Variant report

Variant	nsv518052
Chromosome Location	chr3:119893257-119896657
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119809943..119817218-chr3:119893934..119905581,30	MCF-7	breast:
2	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:
3	chr3:119877444..119878944-chr3:119896183..119899107,2	MCF-7	breast:
4	chr3:119896267..119897823-chr3:119902121..119903746,2	MCF-7	breast:
5	chr3:119810057..119817149-chr3:119894256..119903865,22	MCF-7	breast:
6	chr3:119888337..119890858-chr3:119891647..119894832,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	chromatin interactions
ENSG00000242622	chromatin interactions

Extended variants
information (count: 109 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:109 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1488762	chr3:119893257-119893258	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs540966153	chr3:119893266-119893267	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs559062394	chr3:119893315-119893316	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs528106416	chr3:119893332-119893333	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs139093471	chr3:119893375-119893376	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs79507761	chr3:119893412-119893413	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs530522333	chr3:119893421-119893422	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs78210167	chr3:119893447-119893448	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs567501397	chr3:119893473-119893474	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs557471607	chr3:119893476-119893477	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs73177937	chr3:119893485-119893486	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs1488761	chr3:119893503-119893504	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs539008909	chr3:119893549-119893550	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs187409544	chr3:119893553-119893554	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs575770489	chr3:119893595-119893596	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs190542846	chr3:119893596-119893597	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs181010450	chr3:119893685-119893686	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs1074053	chr3:119893745-119893746	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs145944025	chr3:119893759-119893760	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs1079784	chr3:119893803-119893804	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs577139427	chr3:119893824-119893825	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs544557081	chr3:119893832-119893833	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs564547253	chr3:119893833-119893834	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs2319540	chr3:119893904-119893905	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs139797760	chr3:119893911-119893912	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs143140151	chr3:119893926-119893927	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs529864473	chr3:119893946-119893947	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs372925303	chr3:119893983-119893984	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs369431622	chr3:119893984-119893985	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs370803738	chr3:119893986-119893987	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs370247473	chr3:119893987-119893988	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs373940198	chr3:119893988-119893989	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs375981180	chr3:119893993-119893994	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs370624975	chr3:119893994-119893995	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs572629549	chr3:119894169-119894170	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs546501817	chr3:119894176-119894177	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs566728308	chr3:119894179-119894180	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs538945580	chr3:119894182-119894183	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs371667200	chr3:119894443-119894444	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs552597888	chr3:119894496-119894497	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs9825897	chr3:119894498-119894499	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs68045003	chr3:119894501-119894502	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs112312515	chr3:119894502-119894503	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs116718806	chr3:119894617-119894618	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs574849373	chr3:119894838-119894839	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs534374612	chr3:119894847-119894848	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs554075194	chr3:119894890-119894891	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs189731195	chr3:119894941-119894942	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs546127254	chr3:119894942-119894943	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs114480283	chr3:119895050-119895051	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

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	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
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
Hodgkin''s lymphoma	17606441	CNVD
Developmental delay	22180640	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
lymphocytic leukemia	21291569	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Glioblastoma multiforme	22286061	CNVD
Neurodevelopmental disorder	22521361	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD

Chromatin state (count:176 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119883200-119895800	Weak transcription	Fetal Intestine Small	intestine
3	chr3:119884800-119895600	Weak transcription	Brain Germinal Matrix	brain
4	chr3:119885000-119895800	Weak transcription	Fetal Lung	lung
5	chr3:119887200-119895800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:119888400-119895800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:119888400-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:119888400-119896200	Enhancers	NHDF-Ad	bronchial
9	chr3:119888600-119896000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:119889400-119893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:119890000-119895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:119890400-119893600	Weak transcription	Placenta	Placenta
13	chr3:119890400-119895400	Weak transcription	Psoas Muscle	Psoas
14	chr3:119890400-119895800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:119890400-119895800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:119890600-119893600	Weak transcription	Hela-S3	cervix
17	chr3:119890600-119895600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:119890600-119895800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:119890800-119895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:119890800-119896000	Weak transcription	Right Atrium	heart
21	chr3:119891000-119895800	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:119891200-119895600	Weak transcription	Adipose Nuclei	Adipose
23	chr3:119891200-119895600	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:119891400-119895200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:119891400-119895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:119891400-119895600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:119891400-119895600	Weak transcription	NHLF	lung
28	chr3:119891400-119896200	Weak transcription	Lung	lung
29	chr3:119892000-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:119892200-119893400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:119892200-119893600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:119892200-119895600	Weak transcription	NHEK	skin
33	chr3:119892200-119895800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:119892200-119896000	Weak transcription	Fetal Stomach	stomach
35	chr3:119892400-119914200	Weak transcription	Fetal Brain Female	brain
36	chr3:119892600-119893600	Weak transcription	Osteobl	bone
37	chr3:119892800-119895800	Weak transcription	HSMM	muscle
38	chr3:119892800-119895800	Weak transcription	HSMMtube	muscle
39	chr3:119892800-119896200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:119893000-119895000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:119893000-119895600	Enhancers	A549	lung
42	chr3:119893200-119895000	Enhancers	HMEC	breast
43	chr3:119893200-119896400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:119893400-119893600	Enhancers	Aorta	Aorta
45	chr3:119893400-119896200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:119893600-119894000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:119893600-119894200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:119893600-119895200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr3:119893600-119895600	Enhancers	Hela-S3	cervix
50	chr3:119893600-119896000	Enhancers	Osteobl	bone

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