Variant report

Variant	nsv1013248
Chromosome Location	chr3:84717911-84774750
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	BACH1	chr3:84730033-84730076	H1-hESC	embryonic stem cell:	n/a	n/a
2	BRCA1	chr3:84774057-84774336	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr3:84734687-84734980	Hela-S3	cervix:	n/a	chr3:84734701-84734713
4	CEBPB	chr3:84741121-84741376	HepG2	liver:	n/a	chr3:84741271-84741282
5	CEBPB	chr3:84734630-84734980	H1-hESC	embryonic stem cell:	n/a	chr3:84734701-84734713
6	CEBPB	chr3:84718976-84719301	HepG2	liver:	n/a	chr3:84719116-84719129 chr3:84719190-84719203 chr3:84719117-84719128
7	CEBPB	chr3:84734637-84734996	HepG2	liver:	n/a	chr3:84734701-84734713
8	CEBPB	chr3:84734656-84734969	K562	blood:	n/a	chr3:84734701-84734713
9	CEBPB	chr3:84767168-84767493	HepG2	liver:	n/a	chr3:84767339-84767348 chr3:84767338-84767349 chr3:84767337-84767348
10	CEBPB	chr3:84734635-84734997	IMR90	lung:	n/a	chr3:84734701-84734713
11	CTCF	chr3:84760983-84761034	LNCaP	prostate:	n/a	n/a
12	CTCF	chr3:84760816-84760868	GM13976	blood:	n/a	n/a
13	CTCF	chr3:84770857-84770903	ProgFib	skin:	n/a	n/a
14	CTCF	chr3:84770911-84770979	GM13976	blood:	n/a	n/a
15	CTCF	chr3:84774204-84774274	MCF-7	breast:	n/a	n/a
16	CTCF	chr3:84744700-84744850	WERI-Rb-1	eye:	n/a	n/a
17	CTCF	chr3:84770868-84770893	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:84759548-84759599	LNCaP	prostate:	n/a	n/a
19	CTCF	chr3:84727613-84727639	Kidney_OC	kidney:	n/a	n/a
20	E2F4	chr3:84751273-84751481	MCF10A-Er-Src	breast:	n/a	n/a
21	E2F4	chr3:84754924-84755118	MCF10A-Er-Src	breast:	n/a	n/a
22	E2F4	chr3:84774078-84774317	MCF10A-Er-Src	breast:	n/a	n/a
23	EBF1	chr3:84774102-84774360	GM12878	blood:	n/a	chr3:84774284-84774295
24	EBF1	chr3:84774045-84774680	GM12878	blood:	n/a	chr3:84774284-84774295
25	EP300	chr3:84774119-84774390	Hela-S3	cervix:	n/a	n/a
26	FOS	chr3:84744743-84744964	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr3:84774019-84774461	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr3:84741439-84741755	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr3:84729089-84729090	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr3:84734357-84734555	MCF10A-Er-Src	breast:	n/a	chr3:84734435-84734442
31	FOS	chr3:84774059-84774676	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr3:84744788-84744988	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr3:84741431-84741749	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr3:84741454-84741724	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr3:84744399-84745016	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr3:84744795-84744996	MCF10A-Er-Src	breast:	n/a	n/a
37	FOS	chr3:84773996-84774673	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr3:84774032-84774466	MCF10A-Er-Src	breast:	n/a	n/a
39	FOSL2	chr3:84774017-84774477	SK-N-SH	brain:	n/a	n/a
40	GATA3	chr3:84719200-84719312	SH-SY5Y	brain:	n/a	n/a
41	IRF1	chr3:84747298-84747371	K562	blood:	n/a	n/a
42	JUN	chr3:84774145-84774418	HepG2	liver:	n/a	n/a
43	JUN	chr3:84774050-84774423	Hela-S3	cervix:	n/a	n/a
44	JUND	chr3:84774124-84774418	HepG2	liver:	n/a	chr3:84774274-84774285
45	JUND	chr3:84774056-84774461	Hela-S3	cervix:	n/a	chr3:84774274-84774285
46	JUND	chr3:84734282-84734555	HepG2	liver:	n/a	chr3:84734432-84734443 chr3:84734435-84734442
47	JUND	chr3:84728642-84728841	H1-hESC	embryonic stem cell:	n/a	n/a
48	JUND	chr3:84734352-84734535	H1-hESC	embryonic stem cell:	n/a	chr3:84734432-84734443 chr3:84734435-84734442
49	MAFF	chr3:84728433-84728711	HepG2	liver:	n/a	n/a
50	MAFF	chr3:84729848-84730231	HepG2	liver:	n/a	chr3:84730038-84730056 chr3:84730044-84730058

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:84716502..84719314-chr3:84721003..84723364,2	K562	blood:
2	chr3:84716502..84719314-chr3:84721003..84723364,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VGLL3-9	chr3:84770247-84771053	ucscGeneNc_uc003dqi_2
2	lnc-VGLL3-6	chr3:84715551-84719007	ENSG00000242641.1
3	lnc-VGLL3-10	chr3:84740832-84741742	NONHSAT090650
4	lnc-VGLL3-6	chr3:84732760-84732829	NONHSAT090649
5	lnc-VGLL3-6	chr3:84744516-84744666	NONHSAT090649
6	lnc-VGLL3-6	chr3:84721772-84722056	NONHSAT090649
7	lnc-VGLL3-6	chr3:84744861-84745033	NONHSAT090649
8	lnc-VGLL3-6	chr3:84720735-84720854	NONHSAT090649
9	lnc-VGLL3-6	chr3:84721772-84722056	ENSG00000242641.1
10	lnc-VGLL3-6	chr3:84715551-84719007	NONHSAT090649
11	lnc-VGLL3-6	chr3:84744516-84744666	ENSG00000242641.1
12	lnc-VGLL3-6	chr3:84734791-84734931	ENSG00000242641.1
13	lnc-VGLL3-6	chr3:84732760-84732829	ENSG00000242641.1
14	lnc-VGLL3-6	chr3:84734791-84734931	NONHSAT090649
15	lnc-VGLL3-6	chr3:84744861-84745033	ENSG00000242641.1
16	lnc-VGLL3-6	chr3:84745309-84745492	NONHSAT090649
17	lnc-VGLL3-6	chr3:84745309-84745492	ENSG00000242641.1
18	lnc-VGLL3-6	chr3:84720735-84720854	ENSG00000242641.1

Variant related genes	Relation type
ENSG00000241776	TF binding region

Extended variants
information (count: 860 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:860 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536338041	chr3:84717915-84717916	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs144885450	chr3:84717938-84717939	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs576649473	chr3:84717964-84717965	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs9834714	chr3:84717981-84717982	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs565354331	chr3:84717985-84717986	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs568421310	chr3:84718019-84718020	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs535500011	chr3:84718084-84718085	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs140765728	chr3:84718126-84718127	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs9835018	chr3:84718146-84718147	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs564637454	chr3:84718169-84718170	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs557926040	chr3:84718177-84718178	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs370408158	chr3:84718182-84718183	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs543862621	chr3:84718183-84718184	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs578192104	chr3:84718184-84718185	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs562265429	chr3:84718187-84718188	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs574061344	chr3:84718267-84718268	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs373125926	chr3:84718308-84718309	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs541446285	chr3:84718322-84718323	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs79171792	chr3:84718382-84718383	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs189019901	chr3:84718422-84718423	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs191879604	chr3:84718445-84718446	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs62255480	chr3:84718471-84718472	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs144616355	chr3:84718482-84718483	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs138734033	chr3:84718505-84718506	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs527448306	chr3:84718517-84718518	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs9839313	chr3:84718534-84718535	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs185584000	chr3:84718545-84718546	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs547451152	chr3:84718555-84718556	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs542729607	chr3:84718636-84718637	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs566111280	chr3:84718727-84718728	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs539733697	chr3:84718745-84718746	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs558038212	chr3:84718776-84718777	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs372929589	chr3:84718791-84718792	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs368486252	chr3:84718835-84718836	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs576182536	chr3:84718854-84718855	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs143549132	chr3:84718866-84718867	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs555575976	chr3:84718903-84718904	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs559771309	chr3:84718922-84718923	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs574429146	chr3:84718945-84718946	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs541956012	chr3:84718949-84718950	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs148041251	chr3:84718954-84718955	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs572019380	chr3:84718956-84718957	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs546076325	chr3:84718982-84718983	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs111791869	chr3:84720221-84720222	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs192416805	chr3:84720281-84720282	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs111995901	chr3:84720295-84720296	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs183805270	chr3:84720319-84720320	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs553549511	chr3:84720322-84720323	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs565755477	chr3:84720356-84720357	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs9830050	chr3:84720360-84720361	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Melanoma	18172304	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Wilms tumour	21544195	CNVD
Colorectal cancer	16272173	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Soft tissue tumor	16732325	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
Medulloblastoma	16783165	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Mental retardation	17124404	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Schizophrenia	23813976	CNVD
Lung squamous cell carcinoma	22363434	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:84720200-84722000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:84722000-84729800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:84729800-84730400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:84731600-84732000	Active TSS	Fetal Heart	heart
5	chr3:84732800-84733400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:84741400-84741800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:84744600-84744800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:84744800-84745000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:84759000-84759200	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr3:84759200-84759400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr3:84759200-84759600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:84759400-84759800	Active TSS	Monocytes-CD14+_RO01746	blood
13	chr3:84759800-84760200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:84759800-84760200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:84760200-84762400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:84760200-84762600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:84762400-84762600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:84762600-84763000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:84762600-84763200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr3:84763000-84763400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:84766600-84767400	Enhancers	Psoas Muscle	Psoas
22	chr3:84767200-84767600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:84767200-84767600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:84767200-84767600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:84773800-84775000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr3:84774200-84774800	Enhancers	HSMM	muscle

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