	Esophagus	oesophagus
42	chr20:11282800-11286000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr20:11283000-11283600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr20:11283000-11283600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr20:11283600-11285400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr20:11283600-11285400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:11283600-11285400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr20:11283600-11285400	Weak transcription	HMEC	breast
49	chr20:11283800-11285400	Weak transcription	NHEK	skin
50	chr20:11284400-11284600	Enhancers	Esophagus	oesophagus

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