Variant report

Variant	nsv1014694
Chromosome Location	chr3:84917449-84959329
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:23)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr3:84954233-84954576	HepG2	liver:	n/a	n/a
2	CEBPB	chr3:84958863-84959065	A549	lung:	n/a	chr3:84958954-84958965
3	CEBPB	chr3:84958813-84959139	HepG2	liver:	n/a	chr3:84958954-84958965
4	CEBPB	chr3:84930983-84931198	A549	lung:	n/a	n/a
5	CEBPB	chr3:84930981-84931137	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:84923877-84923947	Lung_OC	lung:	n/a	n/a
7	CTCF	chr3:84934950-84934956	LNCaP	prostate:	n/a	n/a
8	CTCF	chr3:84920920-84921070	MCF-7	breast:	n/a	chr3:84921010-84921028
9	CTCF	chr3:84950240-84950390	HUVEC	blood vessel:	n/a	n/a
10	CTCF	chr3:84957003-84957054	GM13977	blood:	n/a	n/a
11	CTCF	chr3:84929620-84929667	Spleen_OC	spleen:	n/a	n/a
12	CTCF	chr3:84950160-84950310	GM12867	blood:	n/a	n/a
13	E2F4	chr3:84942003-84942163	MCF10A-Er-Src	breast:	n/a	n/a
14	FOXA1	chr3:84943756-84944012	T-47D	breast:	n/a	n/a
15	FOXA1	chr3:84943708-84944084	T-47D	breast:	n/a	n/a
16	FOXA1	chr3:84942280-84942716	T-47D	breast:	n/a	n/a
17	FOXA1	chr3:84934404-84934722	T-47D	breast:	n/a	n/a
18	FOXA1	chr3:84942336-84942612	T-47D	breast:	n/a	n/a
19	FOXA1	chr3:84934418-84934675	T-47D	breast:	n/a	n/a
20	GATA3	chr3:84943614-84944114	T-47D	breast:	n/a	n/a
21	GATA3	chr3:84943690-84944127	T-47D	breast:	n/a	n/a
22	GATA3	chr3:84942290-84942748	T-47D	breast:	n/a	chr3:84942340-84942350
23	GATA3	chr3:84927890-84928248	SH-SY5Y	brain:	n/a	n/a
24	GATA3	chr3:84941026-84941169	SH-SY5Y	brain:	n/a	chr3:84941145-84941155 chr3:84941146-84941153 chr3:84941146-84941153 chr3:84941146-84941153
25	GATA3	chr3:84945849-84946149	T-47D	breast:	n/a	n/a
26	GATA3	chr3:84945858-84946175	T-47D	breast:	n/a	n/a
27	GATA3	chr3:84943744-84944001	SH-SY5Y	brain:	n/a	n/a
28	GATA3	chr3:84942231-84942744	T-47D	breast:	n/a	chr3:84942340-84942350
29	JUND	chr3:84920931-84920961	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAFK	chr3:84952074-84952262	HepG2	liver:	n/a	chr3:84952232-84952247
31	MAFK	chr3:84917855-84918030	HepG2	liver:	n/a	n/a
32	MAFK	chr3:84951991-84952306	HepG2	liver:	n/a	chr3:84952232-84952247
33	MAFK	chr3:84932964-84933136	HepG2	liver:	n/a	chr3:84933069-84933085 chr3:84933070-84933084 chr3:84933072-84933088 chr3:84933067-84933087
34	MYC	chr3:84931757-84931903	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYC	chr3:84919105-84919211	MCF10A-Er-Src	breast:	n/a	n/a
36	MYC	chr3:84954337-84954511	MCF-7	breast:	n/a	n/a
37	POLR2A	chr3:84933920-84933934	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr3:84956448-84956489	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr3:84955223-84955401	MCF-7	breast:	n/a	n/a
40	POLR2A	chr3:84940737-84940760	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr3:84955215-84955218	MCF-7	breast:	n/a	n/a
42	POLR2A	chr3:84955280-84955466	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:84921410-84921442	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr3:84954378-84954393	MCF-7	breast:	n/a	n/a
45	POLR2A	chr3:84947069-84947239	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr3:84954264-84954422	A549	lung:	n/a	n/a
47	POLR2A	chr3:84955415-84955416	MCF-7	breast:	n/a	n/a
48	POLR2A	chr3:84954107-84954160	MCF-7	breast:	n/a	n/a
49	POLR2A	chr3:84954049-84954648	MCF-7	breast:	n/a	n/a
50	POLR2A	chr3:84934812-84934837	MCF-7	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:84919226-84919276	AG04450	lung:	fetal
2	chr3:84919226-84919276	LNCaP	prostate:	n/a
3	chr3:84919226-84919276	Jurkat	blood:	n/a
4	chr3:84919438-84919488	A549	lung:	n/a
5	chr3:84919226-84919276	NHDF-neo	bronchial:	n/a
6	chr3:84919226-84919276	NT2-D1	testis:	n/a
7	chr3:84919438-84919488	GM12891	blood:	n/a
8	chr3:84919438-84919488	CMK	blood:	n/a
9	chr3:84919438-84919488	T-47D	breast:	n/a
10	chr3:84919438-84919488	RPTEC	kidney:	n/a
11	chr3:84919226-84919276	HCPEpiC	choroid plexus:	n/a
12	chr3:84919226-84919276	T-47D	breast:	n/a
13	chr3:84919226-84919276	GM12891	blood:	n/a
14	chr3:84919226-84919276	AG09309	skin:	n/a
15	chr3:84919438-84919488	NT2-D1	testis:	n/a
16	chr3:84919226-84919276	HRE	kidney:	n/a
17	chr3:84919226-84919276	GM12892	blood:	n/a
18	chr3:84919226-84919276	A549	lung:	n/a
19	chr3:84919226-84919276	MCF-7	breast:	n/a
20	chr3:84919438-84919488	SAEC	small airway:	n/a
21	chr3:84919438-84919488	Caco-2	colon:	n/a
22	chr3:84919438-84919488	HL-60	blood:	n/a
23	chr3:84919226-84919276	Hepatocyte	liver:	n/a
24	chr3:84919226-84919276	IMR90	lung:	fetal
25	chr3:84919226-84919276	HAEpiC	amniotic membrane:	n/a
26	chr3:84919438-84919488	HRCEpiC	kidney:	n/a
27	chr3:84919226-84919276	HepG2	liver:	n/a
28	chr3:84919438-84919488	HRE	kidney:	n/a
29	chr3:84919226-84919276	NB4	blood:	n/a
30	chr3:84919438-84919488	HNPCEpiC	eye:	n/a
31	chr3:84919226-84919276	NHBE	bronchial:	n/a
32	chr3:84919438-84919488	MCF10A-Er-Src	breast:	n/a
33	chr3:84919226-84919276	PrEC	prostate:	n/a
34	chr3:84919438-84919488	GM19239	blood:	n/a
35	chr3:84919438-84919488	AG04450	lung:	fetal
36	chr3:84919438-84919488	HCPEpiC	choroid plexus:	n/a
37	chr3:84919438-84919488	ProgFib	skin:	n/a
38	chr3:84919226-84919276	HCM	heart:	n/a
39	chr3:84919438-84919488	HIPEpiC	eye:	n/a
40	chr3:84919226-84919276	CMK	blood:	n/a
41	chr3:84919226-84919276	HMEC	breast:	n/a
42	chr3:84919226-84919276	HNPCEpiC	eye:	n/a
43	chr3:84919226-84919276	HEEpiC	esophagus:	n/a
44	chr3:84919438-84919488	PFSK-1	brain:	n/a
45	chr3:84919226-84919276	SAEC	small airway:	n/a
46	chr3:84919438-84919488	HMEC	breast:	n/a
47	chr3:84919226-84919276	ProgFib	skin:	n/a
48	chr3:84919438-84919488	SK-N-SH_RA	brain:	n/a
49	chr3:84919438-84919488	GM06990	blood:	n/a
50	chr3:84919226-84919276	GM19239	blood:	n/a

No data

(count:23 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VGLL3-6	chr3:84917933-84917994	ENSG00000242641.1
2	lnc-VGLL3-6	chr3:84918429-84918726	NONHSAT090649
3	lnc-VGLL3-9	chr3:84921479-84921613	ucscGeneNc_uc003dqi_2
4	lnc-VGLL3-6	chr3:84918429-84918726	ENSG00000242641.1
5	lnc-VGLL3-6	chr3:84918742-84918779	ENSG00000242641.1
6	lnc-CADM2-1	chr3:84934087-84934274	XLOC_002723
7	lnc-VGLL3-6	chr3:84917749-84917819	ENSG00000242641.1
8	lnc-VGLL3-6	chr3:84930640-84930830	ENSG00000242641.1
9	lnc-VGLL3-9	chr3:84924009-84924132	ucscGeneNc_uc003dqi_2
10	lnc-CADM2-1	chr3:84942083-84942116	XLOC_002723
11	lnc-CADM2-1	chr3:84934086-84934274	NONHSAT090654
12	lnc-CADM2-1	chr3:84942393-84942530	XLOC_002723
13	lnc-VGLL3-6	chr3:84917749-84917819	ENSG00000242641.1
14	lnc-VGLL3-6	chr3:84918054-84918175	ENSG00000242641.1
15	lnc-CADM2-1	chr3:84942082-84942116	NONHSAT090654
16	lnc-VGLL3-6	chr3:84917749-84917819	NONHSAT090649
17	lnc-CADM2-1	chr3:84942392-84942530	NONHSAT090654
18	lnc-VGLL3-6	chr3:84918054-84918175	NONHSAT090649
19	lnc-VGLL3-6	chr3:84918054-84918175	ENSG00000242641.1
20	lnc-VGLL3-6	chr3:84917749-84917819	NONHSAT090652
21	lnc-VGLL3-6	chr3:84918429-84918637	NONHSAT090652
22	lnc-VGLL3-6	chr3:84918054-84918175	NONHSAT090652
23	lnc-VGLL3-6	chr3:84917749-84917819	ENSG00000242641.1

No data

Variant related genes	Relation type
ENSG00000266025	TF binding region
ENSG00000242339	TF binding region
LINC00971	TF binding region
ENSG00000266025	CpG island
ENSG00000242339	CpG island
LINC00971	CpG island
THAP6	miRNA target sites
YES1	miRNA target sites
TCEAL1	miRNA target sites

Extended variants
information (count: 281 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:281 , 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	rs547630662	chr3:84917751-84917752	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs538444917	chr3:84917791-84917792	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs550625280	chr3:84917815-84917816	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs572795685	chr3:84917944-84917945	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs558437377	chr3:84918085-84918086	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs533295463	chr3:84918122-84918123	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs1249036	chr3:84918148-84918149	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs544097307	chr3:84918158-84918159	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs76853375	chr3:84918444-84918445	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs373768108	chr3:84918451-84918452	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs77318742	chr3:84918460-84918461	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs565659907	chr3:84918529-84918530	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs548158105	chr3:84918532-84918533	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs112788851	chr3:84918624-84918625	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs533546061	chr3:84918625-84918626	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs577280358	chr3:84918636-84918637	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs553978184	chr3:84918653-84918654	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs538028018	chr3:84918654-84918655	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs542016143	chr3:84918670-84918671	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs574866905	chr3:84918716-84918717	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs149875685	chr3:84918744-84918745	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs560571781	chr3:84918761-84918762	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs572444363	chr3:84918762-84918763	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs78355077	chr3:84918954-84918955	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs541858712	chr3:84918979-84918980	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs529496330	chr3:84919011-84919012	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs144871068	chr3:84919092-84919093	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs566249323	chr3:84919147-84919148	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs527258706	chr3:84919185-84919186	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs551788587	chr3:84919202-84919203	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs112882798	chr3:84919203-84919204	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs527820305	chr3:84919439-84919440	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
33	rs546200582	chr3:84919443-84919444	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
34	rs558233654	chr3:84919448-84919449	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
35	rs541518242	chr3:84919452-84919453	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
36	rs574879519	chr3:84919487-84919488	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
37	rs551553648	chr3:84920942-84920943	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs570148223	chr3:84920956-84920957	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs537033881	chr3:84920958-84920959	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs377046279	chr3:84920973-84920974	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs9847516	chr3:84921039-84921040	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs9827763	chr3:84921079-84921080	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs535025931	chr3:84921095-84921096	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs114855075	chr3:84921109-84921110	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs577788557	chr3:84921115-84921116	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs112085591	chr3:84921124-84921125	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs541579752	chr3:84921125-84921126	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs576117161	chr3:84921130-84921131	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs9827900	chr3:84921169-84921170	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs149566796	chr3:84921487-84921488	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:79)

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
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
Autism	22102821	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:84926200-84926800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:84926400-84926800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr3:84928200-84928800	Enhancers	Brain Hippocampus Middle	brain
4	chr3:84934200-84934600	ZNF genes & repeats	Pancreas	Pancrea
5	chr3:84953800-84955600	Enhancers	Fetal Muscle Leg	muscle
6	chr3:84954000-84954200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:84954000-84954200	Enhancers	Psoas Muscle	Psoas
8	chr3:84954000-84954200	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr3:84954000-84954200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:84954000-84955600	Enhancers	Fetal Muscle Trunk	muscle
11	chr3:84954200-84954600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:84954200-84954600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:84954200-84954600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:84954200-84954600	Flanking Active TSS	Psoas Muscle	Psoas
15	chr3:84954200-84954600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr3:84954200-84955400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr3:84954600-84954800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:84954600-84955000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:84954600-84955400	Enhancers	Psoas Muscle	Psoas
20	chr3:84955000-84955400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr3:84955400-84955600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:84955400-84955600	Enhancers	Skeletal Muscle Female	skeletal muscle

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