Variant report

Variant	nsv1012748
Chromosome Location	chr4:60385942-60546407
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	chr4:60419115-60419467	GM12878	blood:	n/a	n/a
2	BATF	chr4:60419091-60419374	GM12878	blood:	n/a	n/a
3	BATF	chr4:60401251-60401624	GM12878	blood:	n/a	chr4:60401429-60401440
4	BATF	chr4:60439526-60439802	GM12878	blood:	n/a	n/a
5	BATF	chr4:60439519-60439795	GM12878	blood:	n/a	n/a
6	BATF	chr4:60419100-60419406	GM12878	blood:	n/a	n/a
7	BATF	chr4:60401319-60401538	GM12878	blood:	n/a	chr4:60401429-60401440
8	BATF	chr4:60436963-60437115	GM12878	blood:	n/a	n/a
9	BCL11A	chr4:60419048-60419387	GM12878	blood:	n/a	n/a
10	BCL11A	chr4:60401311-60401576	GM12878	blood:	n/a	n/a
11	BHLHE40	chr4:60401391-60401591	GM12878	blood:	n/a	n/a
12	BHLHE40	chr4:60419045-60419363	GM12878	blood:	n/a	n/a
13	BRCA1	chr4:60432414-60432580	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr4:60477990-60478363	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr4:60404866-60405095	IMR90	lung:	n/a	chr4:60404995-60405006
16	CEBPB	chr4:60426929-60427254	IMR90	lung:	n/a	chr4:60427091-60427104 chr4:60427091-60427102
17	CEBPB	chr4:60461172-60461394	IMR90	lung:	n/a	n/a
18	CEBPB	chr4:60388595-60389160	HepG2	liver:	n/a	chr4:60389093-60389104
19	CEBPB	chr4:60404855-60405120	HepG2	liver:	n/a	chr4:60404995-60405006
20	CEBPB	chr4:60478015-60478369	IMR90	lung:	n/a	n/a
21	CEBPB	chr4:60426979-60427233	A549	lung:	n/a	chr4:60427091-60427104 chr4:60427091-60427102
22	CEBPB	chr4:60511865-60512111	HepG2	liver:	n/a	n/a
23	CEBPB	chr4:60404902-60405102	A549	lung:	n/a	chr4:60404995-60405006
24	CEBPB	chr4:60426929-60427274	HepG2	liver:	n/a	chr4:60427091-60427104 chr4:60427091-60427102
25	CEBPB	chr4:60542291-60542621	HepG2	liver:	n/a	chr4:60542457-60542466 chr4:60542455-60542468 chr4:60542456-60542467
26	CEBPB	chr4:60463619-60463920	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr4:60388967-60389215	IMR90	lung:	n/a	chr4:60389093-60389104
28	CHD1	chr4:60465530-60465688	GM12878	blood:	n/a	n/a
29	CHD2	chr4:60419012-60419365	GM12878	blood:	n/a	n/a
30	CHD2	chr4:60419004-60419384	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr4:60544195-60544260	Lung_OC	lung:	n/a	n/a
32	CTCF	chr4:60481857-60482162	GM12878	blood:	n/a	n/a
33	CTCF	chr4:60419100-60419250	GM12871	blood:	n/a	n/a
34	CTCF	chr4:60531477-60531736	GM12878	blood:	n/a	n/a
35	CTCF	chr4:60401200-60401350	NHDF-neo	bronchial:	n/a	n/a
36	CTCF	chr4:60521893-60521943	Medullo	brain:	n/a	n/a
37	CTCF	chr4:60467853-60467900	LNCaP	prostate:	n/a	n/a
38	CTCF	chr4:60522080-60522116	GM20000	blood:	n/a	n/a
39	CTCF	chr4:60481840-60481990	GM12878	blood:	n/a	n/a
40	CTCF	chr4:60498161-60498213	GM10248	blood:	n/a	n/a
41	CTCF	chr4:60531640-60531790	GM12871	blood:	n/a	n/a
42	CTCF	chr4:60449360-60449396	Kidney_OC	kidney:	n/a	n/a
43	CTCF	chr4:60481880-60482030	GM12873	blood:	n/a	n/a
44	CTCF	chr4:60475480-60475630	WERI-Rb-1	eye:	n/a	n/a
45	CTCF	chr4:60521840-60521990	WERI-Rb-1	eye:	n/a	n/a
46	CTCF	chr4:60419067-60419353	GM12878	blood:	n/a	n/a
47	CTCF	chr4:60466792-60466850	GM20000	blood:	n/a	n/a
48	CTCF	chr4:60462795-60462903	LNCaP	prostate:	n/a	n/a
49	CTCF	chr4:60481942-60481991	GM19238	blood:	n/a	n/a
50	CUX1	chr4:60419486-60419532	GM12878	blood:	n/a	n/a

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	chr4:60543813..60546033-chr4:60553313..60556008,2	K562	blood:
4	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000249392	TF binding region
ENSG00000199780	TF binding region
RUNX2	miRNA target sites

Extended variants
information (count: 3124 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:3124 , 50 per page) page: 1 2 3 4 5 6 7 ... 63

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12505195	chr4:60394507-60394508	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs543774389	chr4:60394544-60394545	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs7679422	chr4:60394555-60394556	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs116120868	chr4:60394586-60394587	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs557433155	chr4:60400403-60400404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs573060153	chr4:60400427-60400428	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs111598402	chr4:60400447-60400448	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs372900477	chr4:60400448-60400449	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs190992263	chr4:60400472-60400473	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs76972772	chr4:60400489-60400490	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs574227423	chr4:60400613-60400614	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs183266138	chr4:60400624-60400625	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs143873157	chr4:60400625-60400626	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs114486024	chr4:60400660-60400661	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs188142516	chr4:60400696-60400697	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs193080643	chr4:60400728-60400729	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs115845513	chr4:60400761-60400762	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs543629183	chr4:60400815-60400816	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs546501859	chr4:60400821-60400822	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs10031779	chr4:60400848-60400849	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs529198949	chr4:60400849-60400850	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs146871741	chr4:60400862-60400863	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs568510513	chr4:60400869-60400870	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs112980430	chr4:60400880-60400881	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs112622673	chr4:60400899-60400900	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs557396174	chr4:60400920-60400921	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs58721032	chr4:60400947-60400948	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs10003133	chr4:60400955-60400956	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs140681734	chr4:60400982-60400983	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs145784900	chr4:60401005-60401006	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs544572393	chr4:60401031-60401032	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs184636023	chr4:60401051-60401052	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs578042110	chr4:60401072-60401073	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs187778999	chr4:60401090-60401091	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs192565732	chr4:60401113-60401114	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs199587387	chr4:60401118-60401119	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs12501563	chr4:60401121-60401122	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs543142680	chr4:60401123-60401124	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs561725734	chr4:60401125-60401126	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs183636970	chr4:60401139-60401140	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs115434575	chr4:60401174-60401175	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs188286863	chr4:60401219-60401220	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs532738808	chr4:60401221-60401222	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs554864076	chr4:60401227-60401228	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs550939277	chr4:60401232-60401233	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs145287920	chr4:60401306-60401307	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs533639247	chr4:60401323-60401324	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs9996367	chr4:60401336-60401337	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs370391821	chr4:60401372-60401373	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs7657798	chr4:60401376-60401377	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	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:232 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:60400400-60402000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr4:60400400-60403600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:60400400-60403600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:60400600-60401000	Enhancers	Primary hematopoietic stem cells	blood
5	chr4:60401200-60401600	Enhancers	Primary hematopoietic stem cells	blood
6	chr4:60401200-60403400	Enhancers	GM12878-XiMat	blood
7	chr4:60402000-60403200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:60402800-60403400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:60402800-60403600	Enhancers	Hela-S3	cervix
10	chr4:60403000-60403400	Enhancers	NHEK	skin
11	chr4:60403000-60403800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:60403200-60403400	Enhancers	Primary hematopoietic stem cells	blood
13	chr4:60403200-60403600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:60403200-60403800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:60405200-60405600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:60405600-60406000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:60406000-60406200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:60406200-60407600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:60407600-60407800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:60407600-60407800	Enhancers	Pancreas	Pancrea
21	chr4:60409400-60410400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:60418400-60419000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:60418400-60419200	Enhancers	Primary hematopoietic stem cells	blood
24	chr4:60418600-60419000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:60418600-60419000	Enhancers	A549	lung
26	chr4:60418600-60419200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr4:60418600-60419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:60418600-60419200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr4:60418600-60419200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:60418600-60419200	Enhancers	Hela-S3	cervix
31	chr4:60418600-60419200	Enhancers	NHDF-Ad	bronchial
32	chr4:60418600-60419400	Enhancers	Dnd41	blood
33	chr4:60418800-60419400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr4:60418800-60419400	Enhancers	HSMM	muscle
35	chr4:60418800-60419600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr4:60419000-60419200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:60419000-60419200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:60419000-60419200	Flanking Active TSS	A549	lung
39	chr4:60419000-60419200	Enhancers	HUVEC	blood vessel
40	chr4:60419000-60419200	Enhancers	NH-A	brain
41	chr4:60419000-60419400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:60419000-60419400	Enhancers	NHEK	skin
43	chr4:60419000-60419600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:60419000-60419600	Active TSS	Adipose Nuclei	Adipose
45	chr4:60419000-60419800	Active TSS	GM12878-XiMat	blood
46	chr4:60419200-60419400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr4:60419200-60419400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:60419200-60419400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:60419200-60419400	Enhancers	Brain Substantia Nigra	brain
50	chr4:60419200-60419400	Active TSS	Gastric	stomach

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