Variant report

Variant	nsv998982
Chromosome Location	chr3:61252469-61364001
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:10)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:61282960..61285286-chr3:61304509..61306852,2	K562	blood:
2	chr3:61125268..61126228-chr3:61279400..61279942,3	MCF-7	breast:
3	chr3:61235142..61237264-chr3:61256166..61257953,2	K562	blood:
4	chr3:61125383..61126228-chr3:61279414..61279942,2	MCF-7	breast:
5	chr3:61296773..61299037-chr3:61299815..61302002,2	MCF-7	breast:
6	chr3:61334249..61335754-chr3:61335765..61337512,2	MCF-7	breast:
7	chr3:61296773..61299037-chr3:61299815..61302002,2	MCF-7	breast:
8	chr3:61282960..61285286-chr3:61304509..61306852,2	K562	blood:
9	chr3:61235706..61237222-chr3:61273811..61275635,2	K562	blood:
10	chr3:61334249..61335754-chr3:61335765..61337512,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPRG-1	chr3:61297641-61297814	XLOC_002680
2	lnc-PTPRG-1	chr3:61284244-61284338	XLOC_002680
3	lnc-PTPRG-1	chr3:61298883-61299032	XLOC_002680
4	lnc-PTPRG-1	chr3:61298882-61299032	NONHSAT090166
5	lnc-PTPRG-1	chr3:61297640-61297814	NONHSAT090166
6	lnc-PTPRG-1	chr3:61284243-61284338	NONHSAT090166

No data

Variant related genes	Relation type
ENSG00000189283	chromatin interactions

Extended variants
information (count: 2309 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:2309 , 50 per page) page: 1 2 3 4 5 6 7 ... 47

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs815719	chr3:61252469-61252470	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs114345420	chr3:61252489-61252490	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs76625165	chr3:61252626-61252627	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs368550876	chr3:61252675-61252676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs80105475	chr3:61252691-61252692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs575719027	chr3:61252703-61252704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs116645070	chr3:61252711-61252712	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs574755133	chr3:61252735-61252736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs541893372	chr3:61252738-61252739	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs377231855	chr3:61252740-61252741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs369671972	chr3:61252743-61252744	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs543794472	chr3:61252785-61252786	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs539775129	chr3:61252793-61252794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs573104090	chr3:61252821-61252822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs540141776	chr3:61252835-61252836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs564700695	chr3:61252850-61252851	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs576644788	chr3:61252901-61252902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs142861002	chr3:61252926-61252927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs180991605	chr3:61253014-61253015	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs184416164	chr3:61253023-61253024	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs10510861	chr3:61253045-61253046	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs573312553	chr3:61253130-61253131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs9871848	chr3:61253182-61253183	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs570173769	chr3:61253238-61253239	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs527948098	chr3:61253300-61253301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs552919643	chr3:61253322-61253323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs150650119	chr3:61253462-61253463	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs550233913	chr3:61253470-61253471	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs1093194	chr3:61253495-61253496	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs372637858	chr3:61253512-61253513	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs544354728	chr3:61253514-61253515	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs149837861	chr3:61253520-61253521	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs189052882	chr3:61253525-61253526	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs182400451	chr3:61253536-61253537	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs377081524	chr3:61253538-61253539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs533867218	chr3:61253556-61253557	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs1093193	chr3:61253578-61253579	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs186297494	chr3:61253662-61253663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs190785193	chr3:61253716-61253717	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs11331420	chr3:61253747-61253748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs398082139	chr3:61253754-61253755	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs397764114	chr3:61253755-61253756	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs576646464	chr3:61253780-61253781	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs543964726	chr3:61253799-61253800	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs562608364	chr3:61253823-61253824	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs815718	chr3:61253888-61253889	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs111335238	chr3:61253895-61253896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs548120192	chr3:61253917-61253918	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs566427213	chr3:61253954-61253955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs12054062	chr3:61253975-61253976	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:88)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	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
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	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 mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Urothelial cell carcinoma	18451213	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Colorectal cancer	16272173	CNVD
Mental retardation	17847001	CNVD
Neuroticism	17667963	CNVD
Squamous cell cancer	19047905	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Cancer	20164920	CNVD
Autism	22102821	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:206 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61248400-61255200	Weak transcription	Left Ventricle	heart
2	chr3:61254400-61256400	Enhancers	Fetal Heart	heart
3	chr3:61254600-61255600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:61254800-61255600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr3:61255000-61255400	Enhancers	Right Ventricle	heart
6	chr3:61255200-61255600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:61255200-61255600	Enhancers	Left Ventricle	heart
8	chr3:61255600-61258200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:61256400-61257400	Weak transcription	Fetal Heart	heart
10	chr3:61257400-61257600	Enhancers	Fetal Heart	heart
11	chr3:61261600-61261800	ZNF genes & repeats	Aorta	Aorta
12	chr3:61261800-61269600	Weak transcription	Aorta	Aorta
13	chr3:61262000-61264200	Enhancers	GM12878-XiMat	blood
14	chr3:61263600-61263800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:61266000-61266400	Enhancers	Fetal Kidney	kidney
16	chr3:61266400-61267000	Enhancers	Fetal Intestine Large	intestine
17	chr3:61268200-61270400	Enhancers	Fetal Brain Male	brain
18	chr3:61269200-61269800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:61269400-61269600	Enhancers	Brain Cingulate Gyrus	brain
20	chr3:61269600-61269800	Enhancers	Aorta	Aorta
21	chr3:61273000-61274000	Enhancers	Brain Hippocampus Middle	brain
22	chr3:61273400-61273600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:61273400-61273800	Enhancers	Brain Anterior Caudate	brain
24	chr3:61273400-61274000	Enhancers	Brain Substantia Nigra	brain
25	chr3:61273400-61274200	Enhancers	Brain Angular Gyrus	brain
26	chr3:61273400-61274800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr3:61273600-61274200	Enhancers	Brain Cingulate Gyrus	brain
28	chr3:61273600-61275200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:61274000-61274800	Weak transcription	Brain Substantia Nigra	brain
30	chr3:61274200-61274600	Weak transcription	Brain Angular Gyrus	brain
31	chr3:61274200-61274800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:61274600-61275000	Enhancers	Brain Angular Gyrus	brain
33	chr3:61274800-61275000	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:61274800-61275200	Enhancers	Brain Substantia Nigra	brain
35	chr3:61275200-61275400	Weak transcription	Brain Substantia Nigra	brain
36	chr3:61275400-61275800	Enhancers	Brain Substantia Nigra	brain
37	chr3:61281000-61281400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:61281000-61281400	Enhancers	H9 Cell Line	embryonic stem cell
39	chr3:61281000-61281600	Enhancers	Fetal Stomach	stomach
40	chr3:61281000-61281800	Enhancers	Fetal Lung	lung
41	chr3:61281200-61281600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr3:61281200-61281600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr3:61281200-61281600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr3:61281200-61284200	Enhancers	Colon Smooth Muscle	Colon
45	chr3:61281400-61285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:61281400-61285000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:61281600-61282800	Weak transcription	Fetal Stomach	stomach
48	chr3:61281600-61285000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:61281600-61285000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:61281600-61285600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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