Variant report

Variant	esv2548666
Chromosome Location	chr2:46909514-46911107
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46709342..46712080-chr2:46908104..46909816,2	K562	blood:
2	chr2:46905228..46908369-chr2:46910696..46912754,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGF-2	chr2:46910457-46910666	XLOC_002087
2	lnc-PIGF-2	chr2:46909764-46910140	XLOC_002087
3	lnc-SOCS5-3	chr2:46908201-46909753	NONHSAT070522

Extended variants
information (count: 58 )
Associated
traits (count: 68 )

Variant overlapped rSNPs/rCNVs (count:58 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs188634520	chr2:46909532-46909533	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
2	rs541278433	chr2:46909534-46909535	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
3	rs559618690	chr2:46909581-46909582	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
4	rs192449785	chr2:46909588-46909589	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
5	rs184358801	chr2:46909624-46909625	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
6	rs542188739	chr2:46909701-46909702	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
7	rs563560132	chr2:46909783-46909784	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
8	rs369025255	chr2:46909788-46909789	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
9	rs62136933	chr2:46909809-46909810	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs4355163	chr2:46909817-46909818	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs564295149	chr2:46909858-46909859	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs528684422	chr2:46909866-46909867	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs189050514	chr2:46909870-46909871	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs35370994	chr2:46909965-46909966	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs112526127	chr2:46909983-46909984	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs535803784	chr2:46909989-46909990	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs72881348	chr2:46909996-46909997	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs184539525	chr2:46910040-46910041	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs28370327	chr2:46910064-46910065	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs558687408	chr2:46910102-46910103	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs570630247	chr2:46910107-46910108	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs534825742	chr2:46910122-46910123	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs189129518	chr2:46910129-46910130	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs200365531	chr2:46910151-46910152	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs373143915	chr2:46910152-46910153	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs574680635	chr2:46910298-46910299	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs369815571	chr2:46910308-46910309	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs574653800	chr2:46910406-46910407	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs375456094	chr2:46910448-46910449	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs73926564	chr2:46910488-46910489	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs112856381	chr2:46910489-46910490	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs575241442	chr2:46910501-46910502	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs62136934	chr2:46910509-46910510	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs370859215	chr2:46910546-46910547	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs546143066	chr2:46910561-46910562	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs146543171	chr2:46910617-46910618	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs528598241	chr2:46910711-46910712	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs540800247	chr2:46910757-46910758	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs562194053	chr2:46910759-46910760	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs529584587	chr2:46910765-46910766	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs564494771	chr2:46910774-46910775	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs72802412	chr2:46910775-46910776	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs530539739	chr2:46910798-46910799	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs552266562	chr2:46910800-46910801	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs570542914	chr2:46910861-46910862	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs534733411	chr2:46910901-46910902	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs553128797	chr2:46910909-46910910	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs143252517	chr2:46910935-46910936	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs115826960	chr2:46910938-46910939	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs78759671	chr2:46910941-46910942	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:68)

Disease	PMID	Source
Breast cancer	17603634	CNVD
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
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
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	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
Myelofibrosis	22110671	CNVD
Hypotonia	17579669	CNVD
Hypotonia-Cystinuria syndrome	16385448	CNVD
Glioblastoma multiforme	17002787	CNVD
Cystinuria	17625506	CNVD
Breast cancer	16272173	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Ovarian cancer	22355333	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Melanoma	20877625	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46902600-46909600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:46905600-46909600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:46906000-46911400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:46907400-46910800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:46907600-46911200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:46907600-46911400	Weak transcription	Osteobl	bone
7	chr2:46907800-46911400	Weak transcription	NHDF-Ad	bronchial
8	chr2:46907800-46911800	Enhancers	Primary B cells from peripheral blood	blood
9	chr2:46908400-46911200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:46908400-46911400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:46908400-46912400	Weak transcription	NHLF	lung
12	chr2:46908600-46909800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:46908800-46909600	Weak transcription	GM12878-XiMat	blood
14	chr2:46909400-46910000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr2:46909600-46909800	Enhancers	GM12878-XiMat	blood
16	chr2:46909600-46910000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:46909600-46910800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr2:46909600-46911200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:46909800-46911200	Weak transcription	GM12878-XiMat	blood
20	chr2:46910000-46911600	Enhancers	Primary B cells from cord blood	blood
21	chr2:46910600-46911600	Enhancers	Fetal Muscle Leg	muscle
22	chr2:46910800-46911000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:46911000-46911200	Bivalent Enhancer	HepG2	liver
24	chr2:46911000-46911400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:46911000-46911800	Enhancers	HSMMtube	muscle
26	chr2:46911000-46912400	Enhancers	Fetal Kidney	kidney

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