Variant report

Variant	nsv1062442
Chromosome Location	chr20:25714010-25754838
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	BATF	chr20:25734352-25734580	GM12878	blood:	n/a	n/a
2	BCL11A	chr20:25737731-25737913	GM12878	blood:	n/a	n/a
3	BHLHE40	chr20:25731988-25732189	K562	blood:	n/a	n/a
4	BRCA1	chr20:25731987-25732070	HepG2	liver:	n/a	n/a
5	CEBPB	chr20:25731932-25732389	HepG2	liver:	n/a	n/a
6	CEBPB	chr20:25726257-25726525	HepG2	liver:	n/a	chr20:25726399-25726410
7	CEBPB	chr20:25741823-25742042	HepG2	liver:	n/a	chr20:25741983-25741994
8	CEBPB	chr20:25741860-25742060	K562	blood:	n/a	chr20:25741983-25741994
9	CEBPB	chr20:25736429-25736642	HepG2	liver:	n/a	chr20:25736503-25736514 chr20:25736533-25736544
10	CEBPB	chr20:25741990-25742017	Hela-S3	cervix:	n/a	n/a
11	CEBPD	chr20:25731486-25732115	HepG2	liver:	n/a	n/a
12	CHD1	chr20:25741744-25742036	IMR90	lung:	n/a	n/a
13	CHD2	chr20:25731489-25731592	HepG2	liver:	n/a	n/a
14	CTCF	chr20:25741900-25742050	HFF	foreskin:	n/a	n/a
15	CTCF	chr20:25741840-25741990	WI-38	lung:	n/a	n/a
16	CTCF	chr20:25742480-25742630	MCF-7	breast:	n/a	n/a
17	CTCF	chr20:25741760-25741910	GM12864	blood:	n/a	n/a
18	CTCF	chr20:25732195-25732293	MCF-7	breast:	n/a	n/a
19	CTCF	chr20:25732194-25732317	MCF-7	breast:	n/a	n/a
20	CTCF	chr20:25740060-25740210	HepG2	liver:	n/a	n/a
21	CTCF	chr20:25732160-25732310	MCF-7	breast:	n/a	n/a
22	CTCF	chr20:25741780-25741930	HCPEpiC	choroid plexus:	n/a	n/a
23	CTCF	chr20:25735404-25735632	LNCaP	prostate:	n/a	n/a
24	CTCF	chr20:25732220-25732370	MCF-7	breast:	n/a	n/a
25	CTCF	chr20:25735410-25735655	LNCaP	prostate:	n/a	n/a
26	CTCF	chr20:25737920-25738070	WI-38	lung:	n/a	n/a
27	CTCF	chr20:25741700-25741850	GM12869	blood:	n/a	n/a
28	CUX1	chr20:25741855-25742028	GM12878	blood:	n/a	n/a
29	CUX1	chr20:25731567-25731602	K562	blood:	n/a	n/a
30	E2F4	chr20:25721500-25721730	MCF10A-Er-Src	breast:	n/a	n/a
31	E2F4	chr20:25721024-25721132	MCF10A-Er-Src	breast:	n/a	n/a
32	E2F6	chr20:25731807-25731981	K562	blood:	n/a	n/a
33	EBF1	chr20:25748749-25748970	GM12878	blood:	n/a	n/a
34	EGR1	chr20:25731443-25732329	MCF-7	breast:	n/a	chr20:25732030-25732040 chr20:25732103-25732127 chr20:25732030-25732039 chr20:25732030-25732041 chr20:25732030-25732040 chr20:25732029-25732042 chr20:25731749-25731758 chr20:25732030-25732041 chr20:25732028-25732042
35	EGR1	chr20:25731924-25732082	K562	blood:	n/a	chr20:25732030-25732040 chr20:25732030-25732039 chr20:25732030-25732041 chr20:25732030-25732040 chr20:25732029-25732042 chr20:25732030-25732041 chr20:25732028-25732042
36	EGR1	chr20:25731806-25732260	ECC-1	luminal epithelium:	n/a	chr20:25732030-25732040 chr20:25732103-25732127 chr20:25732030-25732039 chr20:25732030-25732041 chr20:25732030-25732040 chr20:25732029-25732042 chr20:25732030-25732041 chr20:25732028-25732042
37	EP300	chr20:25740283-25740289	GM12878	blood:	n/a	n/a
38	EP300	chr20:25731536-25731557	HepG2	liver:	n/a	n/a
39	EP300	chr20:25731967-25732126	HepG2	liver:	n/a	n/a
40	FOS	chr20:25718862-25719132	MCF10A-Er-Src	breast:	n/a	chr20:25718937-25718949
41	FOS	chr20:25718895-25719138	MCF10A-Er-Src	breast:	n/a	chr20:25718937-25718949
42	FOS	chr20:25720313-25720625	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr20:25720210-25720679	HUVEC	blood vessel:	n/a	n/a
44	FOS	chr20:25718894-25719152	MCF10A-Er-Src	breast:	n/a	chr20:25718937-25718949
45	FOS	chr20:25720331-25720608	MCF10A-Er-Src	breast:	n/a	n/a
46	FOSL2	chr20:25737379-25737938	HepG2	liver:	n/a	chr20:25737529-25737537
47	FOSL2	chr20:25747596-25747863	HepG2	liver:	n/a	n/a
48	FOSL2	chr20:25746786-25747003	HepG2	liver:	n/a	n/a
49	FOSL2	chr20:25745239-25745473	HepG2	liver:	n/a	n/a
50	FOSL2	chr20:25740561-25740886	HepG2	liver:	n/a	chr20:25740829-25740839

No.	Distal block	Cell Line	Cell type
1	chr20:25675586..25677215-chr20:25728197..25729782,2	MCF-7	breast:
2	chr20:25719439..25721386-chr20:25725863..25727758,2	K562	blood:
3	chr20:25722229..25725727-chr20:25729009..25731451,3	MCF-7	breast:
4	chr20:25724362..25726772-chr20:25730117..25732071,3	MCF-7	breast:
5	chr20:25727469..25729069-chr20:25729208..25731767,2	MCF-7	breast:
6	chr20:25722229..25725727-chr20:25729009..25731451,3	MCF-7	breast:
7	chr20:25719439..25721386-chr20:25725863..25727758,2	K562	blood:
8	chr20:25722430..25724237-chr20:25730774..25732433,2	MCF-7	breast:
9	chr20:25727469..25729069-chr20:25729208..25731767,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GINS1-7	chr20:25714900-25715729	NONHSAT079180
2	lnc-GINS1-2	chr20:25733199-25733422	NONHSAT079183
3	lnc-FAM182B-1	chr20:25730059-25730236	XLOC_013708
4	lnc-FAM182B-1	chr20:25730940-25732440	XLOC_013708
5	lnc-GINS1-2	chr20:25731813-25731974	NONHSAT079184
6	lnc-GINS1-2	chr20:25733199-25733397	ENSG00000226465.1
7	lnc-GINS1-2	chr20:25731854-25731974	ENSG00000226465.1
8	lnc-FAM182B-8	chr20:25754652-25754795	NONHSAT147160
9	lnc-GINS1-2	chr20:25731520-25731591	NONHSAT079183
10	lnc-GINS1-2	chr20:25733199-25733422	NONHSAT079184
11	lnc-FAM182B-8	chr20:25750234-25754795	NONHSAT079187

Variant related genes	Relation type
VN1R108P	TF binding region
ENSG00000226465	TF binding region
ENSG00000226465	chromatin interactions
PTPLAD1	miRNA target sites
PTPMT1	miRNA target sites

Extended variants
information (count: 1912 )
Associated
traits (count: 45 )

Variant overlapped rSNPs/rCNVs (count:1912 , 50 per page) page: 1 2 3 4 5 6 7 ... 39

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534343546	chr20:25714013-25714014	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs188609475	chr20:25714104-25714105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs140828608	chr20:25714132-25714133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs540170633	chr20:25714145-25714146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs191925186	chr20:25714150-25714151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs576421860	chr20:25714152-25714153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs529793522	chr20:25714174-25714175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs184174619	chr20:25714180-25714181	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs117412604	chr20:25714181-25714182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs540791002	chr20:25714211-25714212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs563971867	chr20:25714222-25714223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs533032977	chr20:25714229-25714230	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs188500683	chr20:25714237-25714238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs114816325	chr20:25714241-25714242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs376231849	chr20:25714247-25714248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs548704848	chr20:25714257-25714258	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs368671799	chr20:25714276-25714277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs565752702	chr20:25714290-25714291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs528212064	chr20:25714303-25714304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs547995903	chr20:25714329-25714330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs180914862	chr20:25714338-25714339	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs184309311	chr20:25714364-25714365	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs190475280	chr20:25714398-25714399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs570255245	chr20:25714433-25714434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs528137919	chr20:25714475-25714476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs116114336	chr20:25714481-25714482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs62213470	chr20:25714579-25714580	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs555490596	chr20:25714585-25714586	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs572189815	chr20:25714595-25714596	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs541153141	chr20:25714612-25714613	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs557529028	chr20:25714620-25714621	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs73904659	chr20:25714640-25714641	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs549711994	chr20:25714716-25714717	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs563555072	chr20:25714792-25714793	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs199890787	chr20:25714794-25714795	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs546611358	chr20:25714800-25714801	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs529196996	chr20:25714832-25714833	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs16987989	chr20:25714840-25714841	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs150150267	chr20:25714869-25714870	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs57039225	chr20:25714877-25714878	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs559426045	chr20:25714893-25714894	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs528174437	chr20:25714912-25714913	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
43	rs149368569	chr20:25714934-25714935	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
44	rs571373055	chr20:25715003-25715004	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
45	rs112677809	chr20:25715014-25715015	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
46	rs550128675	chr20:25715049-25715050	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
47	rs570293299	chr20:25715074-25715075	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
48	rs73345246	chr20:25715108-25715109	Weak transcription ZNF genes & repeats	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs551217451	chr20:25715113-25715114	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
50	rs565780796	chr20:25715119-25715120	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:45)

Disease	PMID	Source
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
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Colorectal cancer	16774939	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:389 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25700400-25725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr20:25701200-25720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:25708000-25715800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr20:25708000-25716200	Weak transcription	Thymus	Thymus
5	chr20:25708000-25717200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:25708000-25717600	Weak transcription	Psoas Muscle	Psoas
7	chr20:25708000-25724600	Weak transcription	Brain Substantia Nigra	brain
8	chr20:25708000-25731400	Weak transcription	Esophagus	oesophagus
9	chr20:25711200-25715400	Weak transcription	Gastric	stomach
10	chr20:25711600-25724800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:25713400-25720200	Weak transcription	Primary T cells from cord blood	blood
12	chr20:25713400-25731000	Weak transcription	Left Ventricle	heart
13	chr20:25713600-25720200	Weak transcription	HSMM	muscle
14	chr20:25713600-25721800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr20:25714400-25731200	Weak transcription	Pancreas	Pancrea
16	chr20:25714600-25718600	Weak transcription	NHEK	skin
17	chr20:25714800-25715800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr20:25715400-25715600	ZNF genes & repeats	Aorta	Aorta
19	chr20:25715400-25715600	ZNF genes & repeats	Gastric	stomach
20	chr20:25715600-25716800	Weak transcription	Gastric	stomach
21	chr20:25715600-25731400	Weak transcription	Aorta	Aorta
22	chr20:25718400-25719600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr20:25718600-25718800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr20:25718600-25718800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr20:25718600-25718800	Enhancers	HMEC	breast
26	chr20:25718600-25718800	Enhancers	Osteobl	bone
27	chr20:25718600-25719000	Enhancers	NHEK	skin
28	chr20:25718800-25720200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr20:25719000-25720200	Weak transcription	HMEC	breast
30	chr20:25719000-25720200	Weak transcription	NHEK	skin
31	chr20:25719600-25720000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr20:25719600-25721600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr20:25719800-25721200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr20:25719800-25721200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr20:25719800-25721400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr20:25720000-25721000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr20:25720000-25721600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr20:25720000-25721600	Enhancers	Hela-S3	cervix
39	chr20:25720000-25722200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr20:25720000-25722200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr20:25720200-25720600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr20:25720200-25720800	Enhancers	Primary T cells from cord blood	blood
43	chr20:25720200-25720800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr20:25720200-25720800	Enhancers	HUVEC	blood vessel
45	chr20:25720200-25720800	Enhancers	NHLF	lung
46	chr20:25720200-25721000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:25720200-25721000	Enhancers	Primary T cells fromperipheralblood	blood
48	chr20:25720200-25721000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr20:25720200-25721000	Enhancers	HMEC	breast
50	chr20:25720200-25721000	Enhancers	HSMM	muscle

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