Variant report

Variant	nsv963320
Chromosome Location	chr3:52290168-52291494
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52286679..52290007-chr3:52290235..52292692,3	K562	blood:
2	chr3:52277093..52279461-chr3:52290667..52292256,2	MCF-7	breast:
3	chr3:52290955..52293788-chr3:52297158..52298749,2	MCF-7	breast:
4	chr3:52286492..52290913-chr3:52310452..52313639,5	K562	blood:
5	chr3:52289327..52293774-chr3:52294215..52297996,5	MCF-7	breast:
6	chr3:52282177..52283761-chr3:52291463..52293959,2	K562	blood:

Variant related genes	Relation type
ENSG00000164088	chromatin interactions
ENSG00000164091	chromatin interactions

Extended variants
information (count: 51 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:51 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs538196832	chr3:52290222-52290223	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs183101940	chr3:52290252-52290253	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs73835766	chr3:52290285-52290286	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs61734625	chr3:52290329-52290330	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs369445421	chr3:52290384-52290385	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs376648176	chr3:52290385-52290386	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs376050318	chr3:52290398-52290399	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs61734626	chr3:52290400-52290401	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs578048346	chr3:52290453-52290454	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs369093746	chr3:52290459-52290460	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs572670884	chr3:52290460-52290461	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs541625162	chr3:52290465-52290466	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs149817295	chr3:52290466-52290467	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs1767	chr3:52290474-52290475	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs544211155	chr3:52290481-52290482	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs199585687	chr3:52290489-52290490	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs373313284	chr3:52290496-52290497	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs55803050	chr3:52290537-52290538	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs564491799	chr3:52290546-52290547	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs1769	chr3:52290550-52290551	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs201931854	chr3:52290551-52290552	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs200990295	chr3:52290570-52290571	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs61734627	chr3:52290585-52290586	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs374061140	chr3:52290589-52290590	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs3733067	chr3:52290594-52290595	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs367949796	chr3:52290606-52290607	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs370398785	chr3:52290621-52290622	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs529468160	chr3:52290726-52290727	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs376629633	chr3:52290746-52290747	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs549588821	chr3:52290794-52290795	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs569517974	chr3:52290852-52290853	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs538508523	chr3:52290861-52290862	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs369608227	chr3:52290882-52290883	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs549712547	chr3:52290887-52290888	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs551820010	chr3:52290890-52290891	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs532917834	chr3:52290956-52290957	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs561641883	chr3:52290970-52290971	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs529112539	chr3:52290974-52290975	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs547194048	chr3:52291043-52291044	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs570391498	chr3:52291055-52291056	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs57823393	chr3:52291078-52291079	Strong transcription Weak transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs539175493	chr3:52291134-52291135	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs552601295	chr3:52291188-52291189	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs145915837	chr3:52291194-52291195	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs377579934	chr3:52291206-52291207	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs146545345	chr3:52291224-52291225	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs55653966	chr3:52291283-52291284	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs562806674	chr3:52291312-52291313	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs34922530	chr3:52291374-52291375	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs555122744	chr3:52291379-52291380	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:86)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	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
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Bladder cancer	21909424	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD

Chromatin state (count:141 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52280400-52291200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:52280600-52290800	Weak transcription	Psoas Muscle	Psoas
3	chr3:52280600-52292400	Weak transcription	Fetal Heart	heart
4	chr3:52280800-52292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:52281000-52291800	Strong transcription	Fetal Intestine Small	intestine
6	chr3:52281800-52303400	Weak transcription	Right Atrium	heart
7	chr3:52282000-52298800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:52282000-52299400	Strong transcription	Liver	Liver
9	chr3:52282200-52293200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:52282200-52303000	Strong transcription	Fetal Lung	lung
11	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:52282400-52297200	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:52282400-52309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52282600-52304000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:52282600-52308200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:52282800-52303800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:52282800-52305000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:52283000-52306000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:52283200-52308400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:52283400-52304600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:52283400-52305400	Strong transcription	Brain Germinal Matrix	brain
22	chr3:52283600-52308800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr3:52283800-52309600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:52284400-52291800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:52284400-52304800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:52284600-52293000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:52284600-52305800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:52284800-52300200	Strong transcription	Pancreas	Pancrea
29	chr3:52285000-52302600	Strong transcription	A549	lung
30	chr3:52285200-52291000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:52285600-52292800	Strong transcription	NH-A	brain
32	chr3:52285600-52308400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:52285800-52307400	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr3:52286000-52298200	Strong transcription	Gastric	stomach
35	chr3:52286000-52302200	Strong transcription	Left Ventricle	heart
36	chr3:52286400-52306800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:52286600-52293400	Strong transcription	NHDF-Ad	bronchial
38	chr3:52286600-52303400	Strong transcription	NHLF	lung
39	chr3:52287000-52293400	Strong transcription	HSMMtube	muscle
40	chr3:52287200-52294000	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr3:52287200-52296800	Strong transcription	Right Ventricle	heart
42	chr3:52287400-52291000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:52287400-52295200	Strong transcription	Aorta	Aorta
44	chr3:52287400-52305400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:52287400-52305600	Strong transcription	HepG2	liver
46	chr3:52287600-52293600	Strong transcription	HMEC	breast
47	chr3:52287800-52294600	Strong transcription	Small Intestine	intestine
48	chr3:52287800-52302200	Strong transcription	Lung	lung
49	chr3:52288000-52290200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr3:52288000-52291400	Genic enhancers	Fetal Thymus	thymus

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