Variant report

Variant	nsv979287
Chromosome Location	chr2:47902976-47912715
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSH6-5	chr2:47903897-47904118	NONHSAT070591

Extended variants
information (count: 458 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:458 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs563131640	chr2:47903052-47903053	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs530957363	chr2:47903093-47903094	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs74889028	chr2:47903156-47903157	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs188093450	chr2:47903168-47903169	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs182019576	chr2:47903198-47903199	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs528441297	chr2:47903232-47903233	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs368007046	chr2:47903236-47903237	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs568613362	chr2:47903237-47903238	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs536056445	chr2:47903373-47903374	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs143330935	chr2:47903382-47903383	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs76244477	chr2:47903395-47903396	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs563163553	chr2:47903431-47903432	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs146698652	chr2:47903435-47903436	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs140273275	chr2:47903456-47903457	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs576932708	chr2:47903463-47903464	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs534273547	chr2:47903476-47903477	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs371662008	chr2:47903485-47903486	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs75095531	chr2:47903488-47903489	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs150304333	chr2:47903496-47903497	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs137888767	chr2:47903509-47903510	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs149019576	chr2:47903512-47903513	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs76636608	chr2:47903541-47903542	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs545907924	chr2:47903565-47903566	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs527782107	chr2:47903570-47903571	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs11688709	chr2:47903595-47903596	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs566179908	chr2:47903609-47903610	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs374029941	chr2:47903638-47903639	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs546638431	chr2:47903640-47903641	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs533788164	chr2:47903662-47903663	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs562105173	chr2:47903745-47903746	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs372199028	chr2:47903749-47903750	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs143820788	chr2:47903760-47903761	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs553346759	chr2:47903875-47903876	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs138515601	chr2:47903906-47903907	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs187383423	chr2:47903952-47903953	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs376691273	chr2:47903985-47903986	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs369985668	chr2:47904000-47904001	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs77204584	chr2:47904023-47904024	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs570408788	chr2:47904044-47904045	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs534701880	chr2:47904048-47904049	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs552723359	chr2:47904073-47904074	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs574373137	chr2:47904077-47904078	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs535425156	chr2:47904078-47904079	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs200863942	chr2:47904092-47904093	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs7603494	chr2:47904096-47904097	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs144008817	chr2:47904134-47904135	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs575791388	chr2:47904137-47904138	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs376681295	chr2:47904144-47904145	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs545565951	chr2:47904204-47904205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs373010688	chr2:47904219-47904220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20433910	CNVD
Autism	21701786	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Austim spectrum disorder	21302340	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	20553308	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Mental retardation	19521722	CNVD
Schizophrenia	18990708	CNVD
Schizophrenia	18940311	CNVD
Schizophrenia	19348701	CNVD
Schizophrenia	18945720	CNVD
Schizophrenia	19571808	CNVD
Prostate cancer	16573809	CNVD
Neuroticism	17667963	CNVD
Schizophrenia	19443537	CNVD
Schizophrenia	19546859	CNVD
Autism	17322880	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Cancer	17699850	CNVD
Ovarian cancer	17699850	CNVD
Breast cancer	22522925	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47897400-47915600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47902400-47903600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:47902800-47904000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:47902800-47904200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:47904000-47905000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:47905000-47905200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:47905000-47905200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:47905000-47905600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr2:47905000-47905800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr2:47905000-47906000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr2:47905000-47906000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr2:47905000-47906000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:47905200-47905400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:47905200-47905800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:47905200-47905800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr2:47905200-47906000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr2:47905200-47906200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:47905600-47908200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:47905800-47922000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:47906000-47906200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:47906000-47907000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:47906200-47922000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:47908200-47908400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr2:47909200-47909400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:47909200-47909400	Enhancers	HUVEC	blood vessel
26	chr2:47909400-47910600	Weak transcription	HUVEC	blood vessel
27	chr2:47909400-47915800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:47910600-47910800	Enhancers	HUVEC	blood vessel
29	chr2:47910800-47915800	Weak transcription	HUVEC	blood vessel
30	chr2:47912000-47912200	Enhancers	Pancreas	Pancrea
31	chr2:47912600-47912800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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