Variant report

Variant	nsv876799
Chromosome Location	chr3:53024216-53060637
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53055176..53056730-chr3:53078490..53080404,2	MCF-7	breast:
2	chr3:53047316..53051698-chr3:53056732..53062167,5	MCF-7	breast:
3	chr3:53056801..53057547-chr3:53179048..53179588,2	MCF-7	breast:
4	chr3:53045411..53048406-chr3:53050370..53052257,2	K562	blood:
5	chr3:53037209..53039730-chr3:53079605..53081876,2	MCF-7	breast:
6	chr3:53047316..53051698-chr3:53056732..53062167,5	MCF-7	breast:
7	chr3:53060296..53062382-chr3:53075868..53077771,2	MCF-7	breast:
8	chr3:53025419..53026271-chr3:53080327..53081039,2	MCF-7	breast:
9	chr3:53058305..53060040-chr3:53077970..53080050,2	K562	blood:
10	chr3:53029648..53031787-chr3:53078604..53081365,2	MCF-7	breast:
11	chr3:53059584..53062030-chr3:53075790..53077753,2	K562	blood:
12	chr3:53054569..53056705-chr3:53106775..53108496,2	MCF-7	breast:
13	chr3:53056126..53058134-chr3:53061359..53063994,2	K562	blood:
14	chr3:53045411..53048406-chr3:53050370..53052257,2	K562	blood:
15	chr3:53053108..53056030-chr3:53104834..53107226,3	K562	blood:
16	chr3:53058305..53064318-chr3:53075790..53081540,9	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFT1-5	chr3:53052102-53052244	NONHSAT089975

No data

Variant related genes	Relation type
ENSG00000163935	chromatin interactions

Extended variants
information (count: 1359 )
Associated
traits (count: 94 )

Variant overlapped rSNPs/rCNVs (count:1359 , 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	rs17052697	chr3:53024216-53024217	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs533742287	chr3:53024247-53024248	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs553921670	chr3:53024305-53024306	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs567235817	chr3:53024344-53024345	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs547545991	chr3:53024437-53024438	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs538664157	chr3:53024472-53024473	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs556749142	chr3:53024534-53024535	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs556084235	chr3:53024562-53024563	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs371835431	chr3:53024572-53024573	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs2564934	chr3:53024580-53024581	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs544914462	chr3:53024587-53024588	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs113371102	chr3:53024623-53024624	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs558386207	chr3:53024684-53024685	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs187865524	chr3:53024688-53024689	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs143424099	chr3:53024709-53024710	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs190974846	chr3:53024731-53024732	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs150104248	chr3:53024801-53024802	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs530113501	chr3:53024815-53024816	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs544039742	chr3:53024816-53024817	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs567268856	chr3:53024849-53024850	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs532711045	chr3:53024868-53024869	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs552907514	chr3:53024886-53024887	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs182081801	chr3:53024943-53024944	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs367845282	chr3:53024948-53024949	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs186679763	chr3:53025046-53025047	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs200651223	chr3:53025065-53025066	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs567403417	chr3:53025067-53025068	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs535957723	chr3:53025121-53025122	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs556185773	chr3:53025148-53025149	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs13064820	chr3:53025159-53025160	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs569520822	chr3:53025216-53025217	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs538414840	chr3:53025235-53025236	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs558441276	chr3:53025267-53025268	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs571992155	chr3:53025322-53025323	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs112218739	chr3:53025358-53025359	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs71087045	chr3:53025377-53025378	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs367824522	chr3:53025378-53025379	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs370202851	chr3:53025380-53025381	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs7617569	chr3:53025382-53025383	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs541052986	chr3:53025496-53025497	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs6779505	chr3:53025510-53025511	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs183208707	chr3:53025511-53025512	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs2564935	chr3:53025517-53025518	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs58133068	chr3:53025533-53025534	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs397938186	chr3:53025534-53025535	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs188629371	chr3:53025549-53025550	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs577528764	chr3:53025580-53025581	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs2564936	chr3:53025585-53025586	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs554792618	chr3:53025643-53025644	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs192975720	chr3:53025644-53025645	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:94)

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
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
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
Lung cancer	16618734	CNVD
Neuroblastoma	19686582	CNVD
Renal cell carcinoma	18765545	CNVD
Adrenocortical carcinoma	18281524	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:479 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
2	chr3:53008400-53031000	Weak transcription	Hela-S3	cervix
3	chr3:53012600-53032600	Weak transcription	Pancreas	Pancrea
4	chr3:53016200-53029400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:53018000-53030400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:53018000-53044200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:53018200-53045200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:53018600-53032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:53019000-53057200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:53019200-53032800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:53019200-53039600	Weak transcription	GM12878-XiMat	blood
12	chr3:53019600-53056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:53019800-53024400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:53019800-53044400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:53020400-53024400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:53020600-53057000	Weak transcription	Dnd41	blood
17	chr3:53022600-53030600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:53022600-53043000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:53022600-53050400	Weak transcription	Primary B cells from cord blood	blood
20	chr3:53023000-53025400	Weak transcription	Lung	lung
21	chr3:53023400-53024400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:53023400-53026200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr3:53023800-53025200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:53024000-53025000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:53024200-53024800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:53024200-53025200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:53024200-53025400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:53024200-53025400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:53024400-53025200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:53024400-53025200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:53024400-53025200	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr3:53024400-53026800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:53024800-53025200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:53025200-53025400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:53025200-53025600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:53025200-53032600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:53025200-53039000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:53025400-53025600	Enhancers	Lung	lung
39	chr3:53025400-53025800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:53025400-53026000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:53025400-53026800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:53025600-53026200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:53025600-53061600	Weak transcription	Lung	lung
44	chr3:53026000-53026200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:53026000-53026200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:53026200-53032600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:53026200-53037800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:53026200-53042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:53026200-53044200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:53026800-53027200	Enhancers	Primary T helper cells fromperipheralblood	blood

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