Variant report

Variant	nsv594253
Chromosome Location	chr4:60487235-60549283
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	chr4:60542291-60542621	HepG2	liver:	n/a	chr4:60542457-60542466 chr4:60542455-60542468 chr4:60542456-60542467
3	CTCF	chr4:60498161-60498213	GM10248	blood:	n/a	n/a
4	CTCF	chr4:60544195-60544260	Lung_OC	lung:	n/a	n/a
5	CTCF	chr4:60531477-60531736	GM12878	blood:	n/a	n/a
6	CTCF	chr4:60531640-60531790	GM12871	blood:	n/a	n/a
7	CTCF	chr4:60521840-60521990	WERI-Rb-1	eye:	n/a	n/a
8	CTCF	chr4:60522080-60522116	GM20000	blood:	n/a	n/a
9	CTCF	chr4:60521893-60521943	Medullo	brain:	n/a	n/a
10	E2F4	chr4:60507307-60507495	MCF10A-Er-Src	breast:	n/a	n/a
11	EBF1	chr4:60503498-60503602	GM12878	blood:	n/a	n/a
12	EP300	chr4:60496662-60497025	T-47D	breast:	n/a	chr4:60496978-60496988
13	EP300	chr4:60496523-60497138	T-47D	breast:	n/a	chr4:60497080-60497094 chr4:60496978-60496988 chr4:60497072-60497086 chr4:60497078-60497092
14	EP300	chr4:60495857-60496486	T-47D	breast:	n/a	chr4:60496186-60496196 chr4:60496261-60496275
15	EP300	chr4:60510441-60510472	GM12878	blood:	n/a	n/a
16	EP300	chr4:60494943-60495384	T-47D	breast:	n/a	n/a
17	EP300	chr4:60494722-60495518	T-47D	breast:	n/a	n/a
18	EP300	chr4:60500749-60501226	T-47D	breast:	n/a	n/a
19	ESR1	chr4:60494890-60495330	T-47D	breast:	n/a	n/a
20	ESR1	chr4:60495869-60496362	T-47D	breast:	n/a	n/a
21	ESR1	chr4:60494901-60495355	T-47D	breast:	n/a	n/a
22	ESR1	chr4:60494853-60495407	T-47D	breast:	n/a	n/a
23	FOS	chr4:60512783-60512945	MCF10A-Er-Src	breast:	n/a	chr4:60512834-60512843 chr4:60512835-60512842 chr4:60512834-60512842
24	FOS	chr4:60512692-60513001	MCF10A-Er-Src	breast:	n/a	chr4:60512834-60512843 chr4:60512835-60512842 chr4:60512834-60512842
25	FOS	chr4:60513838-60514017	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr4:60512728-60512981	MCF10A-Er-Src	breast:	n/a	chr4:60512834-60512843 chr4:60512835-60512842 chr4:60512834-60512842
27	FOS	chr4:60512788-60512968	MCF10A-Er-Src	breast:	n/a	chr4:60512834-60512843 chr4:60512835-60512842 chr4:60512834-60512842
28	FOXA1	chr4:60496572-60496995	T-47D	breast:	n/a	n/a
29	FOXA1	chr4:60496030-60496384	T-47D	breast:	n/a	chr4:60496181-60496196
30	FOXA1	chr4:60494786-60495474	T-47D	breast:	n/a	n/a
31	FOXA1	chr4:60500828-60501060	T-47D	breast:	n/a	n/a
32	FOXA1	chr4:60494838-60495429	T-47D	breast:	n/a	n/a
33	FOXA1	chr4:60495847-60496423	T-47D	breast:	n/a	chr4:60496181-60496196
34	FOXA1	chr4:60500890-60501150	T-47D	breast:	n/a	n/a
35	FOXA1	chr4:60496561-60496996	T-47D	breast:	n/a	n/a
36	GATA2	chr4:60542150-60542448	SH-SY5Y	brain:	n/a	chr4:60542235-60542242 chr4:60542235-60542242 chr4:60542233-60542242 chr4:60542235-60542242
37	GATA2	chr4:60545734-60546718	SH-SY5Y	brain:	n/a	n/a
38	GATA3	chr4:60496497-60497086	T-47D	breast:	n/a	n/a
39	GATA3	chr4:60542131-60542340	SH-SY5Y	brain:	n/a	chr4:60542235-60542242 chr4:60542235-60542242 chr4:60542233-60542242 chr4:60542235-60542242
40	GATA3	chr4:60494768-60495537	T-47D	breast:	n/a	n/a
41	GATA3	chr4:60500812-60501206	T-47D	breast:	n/a	n/a
42	GATA3	chr4:60513510-60513694	SH-SY5Y	brain:	n/a	n/a
43	GATA3	chr4:60496713-60497058	MCF-7	breast:	n/a	n/a
44	GATA3	chr4:60494773-60495522	T-47D	breast:	n/a	n/a
45	GATA3	chr4:60500837-60501228	T-47D	breast:	n/a	n/a
46	GATA3	chr4:60545651-60546941	SH-SY5Y	brain:	n/a	n/a
47	GATA3	chr4:60495844-60496392	T-47D	breast:	n/a	n/a
48	GATA3	chr4:60495844-60496424	T-47D	breast:	n/a	n/a
49	GATA3	chr4:60496488-60497032	T-47D	breast:	n/a	n/a
50	JUN	chr4:60532468-60532638	HepG2	liver:	n/a	chr4:60532540-60532549 chr4:60532536-60532549

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:60543813..60546033-chr4:60553313..60556008,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	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: 986 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:986 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6828465	chr4:60487235-60487236	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs571393498	chr4:60487278-60487279	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs532433936	chr4:60487294-60487295	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs75828073	chr4:60487304-60487305	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs565667157	chr4:60487320-60487321	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs186989228	chr4:60487338-60487339	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs536222097	chr4:60487372-60487373	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs542058704	chr4:60489231-60489232	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs563407590	chr4:60489236-60489237	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs143214191	chr4:60489258-60489259	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs182273111	chr4:60489265-60489266	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs564148504	chr4:60489266-60489267	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs528170968	chr4:60489268-60489269	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs78803593	chr4:60489275-60489276	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs185337762	chr4:60489313-60489314	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs56894382	chr4:60489317-60489318	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs529412943	chr4:60489371-60489372	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs551179775	chr4:60489411-60489412	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs572966094	chr4:60489421-60489422	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs569405893	chr4:60489469-60489470	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs540136733	chr4:60489480-60489481	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs370442736	chr4:60489487-60489488	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs148276131	chr4:60489496-60489497	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs141405543	chr4:60489506-60489507	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs6842739	chr4:60489510-60489511	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs147003649	chr4:60489533-60489534	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs371311904	chr4:60489536-60489537	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs57033355	chr4:60489561-60489562	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs541612084	chr4:60489594-60489595	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs138141961	chr4:60489616-60489617	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs112591797	chr4:60489625-60489626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs143616381	chr4:60489675-60489676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs190144862	chr4:60489678-60489679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs12499518	chr4:60489707-60489708	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs183211852	chr4:60489738-60489739	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs73202957	chr4:60489781-60489782	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs539858273	chr4:60489806-60489807	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs561420863	chr4:60489814-60489815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs528962464	chr4:60489849-60489850	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs147178166	chr4:60489884-60489885	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs535668798	chr4:60489903-60489904	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs569477780	chr4:60489940-60489941	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs550852284	chr4:60489948-60489949	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs554358879	chr4:60489962-60489963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs368501647	chr4:60490024-60490025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs138416921	chr4:60490028-60490029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs567184009	chr4:60490068-60490069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs534152453	chr4:60490119-60490120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs116058371	chr4:60490160-60490161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs572687673	chr4:60490163-60490164	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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:60486800-60487400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:60486800-60487400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:60489200-60489600	Enhancers	Liver	Liver
4	chr4:60489600-60495200	Weak transcription	Liver	Liver
5	chr4:60495200-60495600	Enhancers	Liver	Liver
6	chr4:60495600-60495800	Weak transcription	Liver	Liver
7	chr4:60495800-60497000	Enhancers	Liver	Liver
8	chr4:60498800-60499400	Active TSS	Gastric	stomach
9	chr4:60503000-60504400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:60504000-60504400	Enhancers	Liver	Liver
11	chr4:60509200-60510000	Enhancers	Liver	Liver
12	chr4:60514800-60516000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:60515200-60515600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:60515600-60515800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:60516000-60516400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:60516400-60516600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:60516400-60517400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:60516800-60517800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:60521600-60522000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:60521600-60522000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:60521600-60522200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:60521600-60522600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:60528600-60529000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:60534400-60534800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr4:60534400-60535800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:60534600-60534800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr4:60534600-60535200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr4:60534600-60535400	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr4:60534800-60535200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr4:60534800-60535200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr4:60536800-60537200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:60543400-60550000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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