Variant report

Variant	esv3497591
Chromosome Location	chr20:1389046-1390921
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1387186..1389098-chr20:1391471..1393677,2	MCF-7	breast:
2	chr20:1384990..1387871-chr20:1389849..1391425,2	K562	blood:
3	chr20:1389651..1392477-chr20:1392965..1396440,4	K562	blood:
4	chr20:1388186..1390453-chr20:1399929..1402694,2	K562	blood:
5	chr20:1374791..1377395-chr20:1388884..1390483,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FKBP1A-3	chr20:1389013-1389091	NONHSAT078110

Extended variants
information (count: 60 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:60 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540089726	chr20:1389063-1389064	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
2	rs376908470	chr20:1389070-1389071	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs6105081	chr20:1389097-1389098	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs6109838	chr20:1389134-1389135	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs369278599	chr20:1389146-1389147	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs369823643	chr20:1389147-1389148	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs140997298	chr20:1389153-1389154	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs74998469	chr20:1389189-1389190	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs146516947	chr20:1389198-1389199	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs377337698	chr20:1389226-1389227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs60505700	chr20:1389260-1389261	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs192894808	chr20:1389276-1389277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs185292018	chr20:1389281-1389282	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs188517183	chr20:1389288-1389289	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs7263236	chr20:1389337-1389338	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs6074595	chr20:1389383-1389384	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs6074596	chr20:1389388-1389389	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs181327410	chr20:1389404-1389405	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs6074597	chr20:1389414-1389415	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs6074598	chr20:1389415-1389416	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs6514389	chr20:1389425-1389426	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs554935493	chr20:1389614-1389615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs568309496	chr20:1389630-1389631	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs564279963	chr20:1389673-1389674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs7272487	chr20:1389695-1389696	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs13038785	chr20:1389730-1389731	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs75039933	chr20:1389740-1389741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs77516401	chr20:1389743-1389744	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs537226593	chr20:1389748-1389749	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs141496351	chr20:1389749-1389750	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs34205790	chr20:1389766-1389767	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs7263501	chr20:1389773-1389774	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs67138747	chr20:1389810-1389811	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs6109845	chr20:1389863-1389864	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs7271023	chr20:1389881-1389882	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs7271027	chr20:1389896-1389897	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs561722538	chr20:1389935-1389936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs146248537	chr20:1389936-1389937	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs7272681	chr20:1389952-1389953	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs541805560	chr20:1389974-1389975	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs7261672	chr20:1390023-1390024	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs183676898	chr20:1390027-1390028	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs527444601	chr20:1390040-1390041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs6514392	chr20:1390247-1390248	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs7261873	chr20:1390349-1390350	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs548344955	chr20:1390414-1390415	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs8116350	chr20:1390430-1390431	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs138652453	chr20:1390504-1390505	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs8121136	chr20:1390579-1390580	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs6079033	chr20:1390683-1390684	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Glioblastoma multiforme	22286061	CNVD
Hepatocellular carcinoma	22174799	CNVD
Colorectal cancer	19455253	CNVD
Ovarian cancer	20844748	CNVD
Breast cancer	17603634	CNVD
Colorectal cancer	19359472	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Intracranial aneurysm	16715129	CNVD
Colorectal cancer	16774939	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Medulloblastoma	21979893	CNVD
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
lymphocytic leukemia	21291569	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Ewing''s sarcoma	17952124	CNVD
Oral cancer	21386901	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	17363583	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1383800-1396000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr20:1384400-1395600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:1384400-1396000	Weak transcription	HMEC	breast
4	chr20:1388400-1389200	Enhancers	Placenta	Placenta
5	chr20:1389000-1396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr20:1389200-1396400	Weak transcription	Placenta	Placenta
7	chr20:1390200-1390600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr20:1390600-1396600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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