Variant report

Variant	nsv528225
Chromosome Location	chr3:84017630-84024847
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CADM2-3	chr3:84017989-84018105	XLOC_002722
2	lnc-CADM2-3	chr3:84017989-84018105	XLOC_002722
3	lnc-CADM2-3	chr3:84017989-84018105	XLOC_002722
4	lnc-CADM2-3	chr3:84019647-84019724	XLOC_002722
5	lnc-CADM2-3	chr3:84019637-84019724	XLOC_002722

Variant related genes	Relation type
HOXC4	miRNA target sites
VEGFA	miRNA target sites
RUNX2	miRNA target sites

Extended variants
information (count: 273 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:273 , 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	rs4856477	chr3:84017630-84017631	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs193136563	chr3:84017633-84017634	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs546174705	chr3:84017739-84017740	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs34662573	chr3:84017740-84017741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs184376399	chr3:84017741-84017742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs371711383	chr3:84017794-84017795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs144713116	chr3:84017812-84017813	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs532077344	chr3:84017832-84017833	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs62260311	chr3:84017837-84017838	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs148539144	chr3:84017871-84017872	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs536077660	chr3:84017885-84017886	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs548391722	chr3:84017901-84017902	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs566756530	chr3:84017939-84017940	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs62260312	chr3:84017945-84017946	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs558988471	chr3:84017947-84017948	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs577312663	chr3:84017949-84017950	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs374577911	chr3:84017955-84017956	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs9865923	chr3:84018004-84018005	Weak transcription ZNF genes & repeats	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs141905258	chr3:84018054-84018055	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
20	rs544896842	chr3:84018089-84018090	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
21	rs574949874	chr3:84018095-84018096	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
22	rs1590056	chr3:84018151-84018152	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs554380829	chr3:84018160-84018161	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs572398297	chr3:84018180-84018181	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs546088445	chr3:84018210-84018211	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs150610886	chr3:84018219-84018220	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs532016846	chr3:84018276-84018277	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs140044429	chr3:84018284-84018285	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs188470318	chr3:84018290-84018291	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs13080984	chr3:84018298-84018299	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs529813101	chr3:84018325-84018326	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs79808755	chr3:84018375-84018376	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs566676559	chr3:84018435-84018436	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs62260313	chr3:84018441-84018442	Enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs552545020	chr3:84018491-84018492	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs1819037	chr3:84018632-84018633	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs62260314	chr3:84018667-84018668	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs567312893	chr3:84018680-84018681	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs143896262	chr3:84018681-84018682	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs191462998	chr3:84018725-84018726	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs535952935	chr3:84018796-84018797	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs568690339	chr3:84018822-84018823	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs374529147	chr3:84018827-84018828	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs553899703	chr3:84018904-84018905	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs183983192	chr3:84018907-84018908	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs546075945	chr3:84018925-84018926	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs373287845	chr3:84018927-84018928	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs188757752	chr3:84018949-84018950	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs368774671	chr3:84018969-84018970	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs537784030	chr3:84018986-84018987	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:77)

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

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:84016000-84017800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:84016400-84018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:84017800-84019000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
4	chr3:84018200-84018400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:84018200-84018600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr3:84018200-84018600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:84018600-84021400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:84019000-84019400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:84019400-84020000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:84020000-84020400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:84020400-84021000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr3:84020400-84021400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:84020400-84021400	ZNF genes & repeats	Dnd41	blood
14	chr3:84021000-84024000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:84021800-84022000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:84024000-84024400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr3:84024200-84024800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:84024400-84028800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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