Variant report

Variant	nsv879052
Chromosome Location	chr4:60458820-60538549
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	CEBPB	chr4:60511865-60512111	HepG2	liver:	n/a	n/a
2	CEBPB	chr4:60478015-60478369	IMR90	lung:	n/a	n/a
3	CEBPB	chr4:60463619-60463920	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr4:60477990-60478363	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr4:60461172-60461394	IMR90	lung:	n/a	n/a
6	CHD1	chr4:60465530-60465688	GM12878	blood:	n/a	n/a
7	CTCF	chr4:60467853-60467900	LNCaP	prostate:	n/a	n/a
8	CTCF	chr4:60481857-60482162	GM12878	blood:	n/a	n/a
9	CTCF	chr4:60462795-60462903	LNCaP	prostate:	n/a	n/a
10	CTCF	chr4:60498161-60498213	GM10248	blood:	n/a	n/a
11	CTCF	chr4:60481942-60481991	GM19238	blood:	n/a	n/a
12	CTCF	chr4:60521840-60521990	WERI-Rb-1	eye:	n/a	n/a
13	CTCF	chr4:60531640-60531790	GM12871	blood:	n/a	n/a
14	CTCF	chr4:60521893-60521943	Medullo	brain:	n/a	n/a
15	CTCF	chr4:60475480-60475630	WERI-Rb-1	eye:	n/a	n/a
16	CTCF	chr4:60466792-60466850	GM20000	blood:	n/a	n/a
17	CTCF	chr4:60481840-60481990	GM12878	blood:	n/a	n/a
18	CTCF	chr4:60531477-60531736	GM12878	blood:	n/a	n/a
19	CTCF	chr4:60522080-60522116	GM20000	blood:	n/a	n/a
20	CTCF	chr4:60481880-60482030	GM12873	blood:	n/a	n/a
21	E2F4	chr4:60478019-60478413	MCF10A-Er-Src	breast:	n/a	n/a
22	E2F4	chr4:60507307-60507495	MCF10A-Er-Src	breast:	n/a	n/a
23	EBF1	chr4:60503498-60503602	GM12878	blood:	n/a	n/a
24	EP300	chr4:60494722-60495518	T-47D	breast:	n/a	n/a
25	EP300	chr4:60495857-60496486	T-47D	breast:	n/a	chr4:60496186-60496196 chr4:60496261-60496275
26	EP300	chr4:60496662-60497025	T-47D	breast:	n/a	chr4:60496978-60496988
27	EP300	chr4:60478096-60478306	Hela-S3	cervix:	n/a	n/a
28	EP300	chr4:60496523-60497138	T-47D	breast:	n/a	chr4:60497080-60497094 chr4:60496978-60496988 chr4:60497072-60497086 chr4:60497078-60497092
29	EP300	chr4:60494943-60495384	T-47D	breast:	n/a	n/a
30	EP300	chr4:60510441-60510472	GM12878	blood:	n/a	n/a
31	EP300	chr4:60500749-60501226	T-47D	breast:	n/a	n/a
32	ESR1	chr4:60494890-60495330	T-47D	breast:	n/a	n/a
33	ESR1	chr4:60495869-60496362	T-47D	breast:	n/a	n/a
34	ESR1	chr4:60494853-60495407	T-47D	breast:	n/a	n/a
35	ESR1	chr4:60494901-60495355	T-47D	breast:	n/a	n/a
36	FOS	chr4:60474232-60474602	MCF10A-Er-Src	breast:	n/a	chr4:60474578-60474587 chr4:60474577-60474587 chr4:60474577-60474586
37	FOS	chr4:60512728-60512981	MCF10A-Er-Src	breast:	n/a	chr4:60512834-60512843 chr4:60512835-60512842 chr4:60512834-60512842
38	FOS	chr4:60474203-60474640	MCF10A-Er-Src	breast:	n/a	chr4:60474578-60474587 chr4:60474577-60474587 chr4:60474577-60474586
39	FOS	chr4:60477976-60478610	MCF10A-Er-Src	breast:	n/a	n/a
40	FOS	chr4:60477823-60478622	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr4:60474246-60474624	MCF10A-Er-Src	breast:	n/a	chr4:60474578-60474587 chr4:60474577-60474587 chr4:60474577-60474586
42	FOS	chr4:60477006-60477038	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr4:60474231-60474635	MCF10A-Er-Src	breast:	n/a	chr4:60474578-60474587 chr4:60474577-60474587 chr4:60474577-60474586
44	FOS	chr4:60512783-60512945	MCF10A-Er-Src	breast:	n/a	chr4:60512834-60512843 chr4:60512835-60512842 chr4:60512834-60512842
45	FOS	chr4:60513838-60514017	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr4:60477443-60478467	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr4:60477941-60478412	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr4:60512788-60512968	MCF10A-Er-Src	breast:	n/a	chr4:60512834-60512843 chr4:60512835-60512842 chr4:60512834-60512842
49	FOS	chr4:60512692-60513001	MCF10A-Er-Src	breast:	n/a	chr4:60512834-60512843 chr4:60512835-60512842 chr4:60512834-60512842
50	FOXA1	chr4:60495847-60496423	T-47D	breast:	n/a	chr4:60496181-60496196

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:
2	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IGFBP7-7	chr4:60460138-60460197	XLOC_003964
2	lnc-IGFBP7-7	chr4:60495929-60496042	XLOC_003964

Variant related genes	Relation type
ENSG00000249392	TF binding region
RUNX2	miRNA target sites

Extended variants
information (count: 1740 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:1740 , 50 per page) page: 1 2 3 4 5 6 7 ... 35

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs185327018	chr4:60460158-60460159	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs536268603	chr4:60460162-60460163	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs576967622	chr4:60460197-60460198	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs73202907	chr4:60461015-60461016	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs534639528	chr4:60461021-60461022	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs144617605	chr4:60461039-60461040	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs77215302	chr4:60461044-60461045	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs72612792	chr4:60461077-60461078	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs191325086	chr4:60461084-60461085	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs550865769	chr4:60461100-60461101	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs376202819	chr4:60461101-60461102	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs568870928	chr4:60461107-60461108	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs539489479	chr4:60461116-60461117	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs3912319	chr4:60461145-60461146	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs566879060	chr4:60461190-60461191	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs561031465	chr4:60461215-60461216	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs183858616	chr4:60461228-60461229	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs552857966	chr4:60461256-60461257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs574706390	chr4:60461272-60461273	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs535697752	chr4:60461273-60461274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs17089704	chr4:60461284-60461285	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs189414255	chr4:60461367-60461368	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs545860247	chr4:60461399-60461400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs147851529	chr4:60461434-60461435	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs572819143	chr4:60461436-60461437	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs192921177	chr4:60461458-60461459	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs562097826	chr4:60461464-60461465	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs140360176	chr4:60461489-60461490	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs184962265	chr4:60461494-60461495	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs562892403	chr4:60461526-60461527	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs73820445	chr4:60461534-60461535	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs551517211	chr4:60461540-60461541	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs190178089	chr4:60461541-60461542	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs73202910	chr4:60461550-60461551	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs549456489	chr4:60461592-60461593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs181628694	chr4:60461593-60461594	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs535686183	chr4:60461600-60461601	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs557288014	chr4:60461662-60461663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs569211064	chr4:60461699-60461700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs539738946	chr4:60461702-60461703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs557443677	chr4:60461703-60461704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs374294596	chr4:60461791-60461792	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs7694284	chr4:60461798-60461799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs533094430	chr4:60461810-60461811	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs539909613	chr4:60461850-60461851	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs186142397	chr4:60461921-60461922	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs573893886	chr4:60462105-60462106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs544432683	chr4:60462127-60462128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs369308631	chr4:60462159-60462160	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs562825153	chr4:60462170-60462171	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Multiple myeloma	16616336	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Colorectal cancer	16272173	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute monocytic leukemia	16498392	CNVD
Prostate cancer	16573809	CNVD
Osteoporosis	18992858	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Breast cancer	20369283	CNVD
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:60461000-60461200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:60461200-60463600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:60462800-60464400	Enhancers	Brain Substantia Nigra	brain
4	chr4:60462800-60464600	Enhancers	Brain Hippocampus Middle	brain
5	chr4:60462800-60465400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:60463200-60463800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:60463200-60464200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:60463200-60464600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr4:60463200-60464600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr4:60463200-60464600	Enhancers	Fetal Intestine Small	intestine
11	chr4:60463400-60463800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:60463400-60463800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:60463400-60463800	Active TSS	Brain Anterior Caudate	brain
14	chr4:60463400-60464000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:60463400-60464000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:60463400-60464000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr4:60463400-60464200	Enhancers	HMEC	breast
18	chr4:60463600-60464800	Enhancers	Brain Angular Gyrus	brain
19	chr4:60463600-60465000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:60463800-60464000	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr4:60463800-60464200	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:60464000-60464400	Enhancers	Brain Anterior Caudate	brain
23	chr4:60464000-60465000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:60464200-60464800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:60465000-60465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:60465000-60470200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:60470200-60470400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:60473600-60474000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:60473600-60474000	Enhancers	Aorta	Aorta
30	chr4:60473600-60474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:60473600-60474400	Enhancers	HMEC	breast
32	chr4:60473600-60474400	Enhancers	NHEK	skin
33	chr4:60473600-60475400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:60473800-60474400	Enhancers	HSMM	muscle
35	chr4:60473800-60474800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:60474000-60476200	Weak transcription	Aorta	Aorta
37	chr4:60474200-60474600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:60474400-60477200	Weak transcription	HMEC	breast
39	chr4:60474400-60477400	Weak transcription	NHEK	skin
40	chr4:60474600-60474800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:60474800-60477600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:60475400-60475600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:60475400-60477200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:60476200-60476400	Enhancers	Aorta	Aorta
45	chr4:60476800-60478000	Enhancers	HSMMtube	muscle
46	chr4:60477200-60477600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:60477200-60477600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:60477200-60477600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:60477200-60478400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:60477200-60478600	Enhancers	HMEC	breast

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