Variant report

Variant	nsv1066494
Chromosome Location	chr20:1552104-1572439
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr20:1557318-1557553	HepG2	liver:	n/a	chr20:1557460-1557471
2	CEBPB	chr20:1557313-1557606	Hela-S3	cervix:	n/a	chr20:1557460-1557471
3	CEBPB	chr20:1557320-1557574	A549	lung:	n/a	chr20:1557460-1557471
4	CTCF	chr20:1569820-1569970	HRE	kidney:	n/a	n/a
5	CTCF	chr20:1562140-1562290	GM12864	blood:	n/a	n/a
6	CTCF	chr20:1562336-1562338	Gliobla	brain:	n/a	n/a
7	CTCF	chr20:1569800-1569950	GM12864	blood:	n/a	n/a
8	CTCF	chr20:1569809-1569981	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr20:1569768-1570055	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr20:1569890-1569986	ProgFib	skin:	n/a	n/a
11	CTCF	chr20:1569880-1570030	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr20:1552670-1552733	GM10266	blood:	n/a	n/a
13	CTCF	chr20:1569820-1569970	GM12878	blood:	n/a	n/a
14	CTCF	chr20:1569840-1569990	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr20:1569812-1570027	Gliobla	brain:	n/a	n/a
16	CTCF	chr20:1569820-1569970	AG10803	skin:	n/a	n/a
17	CTCF	chr20:1569840-1569990	HCPEpiC	choroid plexus:	n/a	n/a
18	CTCF	chr20:1569820-1569970	HCT-116	colon:	n/a	n/a
19	CTCF	chr20:1569860-1570010	HEEpiC	esophagus:	n/a	n/a
20	CTCF	chr20:1569840-1569990	HRE	kidney:	n/a	n/a
21	CTCF	chr20:1569820-1569970	HEEpiC	esophagus:	n/a	n/a
22	CTCF	chr20:1569782-1570019	HUVEC	blood vessel:	n/a	n/a
23	CTCF	chr20:1569900-1570050	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr20:1569840-1569990	HRPEpiC	eye:	n/a	n/a
25	CTCF	chr20:1556774-1556880	NHEK	skin:	n/a	n/a
26	CTCF	chr20:1562180-1562330	GM12878	blood:	n/a	n/a
27	CTCF	chr20:1562218-1562407	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr20:1562235-1562401	GM12878	blood:	n/a	n/a
29	CTCF	chr20:1569780-1569930	SAEC	small airway:	n/a	n/a
30	CTCF	chr20:1562180-1562330	GM12875	blood:	n/a	n/a
31	CTCF	chr20:1569840-1569990	HAc	cerebellar:	n/a	n/a
32	CTCF	chr20:1562236-1562335	Gliobla	brain:	n/a	n/a
33	CTCF	chr20:1562235-1562365	GM13977	blood:	n/a	n/a
34	CTCF	chr20:1569860-1570007	GM12878	blood:	n/a	n/a
35	CTCF	chr20:1569800-1569950	HCPEpiC	choroid plexus:	n/a	n/a
36	CTCF	chr20:1569844-1569973	GM12878	blood:	n/a	n/a
37	FOS	chr20:1557393-1557685	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr20:1557387-1557630	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr20:1556802-1556896	MCF10A-Er-Src	breast:	n/a	n/a
40	MAFF	chr20:1560210-1560695	HepG2	liver:	n/a	n/a
41	MAFK	chr20:1560215-1560626	HepG2	liver:	n/a	n/a
42	MAFK	chr20:1560178-1560655	IMR90	lung:	n/a	n/a
43	MAFK	chr20:1560184-1560754	HepG2	liver:	n/a	n/a
44	NFIC	chr20:1557967-1558358	GM12878	blood:	n/a	n/a
45	POLR2A	chr20:1571059-1571375	H1-neurons	neurons:	n/a	n/a
46	RAD21	chr20:1569778-1570132	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr20:1569656-1570123	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr20:1562184-1562442	H1-hESC	embryonic stem cell:	n/a	n/a
49	RAD21	chr20:1562161-1562382	GM12878	blood:	n/a	n/a
50	RAD21	chr20:1562181-1562423	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNPH-4	chr20:1572038-1572494	NONHSAT078121
2	lnc-SNPH-5	chr20:1565852-1565996	ucscGeneNc_uc002wfp_1
3	lnc-SNPH-5	chr20:1559583-1559595	ucscGeneNc_uc002wfp_1
4	lnc-SNPH-5	chr20:1562154-1562366	ucscGeneNc_uc002wfp_1

No data

Variant related genes	Relation type
SIRPB1	TF binding region
ENSG00000260861	TF binding region
ENSG00000271523	TF binding region

Extended variants
information (count: 451 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:451 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544976737	chr20:1552129-1552130	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs538933482	chr20:1552168-1552169	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs370509930	chr20:1552245-1552246	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs554092713	chr20:1552253-1552254	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs148454177	chr20:1552267-1552268	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs141714945	chr20:1552324-1552325	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs199938839	chr20:1552332-1552333	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs181352082	chr20:1552343-1552344	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs201016187	chr20:1552349-1552350	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs200711758	chr20:1552350-1552351	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs374927836	chr20:1552352-1552353	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs371715786	chr20:1552353-1552354	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs111658454	chr20:1552355-1552356	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs147171272	chr20:1552360-1552361	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs144175019	chr20:1552368-1552369	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs148690008	chr20:1552369-1552370	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs565483001	chr20:1552389-1552390	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs142083473	chr20:1552399-1552400	Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs369061568	chr20:1552410-1552411	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs386811626	chr20:1552423-1552424	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs560065824	chr20:1552424-1552425	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs386811627	chr20:1552430-1552431	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs144028465	chr20:1552432-1552433	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs146852997	chr20:1552451-1552452	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs16995332	chr20:1552457-1552458	Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs61731659	chr20:1552464-1552465	Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs201202573	chr20:1552475-1552476	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs549516216	chr20:1552489-1552490	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs28694393	chr20:1552502-1552503	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs145431656	chr20:1552519-1552520	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs149215208	chr20:1552520-1552521	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs140374707	chr20:1552528-1552529	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs371319948	chr20:1552529-1552530	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs147864161	chr20:1552554-1552555	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs141668681	chr20:1552578-1552579	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs200471530	chr20:1552587-1552588	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs61733947	chr20:1552591-1552592	Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs111742423	chr20:1552601-1552602	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs543944594	chr20:1552607-1552608	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs186440949	chr20:1552609-1552610	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs369780504	chr20:1552610-1552611	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs577389972	chr20:1552614-1552615	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs541639858	chr20:1552619-1552620	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs113675259	chr20:1552623-1552624	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs559780117	chr20:1552633-1552634	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs386811628	chr20:1552646-1552647	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs150138053	chr20:1552647-1552648	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs77462482	chr20:1552649-1552650	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs373681327	chr20:1552650-1552651	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs149312459	chr20:1552652-1552653	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

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
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
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
Non-syndromic sensorineural hearing loss	17289997	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD
Lung cancer	18438408	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1543800-1568000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr20:1544600-1569000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr20:1548800-1552400	Strong transcription	Primary T cells from cord blood	blood
4	chr20:1550000-1568200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr20:1550600-1552400	Genic enhancers	Primary monocytes fromperipheralblood	blood
6	chr20:1550600-1552400	Genic enhancers	Monocytes-CD14+_RO01746	blood
7	chr20:1550800-1552200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
8	chr20:1551200-1552200	Weak transcription	Hela-S3	cervix
9	chr20:1551400-1552600	Strong transcription	Spleen	Spleen
10	chr20:1551400-1552800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr20:1551600-1552400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr20:1552200-1553000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr20:1552400-1553000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr20:1552400-1553400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr20:1552400-1558000	Weak transcription	Primary T cells from cord blood	blood
16	chr20:1552400-1568000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr20:1552600-1569000	Weak transcription	Spleen	Spleen
18	chr20:1552800-1558400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr20:1553000-1556800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr20:1553000-1556800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr20:1553400-1553600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr20:1553600-1553800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr20:1553800-1556800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr20:1555600-1556800	Weak transcription	Hela-S3	cervix
25	chr20:1556800-1557200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr20:1556800-1557400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:1556800-1557600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr20:1556800-1557600	Enhancers	NHEK	skin
29	chr20:1556800-1558200	Enhancers	Hela-S3	cervix
30	chr20:1556800-1558600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
31	chr20:1556800-1560000	Genic enhancers	Primary monocytes fromperipheralblood	blood
32	chr20:1556800-1560000	Genic enhancers	Monocytes-CD14+_RO01746	blood
33	chr20:1557000-1557400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr20:1558000-1559600	Strong transcription	Primary T cells from cord blood	blood
35	chr20:1558400-1560000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr20:1558600-1559600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr20:1559600-1560400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr20:1559600-1560600	Weak transcription	Primary T cells from cord blood	blood
39	chr20:1560000-1561000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr20:1560000-1561000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr20:1560000-1579200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr20:1560400-1561800	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr20:1560600-1561000	Strong transcription	Primary T cells from cord blood	blood
44	chr20:1561000-1562600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr20:1561000-1563600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr20:1561000-1568000	Weak transcription	Primary T cells from cord blood	blood
47	chr20:1561800-1563800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr20:1563600-1564600	Genic enhancers	Primary monocytes fromperipheralblood	blood
49	chr20:1563800-1565400	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr20:1564600-1565400	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links