Variant report

Variant	nsv1002060
Chromosome Location	chr3:88984502-89047104
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	CCNT2	chr3:88986169-88986369	K562	blood:	n/a	n/a
2	CEBPB	chr3:88991580-88991896	IMR90	lung:	n/a	chr3:88991714-88991725
3	CEBPB	chr3:88991573-88991889	A549	lung:	n/a	chr3:88991714-88991725
4	CEBPB	chr3:89037926-89038148	HepG2	liver:	n/a	chr3:89038034-89038045
5	CEBPB	chr3:89034553-89034901	IMR90	lung:	n/a	chr3:89034706-89034717
6	CEBPB	chr3:89001206-89001427	H1-hESC	embryonic stem cell:	n/a	n/a
7	CEBPB	chr3:89001120-89001467	IMR90	lung:	n/a	n/a
8	CEBPB	chr3:88991571-88991883	HepG2	liver:	n/a	chr3:88991714-88991725
9	CEBPB	chr3:88985956-88986262	HepG2	liver:	n/a	chr3:88986086-88986097
10	CEBPB	chr3:89034609-89034859	A549	lung:	n/a	chr3:89034706-89034717
11	CEBPB	chr3:89034569-89034769	H1-hESC	embryonic stem cell:	n/a	chr3:89034706-89034717
12	CTCF	chr3:89028012-89028091	MCF-7	breast:	n/a	n/a
13	CTCF	chr3:89041820-89041970	HMEC	breast:	n/a	n/a
14	CTCF	chr3:89041740-89041890	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr3:89041640-89041790	HMEC	breast:	n/a	n/a
16	CTCF	chr3:89041740-89041890	NHEK	skin:	n/a	n/a
17	CTCF	chr3:88998987-88999026	GM20000	blood:	n/a	n/a
18	CTCF	chr3:89028036-89028073	MCF-7	breast:	n/a	n/a
19	CTCF	chr3:89030940-89031090	HFF-Myc	foreskin:	n/a	n/a
20	E2F4	chr3:88987662-88987678	MCF10A-Er-Src	breast:	n/a	n/a
21	E2F4	chr3:89028697-89028891	MCF10A-Er-Src	breast:	n/a	chr3:89028757-89028766
22	E2F4	chr3:89014004-89014175	MCF10A-Er-Src	breast:	n/a	n/a
23	FAM48A	chr3:88990888-88990940	GM12878	blood:	n/a	n/a
24	FOS	chr3:89027324-89027459	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr3:89040700-89040971	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr3:89038124-89038321	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr3:89035984-89036427	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr3:89035997-89036369	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr3:89027530-89027620	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr3:89034314-89034323	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr3:89006867-89007345	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr3:89038121-89038397	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr3:89006960-89007218	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr3:89006883-89007295	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr3:89035963-89036422	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr3:89035999-89036416	MCF10A-Er-Src	breast:	n/a	n/a
37	FOS	chr3:89027266-89027557	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr3:89038119-89038411	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr3:89040709-89041030	MCF10A-Er-Src	breast:	n/a	n/a
40	FOS	chr3:89040776-89040976	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr3:89006920-89007298	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr3:89038135-89038404	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr3:89040710-89041040	MCF10A-Er-Src	breast:	n/a	n/a
44	FOSL2	chr3:89006921-89007269	SK-N-SH	brain:	n/a	n/a
45	FOSL2	chr3:89006809-89007414	SK-N-SH	brain:	n/a	n/a
46	FOXA2	chr3:89036529-89036892	A549	lung:	n/a	n/a
47	FOXP2	chr3:89004539-89004727	PFSK-1	brain:	n/a	n/a
48	GATA3	chr3:89006793-89007421	SK-N-SH	brain:	n/a	n/a
49	GATA3	chr3:89006709-89007422	SK-N-SH	brain:	n/a	n/a
50	IRF1	chr3:89024733-89024794	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:89005246..89007637-chr7:93973935..93976038,2	MCF-7	breast:

Variant related genes	Relation type
NARG2P2	TF binding region

Extended variants
information (count: 1373 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:1373 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540358056	chr3:88985432-88985433	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs376386587	chr3:88985438-88985439	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs564178911	chr3:88985446-88985447	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs369427059	chr3:88985457-88985458	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs372910484	chr3:88985526-88985527	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs185791225	chr3:88985556-88985557	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs562790157	chr3:88985563-88985564	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs191093355	chr3:88985605-88985606	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs78972760	chr3:88985619-88985620	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs73845858	chr3:88985630-88985631	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs534170907	chr3:88985675-88985676	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs75199659	chr3:88985702-88985703	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs34157397	chr3:88985759-88985760	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs370419151	chr3:88985885-88985886	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs576800374	chr3:88988020-88988021	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs544174231	chr3:88988025-88988026	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs562377821	chr3:88988036-88988037	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs573916433	chr3:88988040-88988041	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs541435833	chr3:88988045-88988046	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs143413020	chr3:88988046-88988047	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs146748950	chr3:88988051-88988052	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs183374679	chr3:88988163-88988164	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs563186950	chr3:88988199-88988200	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs534078433	chr3:88991203-88991204	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs374169356	chr3:88991214-88991215	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs189877054	chr3:88991258-88991259	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs62271095	chr3:88991259-88991260	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs538051253	chr3:88991269-88991270	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs556471403	chr3:88991271-88991272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs78921242	chr3:88991272-88991273	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs557498416	chr3:88991356-88991357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs544163878	chr3:88991365-88991366	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs181809390	chr3:88991425-88991426	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs141874300	chr3:88991438-88991439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs187502762	chr3:88991453-88991454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs577815241	chr3:88991530-88991531	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs545446638	chr3:88991539-88991540	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs563848126	chr3:88991561-88991562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs532535328	chr3:88991592-88991593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs13088456	chr3:88991757-88991758	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs563179936	chr3:88991786-88991787	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs13088492	chr3:88991797-88991798	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs191491399	chr3:88991919-88991920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs572496487	chr3:88991920-88991921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs566704086	chr3:88991952-88991953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs72911953	chr3:88992027-88992028	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs552666387	chr3:88992048-88992049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs150636673	chr3:88992091-88992092	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs368143010	chr3:88992109-88992110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs556434527	chr3:88992114-88992115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:70)

Disease	PMID	Source
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	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
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Wilms tumour	21544195	CNVD
Soft tissue tumor	16732325	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	21829676	CNVD
Lung cancer	19547694	CNVD
Cancer	20164919	CNVD
Acute myeloid leukemia	19651600	CNVD

Chromatin state (count:202 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88985400-88986000	Enhancers	Fetal Brain Female	brain
2	chr3:88988000-88988200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:88991200-88992400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:88993200-88994400	Enhancers	Fetal Heart	heart
5	chr3:88993800-88994000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:88993800-88994400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:88994000-88995400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:88995400-88995800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:88995400-88997200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:88995400-88997200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:88995800-88996000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:88995800-88996400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:88995800-88996600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:88995800-88997000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:88996000-88996400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:88996000-88996400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:88996000-88996600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr3:89004000-89004400	Enhancers	Osteobl	bone
19	chr3:89004000-89004600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:89004400-89005600	Weak transcription	Osteobl	bone
21	chr3:89004600-89004800	ZNF genes & repeats	HSMM	muscle
22	chr3:89004600-89005400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:89004600-89005400	Enhancers	Fetal Brain Male	brain
24	chr3:89004600-89005800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:89004800-89006200	Weak transcription	HSMM	muscle
26	chr3:89005400-89006200	Weak transcription	Fetal Brain Male	brain
27	chr3:89005400-89006600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:89005600-89006600	Enhancers	Osteobl	bone
29	chr3:89005600-89008600	Enhancers	NH-A	brain
30	chr3:89005800-89006400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:89005800-89006600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:89006000-89007800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:89006000-89007800	Enhancers	HMEC	breast
34	chr3:89006000-89008600	Enhancers	NHDF-Ad	bronchial
35	chr3:89006200-89006400	Enhancers	Fetal Brain Female	brain
36	chr3:89006200-89006600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:89006200-89006800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:89006200-89007600	Enhancers	Fetal Brain Male	brain
39	chr3:89006200-89007800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:89006200-89007800	Enhancers	Fetal Heart	heart
41	chr3:89006200-89007800	Enhancers	NHEK	skin
42	chr3:89006200-89008400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:89006200-89009200	Enhancers	HSMM	muscle
44	chr3:89006400-89007000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:89006400-89007200	Weak transcription	Fetal Brain Female	brain
46	chr3:89006400-89007600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:89006400-89007800	Enhancers	HSMMtube	muscle
48	chr3:89006400-89008200	Enhancers	NHLF	lung
49	chr3:89006600-89007000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:89006600-89007000	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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