Variant report

Variant	nsv979883
Chromosome Location	chr3:138766621-138798997
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	ATF3	chr3:138781829-138782132	HCT-116	colon:	n/a	n/a
2	CBX3	chr3:138793361-138793771	HCT-116	colon:	n/a	n/a
3	CBX3	chr3:138772010-138772439	HCT-116	colon:	n/a	n/a
4	CEBPB	chr3:138781761-138782185	Hela-S3	cervix:	n/a	chr3:138781950-138781961
5	CEBPB	chr3:138781804-138782129	K562	blood:	n/a	chr3:138781950-138781961
6	CEBPB	chr3:138781820-138782022	K562	blood:	n/a	chr3:138781950-138781961
7	CEBPB	chr3:138781811-138782129	A549	lung:	n/a	chr3:138781950-138781961
8	CEBPB	chr3:138791476-138791676	A549	lung:	n/a	n/a
9	CEBPB	chr3:138781617-138782269	HCT-116	colon:	n/a	chr3:138781950-138781961
10	CEBPB	chr3:138781852-138782066	K562	blood:	n/a	chr3:138781950-138781961
11	CEBPB	chr3:138781685-138782326	HCT-116	colon:	n/a	chr3:138781950-138781961
12	CEBPB	chr3:138781844-138782075	H1-hESC	embryonic stem cell:	n/a	chr3:138781950-138781961
13	CEBPB	chr3:138781867-138782114	HepG2	liver:	n/a	chr3:138781950-138781961
14	CTCF	chr3:138792840-138792990	GM12874	blood:	n/a	n/a
15	E2F4	chr3:138797260-138797553	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr3:138782007-138782270	MCF10A-Er-Src	breast:	n/a	n/a
17	EGR1	chr3:138786521-138786613	GM12878	blood:	n/a	n/a
18	EP300	chr3:138781767-138782175	Hela-S3	cervix:	n/a	n/a
19	EP300	chr3:138793539-138793739	GM12878	blood:	n/a	n/a
20	EP300	chr3:138781823-138782086	K562	blood:	n/a	n/a
21	FOS	chr3:138781843-138782109	MCF10A-Er-Src	breast:	n/a	n/a
22	IKZF1	chr3:138793624-138793809	GM12878	blood:	n/a	n/a
23	IRF1	chr3:138771718-138771941	K562	blood:	n/a	n/a
24	JUN	chr3:138791401-138791735	K562	blood:	n/a	n/a
25	KAP1	chr3:138771479-138771936	K562	blood:	n/a	n/a
26	KAP1	chr3:138772285-138772858	K562	blood:	n/a	n/a
27	MAFF	chr3:138787995-138788183	K562	blood:	n/a	n/a
28	MAFK	chr3:138777299-138777357	HepG2	liver:	n/a	n/a
29	MAFK	chr3:138783265-138783268	Hela-S3	cervix:	n/a	n/a
30	MAFK	chr3:138788037-138788209	K562	blood:	n/a	n/a
31	MYC	chr3:138792981-138793027	MCF-7	breast:	n/a	n/a
32	MYC	chr3:138780892-138780939	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:138776035-138776110	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr3:138790532-138790601	ProgFib	skin:	n/a	n/a
35	POLR2A	chr3:138782922-138783073	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr3:138773899-138773963	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:138783034-138783202	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr3:138776810-138776834	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:138773517-138773654	MCF-7	breast:	n/a	n/a
40	REST	chr3:138786547-138786617	PANC-1	pancreas:	n/a	n/a
41	RFX5	chr3:138782215-138782227	K562	blood:	n/a	n/a
42	RUNX3	chr3:138793525-138793849	GM12878	blood:	n/a	n/a
43	RUNX3	chr3:138793502-138793843	GM12878	blood:	n/a	n/a
44	SETDB1	chr3:138772003-138772961	U2OS	brain:	n/a	n/a
45	SETDB1	chr3:138793206-138794007	U2OS	brain:	n/a	n/a
46	SIN3AK20	chr3:138786550-138786648	HepG2	liver:	n/a	n/a
47	SP1	chr3:138781834-138782239	HCT-116	colon:	n/a	n/a
48	STAT3	chr3:138774822-138775004	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT3	chr3:138781718-138782161	MCF10A-Er-Src	breast:	n/a	chr3:138781933-138781944
50	STAT3	chr3:138772043-138772206	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:138793112..138793888-chr7:133044725..133045291,2	MCF-7	breast:
2	chr3:138787678..138789899-chr3:138790996..138793075,2	MCF-7	breast:
3	chr3:138787678..138789899-chr3:138790996..138793075,2	MCF-7	breast:

Variant related genes	Relation type
PRR23C	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:78 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs538820616	chr3:138769000-138769001	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs558428563	chr3:138769052-138769053	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs572845007	chr3:138769089-138769090	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs572375232	chr3:138769136-138769137	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs191756242	chr3:138769147-138769148	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs560883404	chr3:138769160-138769161	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs6763958	chr3:138769164-138769165	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs147450063	chr3:138769294-138769295	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs35145677	chr3:138769305-138769306	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs577174482	chr3:138769311-138769312	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs6788382	chr3:138769329-138769330	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs545585402	chr3:138769338-138769339	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs139201850	chr3:138769367-138769368	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs72491764	chr3:138771444-138771445	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs530611796	chr3:138771450-138771451	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs550890923	chr3:138771467-138771468	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs140609860	chr3:138771472-138771473	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs539305033	chr3:138771506-138771507	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs546211611	chr3:138771592-138771593	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs566098663	chr3:138771599-138771600	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs189982180	chr3:138771602-138771603	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs555241930	chr3:138771617-138771618	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs555149678	chr3:138771625-138771626	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs183183127	chr3:138771639-138771640	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs186528279	chr3:138771720-138771721	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs191801596	chr3:138771739-138771740	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs557482819	chr3:138771761-138771762	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs577633832	chr3:138771786-138771787	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs543933253	chr3:138771866-138771867	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs593539	chr3:138771897-138771898	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs113402564	chr3:138771913-138771914	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs553436357	chr3:138771955-138771956	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs564213198	chr3:138771973-138771974	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs372860126	chr3:138772130-138772131	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs542386930	chr3:138772173-138772174	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs562030289	chr3:138772182-138772183	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs139164483	chr3:138773437-138773438	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs540026270	chr3:138773438-138773439	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs553561195	chr3:138773448-138773449	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs567177611	chr3:138773453-138773454	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs375753840	chr3:138773473-138773474	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs536122095	chr3:138773478-138773479	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs555494836	chr3:138773502-138773503	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs201787509	chr3:138773518-138773519	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs575581218	chr3:138773520-138773521	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs537983790	chr3:138773612-138773613	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs143061250	chr3:138773618-138773619	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs577455653	chr3:138773640-138773641	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs885257	chr3:138773669-138773670	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs559886417	chr3:138773688-138773689	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Developmental delay	21147756	CNVD
lymphocytic leukemia	21291569	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138769000-138769400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:138771400-138772200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr3:138773400-138773800	ZNF genes & repeats	Pancreas	Pancrea
4	chr3:138781800-138782200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr3:138782200-138782600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:138788000-138788200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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