Variant report

Variant	nsv945748
Chromosome Location	chr1:47858512-47862980
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47861286..47863513-chr1:47865315..47867381,2	MCF-7	breast:
2	chr1:47861125..47863393-chr1:47873885..47875951,2	MCF-7	breast:
3	chr1:47859231..47861431-chr1:47871606..47874283,2	K562	blood:
4	chr1:47857694..47860292-chr1:47903399..47906596,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STIL-5	chr1:47859450-47861215	NONHSAT003079

Variant related genes	Relation type
ENSG00000225762	chromatin interactions

Extended variants
information (count: 139 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:139 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs565947697	chr1:47858528-47858529	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs141167289	chr1:47858741-47858742	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs573776568	chr1:47858752-47858753	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs551349236	chr1:47858773-47858774	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs560066999	chr1:47858804-47858805	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs11323397	chr1:47858815-47858816	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs10890479	chr1:47858821-47858822	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs192590658	chr1:47858908-47858909	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs555145978	chr1:47858935-47858936	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs369097544	chr1:47858978-47858979	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs573700398	chr1:47859004-47859005	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs552833600	chr1:47859036-47859037	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs143234614	chr1:47859062-47859063	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs183497109	chr1:47859094-47859095	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs572892057	chr1:47859118-47859119	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs577866882	chr1:47859127-47859128	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs369426675	chr1:47859170-47859171	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs148336348	chr1:47859181-47859182	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs544659399	chr1:47859234-47859235	Bivalent Enhancer Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs575220718	chr1:47859341-47859342	Bivalent Enhancer Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs543038543	chr1:47859392-47859393	Bivalent Enhancer Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs564549270	chr1:47859412-47859413	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs561198081	chr1:47859421-47859422	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs528603669	chr1:47859426-47859427	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs547235743	chr1:47859469-47859470	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs559592395	chr1:47859534-47859535	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs533202429	chr1:47859596-47859597	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs2820991	chr1:47859600-47859601	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs554719890	chr1:47859623-47859624	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs150886174	chr1:47859624-47859625	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs536614621	chr1:47859643-47859644	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs548977266	chr1:47859644-47859645	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs112440010	chr1:47859654-47859655	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs371903431	chr1:47859664-47859665	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs138257476	chr1:47859665-47859666	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs2820992	chr1:47859686-47859687	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs577809585	chr1:47859701-47859702	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs188278532	chr1:47859704-47859705	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs557211757	chr1:47859718-47859719	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs575556312	chr1:47859753-47859754	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs181103699	chr1:47859782-47859783	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs561344884	chr1:47859808-47859809	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
43	rs573210886	chr1:47859880-47859881	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
44	rs115129409	chr1:47859931-47859932	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
45	rs565412098	chr1:47859937-47859938	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
46	rs147315354	chr1:47860010-47860011	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
47	rs545245177	chr1:47860027-47860028	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
48	rs184955874	chr1:47860028-47860029	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
49	rs563540283	chr1:47860044-47860045	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
50	rs528587576	chr1:47860045-47860046	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	17603634	CNVD
Soft tissue tumor	16732325	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Chronic myeloid leukemia	21384125	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Muscle-eye-brain disease	21572526	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Neuroblastoma	21899760	CNVD
Uveal melanoma	20484589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Glioblastoma	20031968	CNVD
Leukemia	18688285	CNVD
Rett syndrome	21593744	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Meckel-Gruber syndrome	21572526	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47847400-47858600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:47847600-47858800	Weak transcription	HSMMtube	muscle
3	chr1:47847600-47865200	Weak transcription	GM12878-XiMat	blood
4	chr1:47847600-47872800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:47849400-47858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:47856600-47861400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:47857000-47858800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:47858400-47860200	Enhancers	HSMM	muscle
9	chr1:47858600-47859400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:47858600-47859400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:47858800-47859000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:47858800-47859200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:47858800-47859200	Enhancers	HSMMtube	muscle
14	chr1:47859000-47859200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:47859000-47859200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:47859000-47859400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:47860600-47861800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:47861400-47861800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:47862400-47866600	Weak transcription	Fetal Intestine Small	intestine

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