Variant report

Variant	nsv1012339
Chromosome Location	chr4:59996783-60022095
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	BATF	chr4:60000562-60000764	GM12878	blood:	n/a	n/a
2	BATF	chr4:60020461-60020690	GM12878	blood:	n/a	n/a
3	CEBPB	chr4:60019549-60019772	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr4:60001178-60001350	H1-hESC	embryonic stem cell:	n/a	n/a
5	CUX1	chr4:60008916-60008952	GM12878	blood:	n/a	n/a
6	EBF1	chr4:60020546-60020735	GM12878	blood:	n/a	n/a
7	EP300	chr4:60020437-60020466	GM12878	blood:	n/a	n/a
8	EP300	chr4:60020468-60020710	GM12878	blood:	n/a	n/a
9	FOS	chr4:59998714-59998785	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr4:60017953-60017991	MCF10A-Er-Src	breast:	n/a	n/a
11	FOXA1	chr4:60015093-60015291	T-47D	breast:	n/a	n/a
12	GATA2	chr4:60003791-60004108	SH-SY5Y	brain:	n/a	n/a
13	GATA2	chr4:60021781-60022163	SH-SY5Y	brain:	n/a	chr4:60022125-60022136 chr4:60022134-60022141 chr4:60022127-60022148 chr4:60022134-60022141 chr4:60022129-60022145 chr4:60022129-60022145 chr4:60022132-60022142 chr4:60022134-60022141
14	GATA3	chr4:60003619-60004104	SH-SY5Y	brain:	n/a	n/a
15	GATA3	chr4:60014057-60014236	SH-SY5Y	brain:	n/a	n/a
16	GATA3	chr4:60021479-60022156	SH-SY5Y	brain:	n/a	chr4:60022125-60022136 chr4:60022134-60022141 chr4:60022127-60022148 chr4:60022134-60022141 chr4:60022129-60022145 chr4:60022129-60022145 chr4:60022132-60022142 chr4:60022134-60022141
17	JUN	chr4:60009785-60010185	K562	blood:	n/a	n/a
18	MAFF	chr4:60009185-60009446	HepG2	liver:	n/a	chr4:60009326-60009344
19	MAFK	chr4:60009172-60009460	HepG2	liver:	n/a	chr4:60009323-60009340 chr4:60009327-60009343 chr4:60009331-60009342 chr4:60009327-60009342 chr4:60009330-60009344
20	MAFK	chr4:60018095-60018435	HepG2	liver:	n/a	chr4:60018259-60018274 chr4:60018255-60018272
21	MAFK	chr4:60010127-60010140	HepG2	liver:	n/a	n/a
22	MAFK	chr4:60018101-60018402	HepG2	liver:	n/a	chr4:60018259-60018274 chr4:60018255-60018272
23	MAFK	chr4:60018110-60018346	IMR90	lung:	n/a	chr4:60018259-60018274 chr4:60018255-60018272
24	MAFK	chr4:60009184-60009492	HepG2	liver:	n/a	chr4:60009323-60009340 chr4:60009327-60009343 chr4:60009331-60009342 chr4:60009327-60009342 chr4:60009330-60009344
25	MXI1	chr4:60000697-60000715	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr4:60022061-60022215	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:60013165-60013219	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr4:60009150-60009296	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr4:59996704-59996904	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr4:60015429-60015508	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr4:60010463-60010606	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr4:60018261-60018452	MCF10A-Er-Src	breast:	n/a	n/a
33	RAD21	chr4:60001161-60001433	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr4:60001111-60001625	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr4:60001161-60001465	H1-hESC	embryonic stem cell:	n/a	n/a
36	RUNX3	chr4:60003789-60004085	GM12878	blood:	n/a	n/a
37	SPI1	chr4:60020574-60020770	GM12891	blood:	n/a	n/a
38	STAT3	chr4:60019101-60019283	MCF10A-Er-Src	breast:	n/a	chr4:60019201-60019212
39	STAT3	chr4:60010829-60011012	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr4:60011767-60011773	MCF10A-Er-Src	breast:	n/a	n/a
41	STAT3	chr4:60009561-60009722	MCF10A-Er-Src	breast:	n/a	n/a
42	ZNF384	chr4:60011445-60011469	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:60001000-60001050	H1-hESC	embryonic stem cell:	embryo
2	chr4:60001000-60001050	IMR90	lung:	fetal
3	chr4:60001000-60001050	BE2_C	brain:	n/a
4	chr4:60001000-60001050	SK-N-MC	brain:	n/a
5	chr4:60001000-60001050	GM06990	blood:	n/a
6	chr4:60001000-60001050	GM12892	blood:	n/a
7	chr4:60001000-60001050	GM12891	blood:	n/a
8	chr4:60001000-60001050	HPAEpiC	pulmonary alveolar:	n/a
9	chr4:60001000-60001050	T-47D	breast:	n/a
10	chr4:60001000-60001050	HUVEC	blood vessel:	n/a
11	chr4:60001000-60001050	HRCEpiC	kidney:	n/a
12	chr4:60001000-60001050	ovcar-3	ovarian:	n/a
13	chr4:60001000-60001050	NT2-D1	testis:	n/a
14	chr4:60001000-60001050	LNCaP	prostate:	n/a
15	chr4:60001000-60001050	NHDF-neo	bronchial:	n/a
16	chr4:60001000-60001050	AoSMC	blood vessel:	n/a
17	chr4:60001000-60001050	Hela-S3	cervix:	n/a
18	chr4:60001000-60001050	SK-N-SH_RA	brain:	n/a
19	chr4:60001000-60001050	HCT-116	colon:	n/a
20	chr4:60001000-60001050	PANC-1	pancreas:	n/a
21	chr4:60001000-60001050	ProgFib	skin:	n/a
22	chr4:60001000-60001050	BJ	skin:	n/a
23	chr4:60001000-60001050	SAEC	small airway:	n/a
24	chr4:60001000-60001050	PrEC	prostate:	n/a
25	chr4:60001000-60001050	NH-A	brain:	n/a
26	chr4:60001000-60001050	AG09319	gingival:	n/a
27	chr4:60001000-60001050	HRE	kidney:	n/a
28	chr4:60001000-60001050	AG04449	skin:	fetal
29	chr4:60001000-60001050	MCF10A-Er-Src	breast:	n/a
30	chr4:60001000-60001050	HCPEpiC	choroid plexus:	n/a
31	chr4:60001000-60001050	Hepatocyte	liver:	n/a
32	chr4:60001000-60001050	HIPEpiC	eye:	n/a
33	chr4:60001000-60001050	HepG2	liver:	n/a
34	chr4:60001000-60001050	NB4	blood:	n/a
35	chr4:60001000-60001050	NHBE	bronchial:	n/a
36	chr4:60001000-60001050	HEK293	kidney:	embryo
37	chr4:60001000-60001050	AG04450	lung:	fetal
38	chr4:60001000-60001050	Caco-2	colon:	n/a
39	chr4:60001000-60001050	HEEpiC	esophagus:	n/a
40	chr4:60001000-60001050	HCF	heart:	n/a
41	chr4:60001000-60001050	HMEC	breast:	n/a
42	chr4:60001000-60001050	SKMC	muscle:	n/a
43	chr4:60001000-60001050	Jurkat	blood:	n/a
44	chr4:60001000-60001050	K562	blood:	n/a
45	chr4:60001000-60001050	U87	brain:	n/a
46	chr4:60001000-60001050	HAEpiC	amniotic membrane:	n/a
47	chr4:60001000-60001050	GM12878	blood:	n/a
48	chr4:60001000-60001050	HNPCEpiC	eye:	n/a
49	chr4:60001000-60001050	GM19239	blood:	n/a
50	chr4:60001000-60001050	HRPEpiC	eye:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LPHN3-7	chr4:60018552-60018604	XLOC_003552

Variant related genes	Relation type
ENSG00000249111	TF binding region
ENSG00000249111	CpG island
HELZ	miRNA target sites

Extended variants
information (count: 283 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:283 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs207464732	chr4:59999803-59999804	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs191996208	chr4:59999821-59999822	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs1039465	chr4:59999831-59999832	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs540610244	chr4:59999909-59999910	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs183939049	chr4:59999917-59999918	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs1039466	chr4:59999983-59999984	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs533650876	chr4:59999987-59999988	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs564479013	chr4:60000092-60000093	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs531592050	chr4:60000185-60000186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs357848	chr4:60000192-60000193	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs561804390	chr4:60000240-60000241	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs562099049	chr4:60000248-60000249	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs562724151	chr4:60000314-60000315	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs35708181	chr4:60000360-60000361	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs371750978	chr4:60000406-60000407	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs577920787	chr4:60000444-60000445	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs542268681	chr4:60000479-60000480	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs529403197	chr4:60000501-60000502	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs560083536	chr4:60000530-60000531	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs546994343	chr4:60000532-60000533	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs549193981	chr4:60000582-60000583	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs369369480	chr4:60000584-60000585	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs188436111	chr4:60000611-60000612	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs531568459	chr4:60000620-60000621	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs550065832	chr4:60000641-60000642	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs112118311	chr4:60000644-60000645	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs147121566	chr4:60000661-60000662	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs357847	chr4:60000662-60000663	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs548017246	chr4:60000685-60000686	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs566122913	chr4:60000706-60000707	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs193075522	chr4:60000717-60000718	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs555137453	chr4:60000755-60000756	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs567294351	chr4:60000788-60000789	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs184274245	chr4:60000802-60000803	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs556184176	chr4:60000874-60000875	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs578030824	chr4:60000895-60000896	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs560495239	chr4:60000911-60000912	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs553967317	chr4:60000930-60000931	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs529300745	chr4:60000947-60000948	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs59477914	chr4:60000948-60000949	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs547246162	chr4:60000954-60000955	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs397959969	chr4:60000956-60000957	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs369503641	chr4:60001000-60001001	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs572110615	chr4:60001003-60001004	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs543128523	chr4:60001048-60001049	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs113921357	chr4:60001050-60001051	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs531607951	chr4:60001065-60001066	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs543452505	chr4:60001104-60001105	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs537425748	chr4:60001115-60001116	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs564934453	chr4:60001116-60001117	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:77)

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

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:59999800-60002000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr4:60000200-60001800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:60000400-60002000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:60000400-60002000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:60000600-60001800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:60001400-60001800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr4:60001400-60002000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr4:60001400-60002000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr4:60001400-60002000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:60001400-60002200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:60018000-60021800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:60021800-60022200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr4:60021800-60022200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr4:60021800-60022200	Enhancers	H9 Cell Line	embryonic stem cell

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