Variant report

Variant	nsv1003847
Chromosome Location	chr4:60406832-60538697
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:278)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:278 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr4:60419115-60419467	GM12878	blood:	n/a	n/a
2	BATF	chr4:60436963-60437115	GM12878	blood:	n/a	n/a
3	BATF	chr4:60419100-60419406	GM12878	blood:	n/a	n/a
4	BATF	chr4:60419091-60419374	GM12878	blood:	n/a	n/a
5	BATF	chr4:60439519-60439795	GM12878	blood:	n/a	n/a
6	BATF	chr4:60439526-60439802	GM12878	blood:	n/a	n/a
7	BCL11A	chr4:60419048-60419387	GM12878	blood:	n/a	n/a
8	BHLHE40	chr4:60419045-60419363	GM12878	blood:	n/a	n/a
9	BRCA1	chr4:60432414-60432580	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr4:60426979-60427233	A549	lung:	n/a	chr4:60427091-60427104 chr4:60427091-60427102
11	CEBPB	chr4:60461172-60461394	IMR90	lung:	n/a	n/a
12	CEBPB	chr4:60511865-60512111	HepG2	liver:	n/a	n/a
13	CEBPB	chr4:60477990-60478363	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr4:60463619-60463920	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr4:60478015-60478369	IMR90	lung:	n/a	n/a
16	CEBPB	chr4:60426929-60427274	HepG2	liver:	n/a	chr4:60427091-60427104 chr4:60427091-60427102
17	CEBPB	chr4:60426929-60427254	IMR90	lung:	n/a	chr4:60427091-60427104 chr4:60427091-60427102
18	CHD1	chr4:60465530-60465688	GM12878	blood:	n/a	n/a
19	CHD2	chr4:60419012-60419365	GM12878	blood:	n/a	n/a
20	CHD2	chr4:60419004-60419384	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr4:60521840-60521990	WERI-Rb-1	eye:	n/a	n/a
22	CTCF	chr4:60531477-60531736	GM12878	blood:	n/a	n/a
23	CTCF	chr4:60467853-60467900	LNCaP	prostate:	n/a	n/a
24	CTCF	chr4:60521893-60521943	Medullo	brain:	n/a	n/a
25	CTCF	chr4:60419067-60419353	GM12878	blood:	n/a	n/a
26	CTCF	chr4:60466792-60466850	GM20000	blood:	n/a	n/a
27	CTCF	chr4:60449360-60449396	Kidney_OC	kidney:	n/a	n/a
28	CTCF	chr4:60481840-60481990	GM12878	blood:	n/a	n/a
29	CTCF	chr4:60419100-60419250	GM12871	blood:	n/a	n/a
30	CTCF	chr4:60462795-60462903	LNCaP	prostate:	n/a	n/a
31	CTCF	chr4:60531640-60531790	GM12871	blood:	n/a	n/a
32	CTCF	chr4:60498161-60498213	GM10248	blood:	n/a	n/a
33	CTCF	chr4:60475480-60475630	WERI-Rb-1	eye:	n/a	n/a
34	CTCF	chr4:60522080-60522116	GM20000	blood:	n/a	n/a
35	CTCF	chr4:60481880-60482030	GM12873	blood:	n/a	n/a
36	CTCF	chr4:60481942-60481991	GM19238	blood:	n/a	n/a
37	CTCF	chr4:60481857-60482162	GM12878	blood:	n/a	n/a
38	CUX1	chr4:60419486-60419532	GM12878	blood:	n/a	n/a
39	CUX1	chr4:60436857-60437132	GM12878	blood:	n/a	n/a
40	E2F4	chr4:60507307-60507495	MCF10A-Er-Src	breast:	n/a	n/a
41	E2F4	chr4:60478019-60478413	MCF10A-Er-Src	breast:	n/a	n/a
42	E2F4	chr4:60411360-60411457	MCF10A-Er-Src	breast:	n/a	n/a
43	EBF1	chr4:60503498-60503602	GM12878	blood:	n/a	n/a
44	EBF1	chr4:60419107-60419441	GM12878	blood:	n/a	n/a
45	EBF1	chr4:60419099-60419432	GM12878	blood:	n/a	n/a
46	EBF1	chr4:60436880-60437080	GM12878	blood:	n/a	n/a
47	EBF1	chr4:60419091-60419438	GM12878	blood:	n/a	n/a
48	EP300	chr4:60495857-60496486	T-47D	breast:	n/a	chr4:60496186-60496196 chr4:60496261-60496275
49	EP300	chr4:60494722-60495518	T-47D	breast:	n/a	n/a
50	EP300	chr4:60419089-60419667	GM12878	blood:	n/a	chr4:60419400-60419414

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:63626389..63627074-chr4:60415889..60416567,2	MCF-7	breast:
2	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:
3	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IGFBP7-7	chr4:60429941-60430063	XLOC_003964
2	lnc-IGFBP7-7	chr4:60460138-60460197	XLOC_003964
3	lnc-IGFBP7-7	chr4:60426719-60426805	XLOC_003964
4	lnc-IGFBP7-7	chr4:60440016-60440076	XLOC_003964
5	lnc-IGFBP7-7	chr4:60495929-60496042	XLOC_003964
6	lnc-IGFBP7-7	chr4:60416860-60416972	XLOC_003964

No data

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

Extended variants
information (count: 2739 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:2739 , 50 per page) page: 1 2 3 4 5 6 7 ... 55

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs115558635	chr4:60406866-60406867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs137937189	chr4:60406895-60406896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs142414147	chr4:60406898-60406899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs529137833	chr4:60406904-60406905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs550506036	chr4:60406982-60406983	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs181234932	chr4:60407015-60407016	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs532948435	chr4:60407053-60407054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs375817120	chr4:60407061-60407062	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs528171886	chr4:60407085-60407086	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs370710084	chr4:60407091-60407092	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs546716666	chr4:60407101-60407102	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs533099342	chr4:60407119-60407120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs551153132	chr4:60407139-60407140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs368518847	chr4:60407240-60407241	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs564838524	chr4:60407247-60407248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs184179524	chr4:60407253-60407254	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs188935944	chr4:60407255-60407256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs551621818	chr4:60407275-60407276	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs549582430	chr4:60407322-60407323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs567898205	chr4:60407333-60407334	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs114236408	chr4:60407363-60407364	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs181684683	chr4:60407416-60407417	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs577919356	chr4:60407430-60407431	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs539038710	chr4:60407443-60407444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs553950045	chr4:60407474-60407475	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs533522028	chr4:60407481-60407482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs572483383	chr4:60407543-60407544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs369627930	chr4:60407600-60407601	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs118014646	chr4:60407668-60407669	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs373171491	chr4:60407720-60407721	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs561538306	chr4:60407723-60407724	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs145943707	chr4:60407728-60407729	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs186205176	chr4:60407741-60407742	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs544059537	chr4:60407777-60407778	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs562455958	chr4:60407782-60407783	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs192059381	chr4:60407788-60407789	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs536668328	chr4:60409413-60409414	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs530848384	chr4:60409426-60409427	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs140925518	chr4:60409431-60409432	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs571390599	chr4:60409452-60409453	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs576846411	chr4:60409553-60409554	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs538774780	chr4:60409562-60409563	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs185263186	chr4:60409568-60409569	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs59723985	chr4:60409584-60409585	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs574693272	chr4:60409602-60409603	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs542076065	chr4:60409605-60409606	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs374627455	chr4:60409618-60409619	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs563656251	chr4:60409655-60409656	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs556735620	chr4:60409678-60409679	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs190490700	chr4:60409694-60409695	Enhancers	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:214 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:60406200-60407600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:60407600-60407800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:60407600-60407800	Enhancers	Pancreas	Pancrea
4	chr4:60409400-60410400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:60418400-60419000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:60418400-60419200	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:60418600-60419000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:60418600-60419000	Enhancers	A549	lung
9	chr4:60418600-60419200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr4:60418600-60419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:60418600-60419200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:60418600-60419200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:60418600-60419200	Enhancers	Hela-S3	cervix
14	chr4:60418600-60419200	Enhancers	NHDF-Ad	bronchial
15	chr4:60418600-60419400	Enhancers	Dnd41	blood
16	chr4:60418800-60419400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr4:60418800-60419400	Enhancers	HSMM	muscle
18	chr4:60418800-60419600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr4:60419000-60419200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:60419000-60419200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:60419000-60419200	Flanking Active TSS	A549	lung
22	chr4:60419000-60419200	Enhancers	HUVEC	blood vessel
23	chr4:60419000-60419200	Enhancers	NH-A	brain
24	chr4:60419000-60419400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:60419000-60419400	Enhancers	NHEK	skin
26	chr4:60419000-60419600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:60419000-60419600	Active TSS	Adipose Nuclei	Adipose
28	chr4:60419000-60419800	Active TSS	GM12878-XiMat	blood
29	chr4:60419200-60419400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr4:60419200-60419400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:60419200-60419400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:60419200-60419400	Enhancers	Brain Substantia Nigra	brain
33	chr4:60419200-60419400	Active TSS	Gastric	stomach
34	chr4:60419200-60419400	Flanking Active TSS	NH-A	brain
35	chr4:60419200-60419400	Flanking Active TSS	NHDF-Ad	bronchial
36	chr4:60419200-60419600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:60419200-60419600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:60419200-60419600	Active TSS	Primary monocytes fromperipheralblood	blood
39	chr4:60419200-60419600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr4:60419200-60419600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr4:60419200-60419600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:60419200-60419600	Active TSS	Duodenum Mucosa	Duodenum
43	chr4:60419200-60419600	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr4:60419200-60419600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr4:60419200-60419600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr4:60419200-60419600	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr4:60419200-60419600	Active TSS	Hela-S3	cervix
48	chr4:60419200-60419600	Active TSS	HMEC	breast
49	chr4:60419200-60419600	Active TSS	HSMMtube	muscle
50	chr4:60419200-60419600	Flanking Active TSS	HUVEC	blood vessel

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