Variant report

Variant	nsv1058890
Chromosome Location	chr20:15234769-15388360
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	ATF2	chr20:15313045-15313880	GM12878	blood:	n/a	chr20:15313332-15313343
2	ATF2	chr20:15299152-15299756	GM12878	blood:	n/a	n/a
3	ATF2	chr20:15297929-15299020	GM12878	blood:	n/a	n/a
4	ATF2	chr20:15299283-15299738	GM12878	blood:	n/a	n/a
5	ATF2	chr20:15299899-15300572	GM12878	blood:	n/a	n/a
6	ATF2	chr20:15298201-15298708	GM12878	blood:	n/a	n/a
7	BATF	chr20:15299346-15299710	GM12878	blood:	n/a	n/a
8	BATF	chr20:15298652-15298919	GM12878	blood:	n/a	n/a
9	BATF	chr20:15298206-15298537	GM12878	blood:	n/a	n/a
10	BATF	chr20:15299357-15299730	GM12878	blood:	n/a	n/a
11	BATF	chr20:15298174-15298614	GM12878	blood:	n/a	n/a
12	BATF	chr20:15376139-15376425	GM12878	blood:	n/a	n/a
13	BATF	chr20:15313268-15313752	GM12878	blood:	n/a	n/a
14	BCLAF1	chr20:15298111-15298900	GM12878	blood:	n/a	n/a
15	BCLAF1	chr20:15313142-15313783	GM12878	blood:	n/a	n/a
16	BCLAF1	chr20:15298185-15298626	GM12878	blood:	n/a	n/a
17	BHLHE40	chr20:15307828-15307979	K562	blood:	n/a	n/a
18	BHLHE40	chr20:15313971-15314073	GM12878	blood:	n/a	n/a
19	BHLHE40	chr20:15298187-15298590	GM12878	blood:	n/a	n/a
20	BHLHE40	chr20:15313573-15313619	GM12878	blood:	n/a	n/a
21	CEBPB	chr20:15291108-15291403	A549	lung:	n/a	chr20:15291183-15291194 chr20:15291271-15291288
22	CEBPB	chr20:15291094-15291349	HepG2	liver:	n/a	chr20:15291183-15291194 chr20:15291271-15291288
23	CEBPB	chr20:15385807-15385885	A549	lung:	n/a	n/a
24	CEBPB	chr20:15331718-15331930	H1-hESC	embryonic stem cell:	n/a	n/a
25	CEBPB	chr20:15323545-15323781	A549	lung:	n/a	n/a
26	CEBPB	chr20:15370303-15370515	HepG2	liver:	n/a	chr20:15370422-15370433
27	CEBPB	chr20:15274199-15274343	HepG2	liver:	n/a	n/a
28	CEBPB	chr20:15303652-15303847	MCF-7	breast:	n/a	chr20:15303752-15303765 chr20:15303752-15303765 chr20:15303752-15303765 chr20:15303754-15303765
29	CEBPB	chr20:15239247-15239316	A549	lung:	n/a	n/a
30	CEBPB	chr20:15291116-15291268	H1-hESC	embryonic stem cell:	n/a	chr20:15291183-15291194
31	CEBPB	chr20:15331750-15331882	A549	lung:	n/a	n/a
32	CEBPB	chr20:15291007-15291432	Hela-S3	cervix:	n/a	chr20:15291183-15291194 chr20:15291271-15291288
33	CEBPB	chr20:15237312-15237381	H1-hESC	embryonic stem cell:	n/a	n/a
34	CEBPB	chr20:15252432-15252620	A549	lung:	n/a	n/a
35	CHD1	chr20:15298854-15299036	GM12878	blood:	n/a	n/a
36	CREB1	chr20:15313150-15313651	GM12878	blood:	n/a	n/a
37	CTCF	chr20:15358900-15359050	WERI-Rb-1	eye:	n/a	chr20:15358978-15358996 chr20:15358981-15358994 chr20:15358980-15359001
38	CTCF	chr20:15323540-15323690	AG09319	gingival:	n/a	n/a
39	CTCF	chr20:15248666-15248672	GM13977	blood:	n/a	n/a
40	CTCF	chr20:15339372-15339435	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr20:15358860-15359010	NHEK	skin:	n/a	chr20:15358978-15358996 chr20:15358981-15358994 chr20:15358980-15359001
42	CTCF	chr20:15248620-15248770	MCF-7	breast:	n/a	n/a
43	CTCF	chr20:15326096-15326204	LNCaP	prostate:	n/a	chr20:15326136-15326154
44	CTCF	chr20:15246593-15246928	GM12878	blood:	n/a	n/a
45	CTCF	chr20:15326069-15326226	MCF-7	breast:	n/a	chr20:15326136-15326154
46	CTCF	chr20:15358854-15359143	IMR90	lung:	n/a	chr20:15358978-15358996 chr20:15358981-15358994 chr20:15358980-15359001
47	CTCF	chr20:15326060-15326210	BE2_C	brain:	n/a	chr20:15326136-15326154
48	CTCF	chr20:15246705-15246797	GM10266	blood:	n/a	n/a
49	CTCF	chr20:15358940-15359090	HBMEC	blood vessel:	n/a	chr20:15358978-15358996 chr20:15358981-15358994 chr20:15358980-15359001
50	CTCF	chr20:15303716-15303869	GM12878	blood:	n/a	chr20:15303781-15303799 chr20:15303784-15303797

No.	Distal block	Cell Line	Cell type
1	chr20:14335576..14337791-chr20:15315333..15317078,2	MCF-7	breast:
2	chr20:15293454..15295061-chr20:15304426..15306908,2	MCF-7	breast:
3	chr20:15279663..15281630-chr20:15285386..15287786,2	MCF-7	breast:
4	chr20:15279663..15281630-chr20:15285386..15287786,2	MCF-7	breast:
5	chr20:15280200..15282422-chr20:15286811..15288380,2	MCF-7	breast:
6	chr20:15293454..15295061-chr20:15304426..15306908,2	MCF-7	breast:
7	chr20:15354524..15357487-chr20:15359360..15362240,2	MCF-7	breast:
8	chr20:15349649..15350459-chr6:35465170..35465747,2	MCF-7	breast:
9	chr20:15354524..15357487-chr20:15359360..15362240,2	MCF-7	breast:
10	chr15:79167275..79169229-chr20:15379751..15381953,2	MCF-7	breast:
11	chr20:15280200..15282422-chr20:15286811..15288380,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP475	TF binding region
ENSG00000185787	chromatin interactions

Extended variants
information (count: 4708 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:4708 , 50 per page) page: 1 2 3 4 5 6 7 ... 95

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10485520	chr20:15234769-15234770	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs189334129	chr20:15234776-15234777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs565616325	chr20:15234807-15234808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs111643871	chr20:15234824-15234825	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs535873944	chr20:15234852-15234853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs554174792	chr20:15234865-15234866	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs113532919	chr20:15234902-15234903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs180882817	chr20:15234962-15234963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs140590835	chr20:15234986-15234987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs4580449	chr20:15235072-15235073	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs559531178	chr20:15235080-15235081	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs4399780	chr20:15235142-15235143	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs4371414	chr20:15235247-15235248	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs543953290	chr20:15235256-15235257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs6079719	chr20:15235277-15235278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs562245503	chr20:15235295-15235296	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs529513461	chr20:15235297-15235298	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs146936985	chr20:15235299-15235300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs6074863	chr20:15235300-15235301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs564149841	chr20:15235316-15235317	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs77996820	chr20:15235322-15235323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs572765708	chr20:15235352-15235353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs111767648	chr20:15235417-15235418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs4473454	chr20:15235424-15235425	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs189408271	chr20:15235492-15235493	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs73614403	chr20:15235503-15235504	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs549920480	chr20:15235555-15235556	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs568379523	chr20:15235600-15235601	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs75017119	chr20:15235601-15235602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs74179767	chr20:15235608-15235609	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs73101205	chr20:15235663-15235664	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs141512331	chr20:15235698-15235699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs369060583	chr20:15235732-15235733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs181822560	chr20:15235773-15235774	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs547842167	chr20:15235796-15235797	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs544026454	chr20:15235805-15235806	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs73262749	chr20:15235839-15235840	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs186184264	chr20:15235850-15235851	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs529595431	chr20:15235855-15235856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs555362064	chr20:15235881-15235882	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs576433957	chr20:15235882-15235883	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs549427177	chr20:15235917-15235918	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs150548314	chr20:15235935-15235936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs528477557	chr20:15235973-15235974	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs149616884	chr20:15236000-15236001	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs574026241	chr20:15236004-15236005	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs190463197	chr20:15236008-15236009	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs74179768	chr20:15236079-15236080	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs7274642	chr20:15236087-15236088	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs571936185	chr20:15236092-15236093	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

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
Glioblastoma multiforme	21138945	CNVD
Cancer	20164919	CNVD
Multiple sclerosis	20663923	CNVD
Schizophrenia	20663923	CNVD
brain infarct	20663923	CNVD
Breast cancer	22522925	CNVD
Cancer	20164920	CNVD
Schizophrenia	23813976	CNVD
Esophageal adenocarcinoma	18519675	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	21364760	CNVD
Non-small cell lung cancer	16651412	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:249 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15234000-15236000	Weak transcription	Gastric	stomach
2	chr20:15236000-15236200	Enhancers	Gastric	stomach
3	chr20:15237200-15238400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:15237600-15238400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:15237800-15238200	Enhancers	HMEC	breast
6	chr20:15244200-15245200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:15245200-15246000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:15245200-15246600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr20:15245400-15246200	Enhancers	Fetal Intestine Large	intestine
10	chr20:15245400-15246200	Enhancers	Fetal Intestine Small	intestine
11	chr20:15245800-15246600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:15245800-15246800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr20:15246200-15247000	Weak transcription	Fetal Intestine Large	intestine
14	chr20:15246400-15249600	Enhancers	GM12878-XiMat	blood
15	chr20:15247000-15247200	Enhancers	Fetal Intestine Large	intestine
16	chr20:15248600-15250000	Enhancers	Primary B cells from peripheral blood	blood
17	chr20:15249600-15250000	Flanking Active TSS	GM12878-XiMat	blood
18	chr20:15250000-15250200	Enhancers	GM12878-XiMat	blood
19	chr20:15253400-15253800	Enhancers	Fetal Stomach	stomach
20	chr20:15257600-15259600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr20:15257800-15259800	Enhancers	HMEC	breast
22	chr20:15258000-15259400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr20:15258200-15259400	Enhancers	NHEK	skin
24	chr20:15258400-15259600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:15259400-15277600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:15270400-15271800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr20:15270600-15271800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr20:15271000-15271800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr20:15271000-15272000	Enhancers	Brain Germinal Matrix	brain
30	chr20:15271200-15272400	Enhancers	GM12878-XiMat	blood
31	chr20:15271400-15272000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr20:15276400-15276600	Enhancers	Gastric	stomach
33	chr20:15276400-15279600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr20:15277000-15277600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr20:15277200-15277600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr20:15277600-15277800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr20:15277600-15277800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:15277800-15282200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr20:15277800-15285000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr20:15281600-15282000	Enhancers	Lung	lung
41	chr20:15282600-15283000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr20:15284800-15285200	Enhancers	NHEK	skin
43	chr20:15285000-15285400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr20:15285000-15285800	Enhancers	HMEC	breast
45	chr20:15285800-15291000	Weak transcription	HMEC	breast
46	chr20:15289400-15290800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr20:15290600-15291600	Enhancers	HUVEC	blood vessel
48	chr20:15290600-15292600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr20:15290800-15291000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr20:15291000-15291400	Enhancers	HMEC	breast

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