Variant report

Variant	nsv590320
Chromosome Location	chr3:53027983-53055842
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:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53037209..53039730-chr3:53079605..53081876,2	MCF-7	breast:
2	chr3:53053108..53056030-chr3:53104834..53107226,3	K562	blood:
3	chr3:53055176..53056730-chr3:53078490..53080404,2	MCF-7	breast:
4	chr3:53045411..53048406-chr3:53050370..53052257,2	K562	blood:
5	chr3:53054569..53056705-chr3:53106775..53108496,2	MCF-7	breast:
6	chr3:53029648..53031787-chr3:53078604..53081365,2	MCF-7	breast:
7	chr3:53045411..53048406-chr3:53050370..53052257,2	K562	blood:
8	chr3:53047316..53051698-chr3:53056732..53062167,5	MCF-7	breast:

(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: 1058 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:1058 , 50 per page) page: 1 2 3 4 5 6 7 ... 22

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2246556	chr3:53027983-53027984	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs114914174	chr3:53028002-53028003	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs546997830	chr3:53028020-53028021	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs190150043	chr3:53028038-53028039	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs181563764	chr3:53028054-53028055	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs2336720	chr3:53028061-53028062	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs569438912	chr3:53028066-53028067	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs13326633	chr3:53028090-53028091	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs545910094	chr3:53028124-53028125	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs60579787	chr3:53028161-53028162	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs577901944	chr3:53028191-53028192	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs539092750	chr3:53028208-53028209	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs185927570	chr3:53028231-53028232	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs536308277	chr3:53028236-53028237	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs545033689	chr3:53028318-53028319	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs2336721	chr3:53028375-53028376	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs190723604	chr3:53028390-53028391	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs561598230	chr3:53028403-53028404	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs556879378	chr3:53028453-53028454	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs75126190	chr3:53028464-53028465	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs75972307	chr3:53028465-53028466	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs143040203	chr3:53028546-53028547	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs183238103	chr3:53028551-53028552	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs548328375	chr3:53028602-53028603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs562111027	chr3:53028606-53028607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs533264849	chr3:53028673-53028674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs561080949	chr3:53028674-53028675	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs185057987	chr3:53028675-53028676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs190937348	chr3:53028681-53028682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs78249790	chr3:53028726-53028727	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs529226967	chr3:53028735-53028736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs200634264	chr3:53028743-53028744	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs183219415	chr3:53028751-53028752	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs374647267	chr3:53028798-53028799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs528645306	chr3:53028807-53028808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs188100843	chr3:53028812-53028813	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs551556144	chr3:53028925-53028926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs72961763	chr3:53028931-53028932	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs56384586	chr3:53029006-53029007	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs554122281	chr3:53029011-53029012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs568793175	chr3:53029020-53029021	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs536013982	chr3:53029023-53029024	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs78223031	chr3:53029048-53029049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs535070536	chr3:53029049-53029050	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs539614294	chr3:53029139-53029140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs192961120	chr3:53029275-53029276	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs77489783	chr3:53029290-53029291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs544468842	chr3:53029382-53029383	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs373690591	chr3:53029386-53029387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs565394565	chr3:53029431-53029432	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

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
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:348 , 50 per page) page: 1 2 3 4 5 6 7

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	chr3:53019800-53044400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:53020600-53057000	Weak transcription	Dnd41	blood
15	chr3:53022600-53030600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:53022600-53043000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:53022600-53050400	Weak transcription	Primary B cells from cord blood	blood
18	chr3:53025200-53032600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:53025200-53039000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:53025600-53061600	Weak transcription	Lung	lung
21	chr3:53026200-53032600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:53026200-53037800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:53026200-53042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:53026200-53044200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:53026800-53028600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:53027200-53043400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:53027600-53061600	Weak transcription	Liver	Liver
28	chr3:53027800-53051000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:53028000-53032800	Weak transcription	Esophagus	oesophagus
30	chr3:53028400-53044200	Weak transcription	Adipose Nuclei	Adipose
31	chr3:53028600-53032600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:53028800-53032400	Weak transcription	Fetal Stomach	stomach
33	chr3:53029400-53029600	Enhancers	A549	lung
34	chr3:53029400-53030600	Strong transcription	Fetal Intestine Small	intestine
35	chr3:53029600-53033200	Weak transcription	A549	lung
36	chr3:53029800-53032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:53030000-53033200	Weak transcription	Brain Angular Gyrus	brain
38	chr3:53030200-53034200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:53030200-53059400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:53030400-53030800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:53030400-53052400	Weak transcription	Primary T cells from cord blood	blood
42	chr3:53030600-53031400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:53030600-53031400	Weak transcription	Fetal Intestine Small	intestine
44	chr3:53030800-53050400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:53031000-53031400	Enhancers	Brain Cingulate Gyrus	brain
46	chr3:53031000-53031400	Enhancers	Hela-S3	cervix
47	chr3:53031000-53033200	Weak transcription	Gastric	stomach
48	chr3:53031000-53039800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:53031400-53031600	Flanking Active TSS	Hela-S3	cervix
50	chr3:53031400-53032800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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