Variant report

Variant	esv3320264
Chromosome Location	chr1:78833811-78835858
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTGFR-1	chr1:78834968-78835149	ENSG00000237413.1
2	lnc-PTGFR-1	chr1:78834222-78834412	NONHSAT004072
3	lnc-PTGFR-1	chr1:78834222-78834412	ENSG00000237413.1
4	lnc-PTGFR-1	chr1:78834968-78835147	NONHSAT004072

Extended variants
information (count: 54 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:54 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs554192179	chr1:78833994-78833995	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs566337139	chr1:78834037-78834038	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs534132287	chr1:78834038-78834039	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs558553558	chr1:78834057-78834058	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs577041195	chr1:78834059-78834060	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs544432121	chr1:78834061-78834062	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs185205292	chr1:78834101-78834102	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs190946210	chr1:78834128-78834129	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs544101370	chr1:78834161-78834162	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs182714226	chr1:78834162-78834163	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs6424768	chr1:78834258-78834259	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs188229204	chr1:78834259-78834260	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs540949610	chr1:78834284-78834285	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs192795620	chr1:78834290-78834291	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs532801087	chr1:78834292-78834293	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs550765421	chr1:78834318-78834319	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs574631489	chr1:78834386-78834387	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs529781557	chr1:78834439-78834440	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs540324721	chr1:78834444-78834445	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs183470554	chr1:78834448-78834449	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs560139660	chr1:78834556-78834557	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs114491443	chr1:78834575-78834576	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs552119128	chr1:78834742-78834743	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs11809460	chr1:78834864-78834865	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs11809462	chr1:78834898-78834899	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs556442616	chr1:78834957-78834958	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs569168794	chr1:78835007-78835008	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs538182996	chr1:78835010-78835011	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs574673276	chr1:78835094-78835095	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs557945090	chr1:78835143-78835144	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs577916935	chr1:78835183-78835184	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs554743052	chr1:78835191-78835192	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs573260550	chr1:78835198-78835199	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs540284209	chr1:78835226-78835227	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs563060799	chr1:78835293-78835294	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs534009679	chr1:78835321-78835322	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs565236711	chr1:78835391-78835392	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs6424769	chr1:78835491-78835492	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs574086730	chr1:78835522-78835523	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs542989513	chr1:78835559-78835560	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs562591261	chr1:78835563-78835564	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs187403084	chr1:78835642-78835643	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs145132433	chr1:78835668-78835669	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs12755166	chr1:78835673-78835674	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs192350331	chr1:78835688-78835689	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs530211158	chr1:78835691-78835692	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs548349771	chr1:78835692-78835693	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs565107131	chr1:78835724-78835725	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs560008933	chr1:78835758-78835759	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs12023080	chr1:78835761-78835762	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:102)

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
Breast cancer	17133270	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Ewing''s sarcoma	17952124	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
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Colorectal cancer	16774939	CNVD
Schizophrenia	23813976	CNVD
Pancreatic cancer	17952125	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78832400-78837800	Weak transcription	Pancreas	Pancrea
2	chr1:78833600-78837600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:78833800-78836800	Enhancers	NHDF-Ad	bronchial
4	chr1:78833800-78837600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:78833800-78837600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:78834000-78834200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:78834000-78836200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:78834200-78834800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:78834200-78835000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:78834600-78837600	Enhancers	HMEC	breast
11	chr1:78834600-78837800	Enhancers	HSMM	muscle
12	chr1:78834800-78837600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:78834800-78837800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:78835000-78835400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:78835400-78835800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr1:78835400-78837000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:78835600-78837400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:78835600-78837400	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links