Variant report

Variant	nsv880600
Chromosome Location	chr5:52342760-52362765
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52352312..52354080-chr5:52355424..52357750,2	K562	blood:
2	chr5:52340133..52343071-chr5:52343982..52345648,2	K562	blood:
3	chr5:52351776..52352321-chr9:91925750..91926479,2	MCF-7	breast:
4	chr5:52352312..52354080-chr5:52355424..52357750,2	K562	blood:
5	chr5:52340133..52343071-chr5:52343982..52345648,2	K562	blood:
6	chr5:52342580..52344559-chr5:52347867..52350544,2	K562	blood:
7	chr5:52342580..52344559-chr5:52347867..52350544,2	K562	blood:

Variant related genes	Relation type
ENSG00000123975	chromatin interactions

Extended variants
information (count: 792 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:792 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3212472	chr5:52342760-52342761	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs545521458	chr5:52342765-52342766	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs560530587	chr5:52342780-52342781	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs3212473	chr5:52342798-52342799	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs376323277	chr5:52342806-52342807	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs183039346	chr5:52342822-52342823	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs117617965	chr5:52342890-52342891	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs532063886	chr5:52342937-52342938	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs373049037	chr5:52342968-52342969	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs550049459	chr5:52342978-52342979	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs144431559	chr5:52343080-52343081	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs35599315	chr5:52343107-52343108	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs187668187	chr5:52343179-52343180	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs199651111	chr5:52343187-52343188	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs386687983	chr5:52343188-52343189	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs3212475	chr5:52343189-52343190	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs533631470	chr5:52343209-52343210	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs557392960	chr5:52343231-52343232	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs555572818	chr5:52343247-52343248	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs567339781	chr5:52343263-52343264	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs533592242	chr5:52343292-52343293	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs538189458	chr5:52343308-52343309	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs148409215	chr5:52343327-52343328	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs3212476	chr5:52343356-52343357	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs545384885	chr5:52343387-52343388	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs3212477	chr5:52343451-52343452	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs574878958	chr5:52343483-52343484	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs542738445	chr5:52343503-52343504	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs561566207	chr5:52343517-52343518	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs539996840	chr5:52343519-52343520	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs3212478	chr5:52343561-52343562	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs187763745	chr5:52343582-52343583	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs565207258	chr5:52343591-52343592	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs574022684	chr5:52343593-52343594	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs532788603	chr5:52343594-52343595	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs144025432	chr5:52343613-52343614	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs3212479	chr5:52343628-52343629	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs182399724	chr5:52343736-52343737	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs548802101	chr5:52343769-52343770	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs567458680	chr5:52343783-52343784	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs537998052	chr5:52343789-52343790	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs3212480	chr5:52343793-52343794	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs552724942	chr5:52343796-52343797	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs3212481	chr5:52343802-52343803	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs187028948	chr5:52343857-52343858	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs3212482	chr5:52343872-52343873	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs572337955	chr5:52343875-52343876	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs3212483	chr5:52343901-52343902	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs12519933	chr5:52343910-52343911	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs554716536	chr5:52343921-52343922	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Cancer	16751803	CNVD
Autism	22495311	CNVD
Intellectual disability	22102821	CNVD
Prostate cancer	21965145	CNVD
Cancer	21183584	CNVD
Ovarian cancer	20844748	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Esophageal cancer	20955586	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
adenomatous polyposis	22470819	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	20729466	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Hepatocellular carcinoma	16750200	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Bladder cancer	21909424	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	21911935	CNVD
Breast cancer	17133270	CNVD
Breast cancer	19602461	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:258 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
6	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
8	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
10	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:52334600-52343400	Weak transcription	Gastric	stomach
12	chr5:52334600-52348400	Weak transcription	Lung	lung
13	chr5:52334800-52343400	Weak transcription	Esophagus	oesophagus
14	chr5:52334800-52343800	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:52334800-52343800	Weak transcription	Pancreas	Pancrea
16	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
17	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
18	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:52337200-52353400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:52337400-52346400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:52337400-52348800	Weak transcription	A549	lung
23	chr5:52337400-52355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:52337800-52343200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:52338000-52348200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:52341200-52343000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:52341200-52343200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:52341200-52343200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:52341200-52343200	Weak transcription	NHLF	lung
32	chr5:52341200-52346400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:52341200-52396400	Strong transcription	HMEC	breast
34	chr5:52341400-52343000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:52341400-52343200	Weak transcription	HepG2	liver
36	chr5:52341400-52345800	Weak transcription	NH-A	brain
37	chr5:52341400-52346400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:52341400-52348600	Weak transcription	Dnd41	blood
39	chr5:52341400-52359000	Weak transcription	NHDF-Ad	bronchial
40	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:52341600-52343400	Weak transcription	HUVEC	blood vessel
42	chr5:52341800-52343200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:52341800-52347800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:52341800-52358800	Weak transcription	Osteobl	bone
45	chr5:52342000-52343400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:52342000-52367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:52342400-52363600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:52342600-52344600	Strong transcription	Hela-S3	cervix
49	chr5:52342600-52383800	Strong transcription	NHEK	skin
50	chr5:52343000-52343400	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links