Variant report

Variant	nsv546467
Chromosome Location	chr1:71245703-71249485
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTGER3-8	chr1:71246141-71247581	NONHSAT003868

Extended variants
information (count: 65 )
Associated
traits (count: 110 )

Variant overlapped rSNPs/rCNVs (count:65 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12046339	chr1:71245703-71245704	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs74440220	chr1:71245710-71245711	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs570443448	chr1:71245761-71245762	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs539236704	chr1:71245773-71245774	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs546791424	chr1:71245797-71245798	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs565991115	chr1:71245815-71245816	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs111788996	chr1:71245823-71245824	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs554804373	chr1:71245857-71245858	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs7523175	chr1:71245866-71245867	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs537470116	chr1:71245875-71245876	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs138843616	chr1:71245904-71245905	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs184689366	chr1:71245916-71245917	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs546051962	chr1:71246008-71246009	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs554651464	chr1:71246051-71246052	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs559900335	chr1:71246052-71246053	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs575937833	chr1:71246081-71246082	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs189007017	chr1:71246082-71246083	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs77242863	chr1:71246090-71246091	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs115701116	chr1:71246155-71246156	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs192601474	chr1:71246223-71246224	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs530405569	chr1:71246237-71246238	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs184993702	chr1:71246283-71246284	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs116187050	chr1:71246334-71246335	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs533256229	chr1:71246342-71246343	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs543365489	chr1:71246350-71246351	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs79670106	chr1:71246353-71246354	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs566647962	chr1:71246386-71246387	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs529121057	chr1:71246427-71246428	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs564832351	chr1:71246485-71246486	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs2148800	chr1:71246574-71246575	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs537407049	chr1:71246576-71246577	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs545209983	chr1:71246628-71246629	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs1536536	chr1:71246668-71246669	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs571110989	chr1:71246672-71246673	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs540134797	chr1:71246797-71246798	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs553431071	chr1:71246850-71246851	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs573383276	chr1:71246859-71246860	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs148990919	chr1:71246962-71246963	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs377565510	chr1:71247001-71247002	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs528004136	chr1:71247039-71247040	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs72928399	chr1:71247059-71247060	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs575013658	chr1:71247071-71247072	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs143760616	chr1:71247078-71247079	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs563746281	chr1:71247109-71247110	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs148174439	chr1:71247141-71247142	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs540516339	chr1:71247155-71247156	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs546377606	chr1:71247218-71247219	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs114671327	chr1:71247219-71247220	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs549213565	chr1:71247268-71247269	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
50	rs180927612	chr1:71247283-71247284	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:110)

Disease	PMID	Source
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
Glioblastoma multiforme	21080181	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
Papillary thyroid carcinoma	21436994	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
Breast cancer	17603634	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
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
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17133270	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
abnormal development	18461090	CNVD
Ewing''s sarcoma	17952124	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Poland''s syndrome	22110015	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma multiforme	21922591	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Cancer	22429812	CNVD
Effusion lymphoma	18079361	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71243000-71247000	Enhancers	NHDF-Ad	bronchial
2	chr1:71244800-71245800	Enhancers	HSMM	muscle
3	chr1:71245200-71246200	Weak transcription	Osteobl	bone
4	chr1:71245400-71246200	Enhancers	NHLF	lung
5	chr1:71245600-71245800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:71245600-71245800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:71245800-71246200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:71245800-71247000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:71246400-71246600	Enhancers	Osteobl	bone

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