Variant report

Variant	nsv437183
Chromosome Location	chr20:1546450-1569563
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr20:1550229-1550409	K562	blood:	n/a	n/a
2	ATF1	chr20:1550073-1550394	K562	blood:	n/a	n/a
3	BACH1	chr20:1550102-1550372	K562	blood:	n/a	n/a
4	BHLHE40	chr20:1549969-1550250	K562	blood:	n/a	n/a
5	BRCA1	chr20:1550123-1550444	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr20:1549872-1550575	HCT-116	colon:	n/a	chr20:1549945-1549956
7	CEBPB	chr20:1550079-1550429	K562	blood:	n/a	n/a
8	CEBPB	chr20:1549828-1550670	HCT-116	colon:	n/a	chr20:1549945-1549956
9	CEBPB	chr20:1557318-1557553	HepG2	liver:	n/a	chr20:1557460-1557471
10	CEBPB	chr20:1550121-1550426	IMR90	lung:	n/a	n/a
11	CEBPB	chr20:1549993-1550495	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr20:1548089-1548620	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr20:1550060-1550411	MCF-7	breast:	n/a	n/a
14	CEBPB	chr20:1550069-1550318	K562	blood:	n/a	n/a
15	CEBPB	chr20:1549987-1550512	A549	lung:	n/a	n/a
16	CEBPB	chr20:1550062-1550405	A549	lung:	n/a	n/a
17	CEBPB	chr20:1557320-1557574	A549	lung:	n/a	chr20:1557460-1557471
18	CEBPB	chr20:1550085-1550450	A549	lung:	n/a	n/a
19	CEBPB	chr20:1550076-1550409	HepG2	liver:	n/a	n/a
20	CEBPB	chr20:1557313-1557606	Hela-S3	cervix:	n/a	chr20:1557460-1557471
21	CHD2	chr20:1548232-1548651	Hela-S3	cervix:	n/a	n/a
22	CHD2	chr20:1550074-1550408	Hela-S3	cervix:	n/a	n/a
23	CREB1	chr20:1550008-1550399	K562	blood:	n/a	n/a
24	CTCF	chr20:1562140-1562290	GM12864	blood:	n/a	n/a
25	CTCF	chr20:1562180-1562330	GM12878	blood:	n/a	n/a
26	CTCF	chr20:1552670-1552733	GM10266	blood:	n/a	n/a
27	CTCF	chr20:1562336-1562338	Gliobla	brain:	n/a	n/a
28	CTCF	chr20:1550540-1550690	NB4	blood:	n/a	n/a
29	CTCF	chr20:1550471-1550587	K562	blood:	n/a	n/a
30	CTCF	chr20:1562180-1562330	GM12875	blood:	n/a	n/a
31	CTCF	chr20:1556774-1556880	NHEK	skin:	n/a	n/a
32	CTCF	chr20:1562236-1562335	Gliobla	brain:	n/a	n/a
33	CTCF	chr20:1562235-1562401	GM12878	blood:	n/a	n/a
34	CTCF	chr20:1562218-1562407	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr20:1562235-1562365	GM13977	blood:	n/a	n/a
36	E2F4	chr20:1550155-1550481	MCF10A-Er-Src	breast:	n/a	n/a
37	EP300	chr20:1549951-1550436	Hela-S3	cervix:	n/a	n/a
38	EP300	chr20:1550067-1550405	K562	blood:	n/a	n/a
39	EP300	chr20:1548112-1548657	Hela-S3	cervix:	n/a	n/a
40	FOS	chr20:1547412-1547722	MCF10A-Er-Src	breast:	n/a	chr20:1547544-1547552 chr20:1547547-1547555 chr20:1547416-1547428
41	FOS	chr20:1556802-1556896	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr20:1549885-1550514	MCF10A-Er-Src	breast:	n/a	chr20:1550241-1550249 chr20:1550240-1550250 chr20:1550239-1550251 chr20:1550239-1550250
43	FOS	chr20:1550024-1550457	MCF10A-Er-Src	breast:	n/a	chr20:1550241-1550249 chr20:1550240-1550250 chr20:1550239-1550251 chr20:1550239-1550250
44	FOS	chr20:1548038-1549062	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr20:1548038-1549064	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr20:1547417-1547722	MCF10A-Er-Src	breast:	n/a	chr20:1547544-1547552 chr20:1547547-1547555
47	FOS	chr20:1547519-1547719	MCF10A-Er-Src	breast:	n/a	chr20:1547544-1547552 chr20:1547547-1547555
48	FOS	chr20:1557393-1557685	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr20:1547896-1548917	HUVEC	blood vessel:	n/a	n/a
50	FOS	chr20:1548179-1549018	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1544908..1546600-chr20:1698607..1700315,2	MCF-7	breast:
2	chr20:1547054..1548894-chr20:1756067..1757690,2	K562	blood:

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

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

Extended variants
information (count: 656 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:656 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2253821	chr20:1546450-1546451	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs370361511	chr20:1546452-1546453	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs561332901	chr20:1546498-1546499	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs6135315	chr20:1546506-1546507	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs572292047	chr20:1546544-1546545	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs542564812	chr20:1546548-1546549	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs116264607	chr20:1546564-1546565	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs374752158	chr20:1546595-1546596	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs368544292	chr20:1546613-1546614	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs543901118	chr20:1546641-1546642	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs115564175	chr20:1546689-1546690	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs190691374	chr20:1546705-1546706	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs527585630	chr20:1546723-1546724	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs2243602	chr20:1546742-1546743	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs78745462	chr20:1546769-1546770	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs146905696	chr20:1546780-1546781	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs111403092	chr20:1546802-1546803	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs62623705	chr20:1546805-1546806	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs374551011	chr20:1546813-1546814	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs267605841	chr20:1546817-1546818	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs377447664	chr20:1546830-1546831	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs531223992	chr20:1546838-1546839	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs370255651	chr20:1546853-1546854	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs376340612	chr20:1546857-1546858	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs549401753	chr20:1546866-1546867	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs267605842	chr20:1546871-1546872	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs570990498	chr20:1546882-1546883	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs538384111	chr20:1546885-1546886	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs140560100	chr20:1546886-1546887	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs267605843	chr20:1546890-1546891	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs11907593	chr20:1546906-1546907	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs148162147	chr20:1546907-1546908	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs2243603	chr20:1546911-1546912	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs576438918	chr20:1546984-1546985	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs537420959	chr20:1547012-1547013	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs112911644	chr20:1547042-1547043	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs577407547	chr20:1547064-1547065	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs532539136	chr20:1547092-1547093	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs61741656	chr20:1547124-1547125	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs541176866	chr20:1547161-1547162	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs559852954	chr20:1547176-1547177	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs558134045	chr20:1547183-1547184	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs114854215	chr20:1547212-1547213	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs4814327	chr20:1547213-1547214	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs375022301	chr20:1547220-1547221	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs563626229	chr20:1547238-1547239	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs35048020	chr20:1547241-1547242	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs79248427	chr20:1547251-1547252	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs549365414	chr20:1547258-1547259	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs564545322	chr20:1547260-1547261	Enhancers Genic enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:69)

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
Prostate cancer	21551127	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Alcoholism	21790672	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD
Lung cancer	18438408	CNVD

Chromatin state (count:162 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1537000-1551600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr20:1543200-1550400	Weak transcription	Thymus	Thymus
3	chr20:1543600-1548600	Genic enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:1543800-1568000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr20:1544600-1569000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr20:1544800-1548200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr20:1545000-1548000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr20:1545200-1547400	Strong transcription	Primary T cells from cord blood	blood
9	chr20:1545400-1546600	Strong transcription	Spleen	Spleen
10	chr20:1545800-1546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:1545800-1549400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr20:1546000-1547000	ZNF genes & repeats	Lung	lung
13	chr20:1546200-1547800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr20:1546600-1551200	Enhancers	Hela-S3	cervix
15	chr20:1546600-1551400	Weak transcription	Spleen	Spleen
16	chr20:1546800-1550800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:1546800-1551000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:1547000-1547800	Enhancers	NHEK	skin
19	chr20:1547000-1550800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:1547000-1551000	Enhancers	HMEC	breast
21	chr20:1547200-1549000	Enhancers	NH-A	brain
22	chr20:1547200-1549400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:1547200-1551000	Enhancers	HUVEC	blood vessel
24	chr20:1547400-1548000	Enhancers	A549	lung
25	chr20:1547400-1548800	Weak transcription	Primary T cells from cord blood	blood
26	chr20:1547400-1549000	Enhancers	Osteobl	bone
27	chr20:1547800-1548000	Genic enhancers	Monocytes-CD14+_RO01746	blood
28	chr20:1547800-1548200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr20:1547800-1548600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr20:1547800-1548800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr20:1547800-1548800	Flanking Active TSS	NHEK	skin
32	chr20:1547800-1550200	Enhancers	NHDF-Ad	bronchial
33	chr20:1548000-1548200	Active TSS	A549	lung
34	chr20:1548000-1548400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr20:1548000-1548400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr20:1548000-1548400	Enhancers	Esophagus	oesophagus
37	chr20:1548000-1548400	Enhancers	NHLF	lung
38	chr20:1548000-1548800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr20:1548000-1549000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr20:1548000-1549000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr20:1548000-1549000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
42	chr20:1548200-1548600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr20:1548200-1548600	Flanking Active TSS	A549	lung
44	chr20:1548200-1551400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr20:1548400-1548600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr20:1548400-1548800	Weak transcription	Esophagus	oesophagus
47	chr20:1548400-1550200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr20:1548600-1549000	Enhancers	Primary hematopoietic stem cells	blood
49	chr20:1548600-1550600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr20:1548600-1550600	Enhancers	A549	lung

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