Variant report

Variant	nsv536616
Chromosome Location	chr3:84653836-84773582
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	BHLHE40	chr3:84709346-84709352	GM12878	blood:	n/a	n/a
3	CEBPB	chr3:84688021-84688329	HepG2	liver:	n/a	n/a
4	CEBPB	chr3:84686449-84686790	HepG2	liver:	n/a	chr3:84686617-84686630 chr3:84686618-84686629
5	CEBPB	chr3:84767168-84767493	HepG2	liver:	n/a	chr3:84767339-84767348 chr3:84767338-84767349 chr3:84767337-84767348
6	CEBPB	chr3:84715385-84715534	A549	lung:	n/a	chr3:84715471-84715482 chr3:84715472-84715483 chr3:84715471-84715484
7	CEBPB	chr3:84711442-84711590	HepG2	liver:	n/a	chr3:84711547-84711558
8	CEBPB	chr3:84686470-84686764	A549	lung:	n/a	chr3:84686617-84686630 chr3:84686618-84686629
9	CEBPB	chr3:84734630-84734980	H1-hESC	embryonic stem cell:	n/a	chr3:84734701-84734713
10	CEBPB	chr3:84688124-84688292	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr3:84741121-84741376	HepG2	liver:	n/a	chr3:84741271-84741282
12	CEBPB	chr3:84686451-84686799	H1-hESC	embryonic stem cell:	n/a	chr3:84686617-84686630 chr3:84686618-84686629
13	CEBPB	chr3:84734687-84734980	Hela-S3	cervix:	n/a	chr3:84734701-84734713
14	CEBPB	chr3:84734656-84734969	K562	blood:	n/a	chr3:84734701-84734713
15	CEBPB	chr3:84715380-84715618	HepG2	liver:	n/a	chr3:84715471-84715482 chr3:84715472-84715483 chr3:84715471-84715484
16	CEBPB	chr3:84734637-84734996	HepG2	liver:	n/a	chr3:84734701-84734713
17	CEBPB	chr3:84734635-84734997	IMR90	lung:	n/a	chr3:84734701-84734713
18	CEBPB	chr3:84718976-84719301	HepG2	liver:	n/a	chr3:84719116-84719129 chr3:84719190-84719203 chr3:84719117-84719128
19	CTCF	chr3:84770868-84770893	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:84670060-84670210	GM12869	blood:	n/a	n/a
21	CTCF	chr3:84760983-84761034	LNCaP	prostate:	n/a	n/a
22	CTCF	chr3:84770857-84770903	ProgFib	skin:	n/a	n/a
23	CTCF	chr3:84744700-84744850	WERI-Rb-1	eye:	n/a	n/a
24	CTCF	chr3:84760816-84760868	GM13976	blood:	n/a	n/a
25	CTCF	chr3:84770911-84770979	GM13976	blood:	n/a	n/a
26	CTCF	chr3:84759548-84759599	LNCaP	prostate:	n/a	n/a
27	CTCF	chr3:84657236-84657281	GM20000	blood:	n/a	n/a
28	CTCF	chr3:84706186-84706278	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr3:84727613-84727639	Kidney_OC	kidney:	n/a	n/a
30	E2F4	chr3:84712771-84712951	MCF10A-Er-Src	breast:	n/a	n/a
31	E2F4	chr3:84676270-84676535	MCF10A-Er-Src	breast:	n/a	n/a
32	E2F4	chr3:84656150-84656294	MCF10A-Er-Src	breast:	n/a	n/a
33	E2F4	chr3:84700262-84700458	MCF10A-Er-Src	breast:	n/a	n/a
34	E2F4	chr3:84751273-84751481	MCF10A-Er-Src	breast:	n/a	n/a
35	E2F4	chr3:84754924-84755118	MCF10A-Er-Src	breast:	n/a	n/a
36	E2F4	chr3:84672238-84672346	MCF10A-Er-Src	breast:	n/a	n/a
37	FOS	chr3:84729089-84729090	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr3:84715652-84715990	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr3:84734357-84734555	MCF10A-Er-Src	breast:	n/a	chr3:84734435-84734442
40	FOS	chr3:84710018-84710171	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr3:84744399-84745016	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr3:84744795-84744996	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr3:84715659-84716008	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr3:84688620-84688686	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr3:84741439-84741755	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr3:84715650-84716008	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr3:84741431-84741749	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr3:84741454-84741724	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr3:84657481-84657737	MCF10A-Er-Src	breast:	n/a	chr3:84657591-84657599 chr3:84657592-84657599
50	FOS	chr3:84744788-84744988	MCF10A-Er-Src	breast:	n/a	n/a

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-VGLL3-6	chr3:84734791-84734931	NONHSAT090649
2	lnc-VGLL3-9	chr3:84770247-84771053	ucscGeneNc_uc003dqi_2
3	lnc-VGLL3-6	chr3:84745309-84745492	ENSG00000242641.1
4	lnc-VGLL3-6	chr3:84721772-84722056	ENSG00000242641.1
5	lnc-VGLL3-6	chr3:84687557-84688363	ENSG00000242641.1
6	lnc-VGLL3-6	chr3:84732760-84732829	ENSG00000242641.1
7	lnc-VGLL3-6	chr3:84734791-84734931	ENSG00000242641.1
8	lnc-VGLL3-6	chr3:84744861-84745033	NONHSAT090649
9	lnc-VGLL3-6	chr3:84687556-84688363	NONHSAT090649
10	lnc-VGLL3-6	chr3:84721772-84722056	NONHSAT090649
11	lnc-VGLL3-6	chr3:84745309-84745492	NONHSAT090649
12	lnc-VGLL3-10	chr3:84740832-84741742	NONHSAT090650
13	lnc-VGLL3-6	chr3:84693364-84693437	NONHSAT090649
14	lnc-VGLL3-6	chr3:84715551-84719007	ENSG00000242641.1
15	lnc-VGLL3-6	chr3:84744861-84745033	ENSG00000242641.1
16	lnc-VGLL3-6	chr3:84720735-84720854	NONHSAT090649
17	lnc-VGLL3-6	chr3:84693364-84693437	ENSG00000242641.1
18	lnc-VGLL3-6	chr3:84732760-84732829	NONHSAT090649
19	lnc-VGLL3-6	chr3:84715551-84719007	NONHSAT090649
20	lnc-VGLL3-6	chr3:84720735-84720854	ENSG00000242641.1
21	lnc-VGLL3-6	chr3:84744516-84744666	ENSG00000242641.1
22	lnc-VGLL3-6	chr3:84744516-84744666	NONHSAT090649

Variant related genes	Relation type
ENSG00000241776	TF binding region

Extended variants
information (count: 1400 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:1400 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs530180526	chr3:84658463-84658464	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs182921360	chr3:84658466-84658467	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs540909890	chr3:84658472-84658473	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs550442291	chr3:84658481-84658482	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs527952320	chr3:84658485-84658486	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs371637147	chr3:84658521-84658522	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs570917134	chr3:84658524-84658525	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs538176129	chr3:84658529-84658530	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs117096569	chr3:84658535-84658536	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs376942994	chr3:84658640-84658641	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs1905846	chr3:84658657-84658658	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs80114335	chr3:84658692-84658693	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs536388995	chr3:84658854-84658855	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs554573357	chr3:84658863-84658864	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs566494485	chr3:84658869-84658870	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs534031592	chr3:84658880-84658881	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs558897923	chr3:84658888-84658889	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs577100460	chr3:84658938-84658939	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs544390430	chr3:84658944-84658945	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs367637109	chr3:84658983-84658984	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs35660448	chr3:84659001-84659002	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs144568612	chr3:84659029-84659030	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs557735908	chr3:84659064-84659065	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs574858744	chr3:84659084-84659085	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs541934874	chr3:84659100-84659101	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs11127854	chr3:84659102-84659103	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs377221114	chr3:84659130-84659131	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs527689330	chr3:84659194-84659195	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs545834166	chr3:84659206-84659207	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs564798224	chr3:84659219-84659220	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs577330643	chr3:84659225-84659226	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs73845516	chr3:84659228-84659229	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs187613739	chr3:84659233-84659234	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs546170058	chr3:84659296-84659297	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs192053676	chr3:84659299-84659300	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs529788773	chr3:84659372-84659373	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs548543751	chr3:84659374-84659375	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs147819120	chr3:84659394-84659395	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs566432215	chr3:84659403-84659404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs184980653	chr3:84659437-84659438	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs533758041	chr3:84659448-84659449	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs551932143	chr3:84659496-84659497	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs570703605	chr3:84659500-84659501	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs537783600	chr3:84659546-84659547	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs116141682	chr3:84662453-84662454	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs557480186	chr3:84662519-84662520	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs577560658	chr3:84662589-84662590	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs543301359	chr3:84662619-84662620	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs9812194	chr3:84662644-84662645	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs577825426	chr3:84662727-84662728	Enhancers	n/a	n/a	Overlapped CNVs	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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:84658400-84659600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:84662400-84662800	Enhancers	Adipose Nuclei	Adipose
3	chr3:84677000-84677800	Active TSS	Brain Substantia Nigra	brain
4	chr3:84677000-84678200	Active TSS	Brain Hippocampus Middle	brain
5	chr3:84677200-84677800	Active TSS	Brain Anterior Caudate	brain
6	chr3:84677200-84677800	Active TSS	Brain Cingulate Gyrus	brain
7	chr3:84677600-84678200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:84677800-84678200	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:84682200-84682800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:84686400-84686800	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:84703000-84703200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:84703200-84711600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:84707000-84707800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:84709000-84710000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:84709600-84710800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:84710400-84710800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:84720200-84722000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:84722000-84729800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:84729800-84730400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:84731600-84732000	Active TSS	Fetal Heart	heart
21	chr3:84732800-84733400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr3:84741400-84741800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:84744600-84744800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:84744800-84745000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:84759000-84759200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr3:84759200-84759400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr3:84759200-84759600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:84759400-84759800	Active TSS	Monocytes-CD14+_RO01746	blood
29	chr3:84759800-84760200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:84759800-84760200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr3:84760200-84762400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:84760200-84762600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:84762400-84762600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr3:84762600-84763000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:84762600-84763200	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr3:84763000-84763400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:84766600-84767400	Enhancers	Psoas Muscle	Psoas
38	chr3:84767200-84767600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:84767200-84767600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:84767200-84767600	Enhancers	Skeletal Muscle Female	skeletal muscle

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