Variant report

Variant	nsv965391
Chromosome Location	chr3:109419757-109431296
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	ATF2	chr3:109421148-109421485	GM12878	blood:	n/a	n/a
2	BCL11A	chr3:109430390-109430615	GM12878	blood:	n/a	n/a
3	CEBPB	chr3:109421119-109421540	Hela-S3	cervix:	n/a	chr3:109421333-109421346
4	CEBPB	chr3:109421089-109421474	ECC-1	luminal epithelium:	n/a	chr3:109421333-109421346
5	CEBPB	chr3:109421134-109421500	IMR90	lung:	n/a	chr3:109421333-109421346
6	EP300	chr3:109426525-109426847	SK-N-SH_RA	brain:	n/a	n/a
7	EP300	chr3:109421228-109421504	Hela-S3	cervix:	n/a	chr3:109421334-109421348 chr3:109421335-109421343
8	EP300	chr3:109420945-109421612	SK-N-SH	brain:	n/a	chr3:109421334-109421348 chr3:109421335-109421343
9	EP300	chr3:109426596-109426916	SK-N-SH_RA	brain:	n/a	n/a
10	EP300	chr3:109421077-109421332	SK-N-SH_RA	brain:	n/a	n/a
11	EP300	chr3:109421200-109421437	GM12878	blood:	n/a	chr3:109421334-109421348 chr3:109421335-109421343
12	EP300	chr3:109426351-109427038	SK-N-SH	brain:	n/a	n/a
13	EP300	chr3:109421099-109421398	SK-N-SH_RA	brain:	n/a	chr3:109421334-109421348 chr3:109421335-109421343
14	EP300	chr3:109421096-109421584	SK-N-SH	brain:	n/a	chr3:109421334-109421348 chr3:109421335-109421343
15	FOS	chr3:109421172-109421396	MCF10A-Er-Src	breast:	n/a	n/a
16	FOSL2	chr3:109420978-109421628	SK-N-SH	brain:	n/a	chr3:109421139-109421153
17	GABPA	chr3:109430474-109430578	Hela-S3	cervix:	n/a	n/a
18	GATA2	chr3:109426505-109426836	SH-SY5Y	brain:	n/a	chr3:109426515-109426531 chr3:109426519-109426528 chr3:109426695-109426708 chr3:109426512-109426533 chr3:109426519-109426526 chr3:109426518-109426528 chr3:109426516-109426526 chr3:109426697-109426705 chr3:109426519-109426526 chr3:109426519-109426526
19	GATA3	chr3:109420747-109421803	SK-N-SH	brain:	n/a	chr3:109421120-109421136
20	GATA3	chr3:109420888-109421829	SK-N-SH	brain:	n/a	chr3:109421120-109421136
21	GATA3	chr3:109426399-109427199	SK-N-SH	brain:	n/a	chr3:109426515-109426531 chr3:109426519-109426528 chr3:109426695-109426708 chr3:109426512-109426533 chr3:109426519-109426526 chr3:109426518-109426528 chr3:109426516-109426526 chr3:109426697-109426705 chr3:109426519-109426526 chr3:109426519-109426526
22	GATA3	chr3:109426438-109426849	SH-SY5Y	brain:	n/a	chr3:109426515-109426531 chr3:109426519-109426528 chr3:109426695-109426708 chr3:109426512-109426533 chr3:109426519-109426526 chr3:109426518-109426528 chr3:109426516-109426526 chr3:109426697-109426705 chr3:109426519-109426526 chr3:109426519-109426526
23	GATA3	chr3:109426476-109427016	MCF-7	breast:	n/a	chr3:109426515-109426531 chr3:109426519-109426528 chr3:109426695-109426708 chr3:109426512-109426533 chr3:109426519-109426526 chr3:109426518-109426528 chr3:109426516-109426526 chr3:109426697-109426705 chr3:109426519-109426526 chr3:109426519-109426526
24	GATA3	chr3:109424440-109424616	SH-SY5Y	brain:	n/a	n/a
25	GATA3	chr3:109426276-109427154	SK-N-SH	brain:	n/a	chr3:109426515-109426531 chr3:109426519-109426528 chr3:109426695-109426708 chr3:109426512-109426533 chr3:109426519-109426526 chr3:109426518-109426528 chr3:109426516-109426526 chr3:109426697-109426705 chr3:109426519-109426526 chr3:109426519-109426526
26	GATA3	chr3:109426324-109426853	A549	lung:	n/a	chr3:109426515-109426531 chr3:109426519-109426528 chr3:109426695-109426708 chr3:109426512-109426533 chr3:109426519-109426526 chr3:109426518-109426528 chr3:109426516-109426526 chr3:109426697-109426705 chr3:109426519-109426526 chr3:109426519-109426526
27	JUND	chr3:109426457-109427032	SK-N-SH	brain:	n/a	n/a
28	JUND	chr3:109426405-109426962	SK-N-SH	brain:	n/a	n/a
29	MAX	chr3:109421065-109421501	SK-N-SH	brain:	n/a	chr3:109421336-109421345
30	MAX	chr3:109421114-109421394	Hela-S3	cervix:	n/a	chr3:109421336-109421345
31	MYC	chr3:109421302-109421341	NB4	blood:	n/a	n/a
32	MYC	chr3:109424992-109424999	MCF-7	breast:	n/a	n/a
33	NFIC	chr3:109426477-109426856	SK-N-SH	brain:	n/a	n/a
34	NFIC	chr3:109426378-109426954	ECC-1	luminal epithelium:	n/a	n/a
35	NFIC	chr3:109426428-109426960	ECC-1	luminal epithelium:	n/a	n/a
36	NFIC	chr3:109426380-109427116	SK-N-SH	brain:	n/a	n/a
37	NFIC	chr3:109420963-109421762	SK-N-SH	brain:	n/a	n/a
38	NFIC	chr3:109421083-109421455	GM12878	blood:	n/a	n/a
39	NR2F2	chr3:109426413-109426944	MCF-7	breast:	n/a	n/a
40	NR3C1	chr3:109421128-109421397	ECC-1	luminal epithelium:	n/a	n/a
41	PBX3	chr3:109426447-109427032	SK-N-SH	brain:	n/a	n/a
42	PBX3	chr3:109420992-109421664	SK-N-SH	brain:	n/a	n/a
43	PBX3	chr3:109421076-109421619	SK-N-SH	brain:	n/a	n/a
44	PBX3	chr3:109426458-109427002	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr3:109429261-109429282	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:109429169-109429223	A549	lung:	n/a	n/a
47	POLR2A	chr3:109421080-109421462	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr3:109421676-109421685	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:109429236-109429239	Gliobla	brain:	n/a	n/a
50	POLR2A	chr3:109427090-109427195	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:109414982..109417591-chr3:109417920..109420582,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DPPA4-2	chr3:109420303-109421065	NONHSAT091126

Variant related genes	Relation type
ENSG00000271249	TF binding region

Extended variants
information (count: 334 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:334 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs562752957	chr3:109419839-109419840	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs531514225	chr3:109419861-109419862	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs186023009	chr3:109419874-109419875	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs546666584	chr3:109419914-109419915	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs564492856	chr3:109419922-109419923	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs568054484	chr3:109419928-109419929	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs386664508	chr3:109419929-109419930	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs376093802	chr3:109419937-109419938	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs533400877	chr3:109419968-109419969	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs547109552	chr3:109419969-109419970	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs566901350	chr3:109420006-109420007	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs138933633	chr3:109420017-109420018	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs191135175	chr3:109420064-109420065	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs116152113	chr3:109420069-109420070	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs569500571	chr3:109420102-109420103	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs538179106	chr3:109420112-109420113	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs551687638	chr3:109420213-109420214	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs61353692	chr3:109420220-109420221	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs1164063	chr3:109420249-109420250	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs199781293	chr3:109420252-109420253	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs183350767	chr3:109420310-109420311	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs188022004	chr3:109420326-109420327	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs553448019	chr3:109420351-109420352	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs573654731	chr3:109420353-109420354	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs192354921	chr3:109420360-109420361	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs182614158	chr3:109420372-109420373	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs58988227	chr3:109420398-109420399	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs76184573	chr3:109420456-109420457	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs541649323	chr3:109420466-109420467	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs565220292	chr3:109420497-109420498	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs202045781	chr3:109420512-109420513	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs75025322	chr3:109420513-109420514	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs561952808	chr3:109420646-109420647	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs71323112	chr3:109420648-109420649	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs368707443	chr3:109420651-109420652	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs530113286	chr3:109420660-109420661	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs570254678	chr3:109420672-109420673	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs370925723	chr3:109420753-109420754	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs529385504	chr3:109420760-109420761	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs370642965	chr3:109420763-109420764	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs549527816	chr3:109420771-109420772	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs562919753	chr3:109420785-109420786	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs531819648	chr3:109420796-109420797	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs144142048	chr3:109420814-109420815	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs571652846	chr3:109420825-109420826	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs74839448	chr3:109420829-109420830	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs533496039	chr3:109420831-109420832	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs543905407	chr3:109420835-109420836	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs146499069	chr3:109420845-109420846	Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs535986094	chr3:109421006-109421007	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

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
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	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
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18765545	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21858162	CNVD
Multiple myeloma	17550852	CNVD
Ductal carcinoma	22052326	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic cancer	17952125	CNVD
T-cell lymphomas	22341440	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109418600-109423600	Enhancers	Dnd41	blood
2	chr3:109420400-109420600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:109420600-109421000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:109420800-109422000	Enhancers	HSMM	muscle
5	chr3:109421000-109422200	Enhancers	NH-A	brain
6	chr3:109421000-109422400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:109421200-109421800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:109421400-109421800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:109421400-109421800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:109421400-109421800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:109421400-109421800	Enhancers	HMEC	breast
12	chr3:109421400-109421800	Enhancers	HSMMtube	muscle
13	chr3:109423600-109426400	Weak transcription	Dnd41	blood
14	chr3:109426400-109427000	Enhancers	Dnd41	blood
15	chr3:109426600-109426800	Enhancers	Pancreas	Pancrea
16	chr3:109426600-109427000	Enhancers	Hela-S3	cervix
17	chr3:109426800-109429000	Weak transcription	Pancreas	Pancrea
18	chr3:109429000-109429400	ZNF genes & repeats	Pancreas	Pancrea
19	chr3:109429200-109429400	Enhancers	Gastric	stomach

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