Variant report

Variant	nsv1008596
Chromosome Location	chr2:57407624-57447386
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:56410837..56411593-chr2:57429009..57429668,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VRK2-4	chr2:57419954-57420014	ENSG00000255922
2	lnc-VRK2-4	chr2:57422543-57422644	ENSG00000255922
3	lnc-VRK2-4	chr2:57425380-57425788	ENSG00000255922

Variant related genes	Relation type
ENSG00000055813	chromatin interactions

Extended variants
information (count: 1311 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:1311 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1424638	chr2:57407649-57407650	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs572387798	chr2:57407650-57407651	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs536134640	chr2:57407661-57407662	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs561162679	chr2:57407687-57407688	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs201337084	chr2:57407714-57407715	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs183583132	chr2:57407729-57407730	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs72811394	chr2:57407733-57407734	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs146897824	chr2:57407743-57407744	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs539933027	chr2:57407756-57407757	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs188253137	chr2:57407761-57407762	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs565673746	chr2:57407792-57407793	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs528069252	chr2:57407794-57407795	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs13028231	chr2:57407809-57407810	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs567612929	chr2:57407810-57407811	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs180944059	chr2:57407847-57407848	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs139287873	chr2:57407865-57407866	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs534170113	chr2:57407965-57407966	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs557730422	chr2:57407977-57407978	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs184736643	chr2:57407981-57407982	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs149979205	chr2:57408013-57408014	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs79178152	chr2:57408018-57408019	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs189600514	chr2:57408022-57408023	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs548967046	chr2:57408040-57408041	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs563134366	chr2:57408041-57408042	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs572489143	chr2:57408080-57408081	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs557285493	chr2:57408112-57408113	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs143208399	chr2:57408176-57408177	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs72811398	chr2:57408196-57408197	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs543754685	chr2:57408199-57408200	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs563444423	chr2:57408222-57408223	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs532312138	chr2:57408226-57408227	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs545712687	chr2:57408227-57408228	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs559387696	chr2:57408238-57408239	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs181609520	chr2:57408239-57408240	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs116756965	chr2:57408248-57408249	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs369560390	chr2:57408284-57408285	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs147076283	chr2:57408357-57408358	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs530304139	chr2:57408400-57408401	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs550041614	chr2:57408426-57408427	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs76859735	chr2:57408432-57408433	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs539214924	chr2:57408443-57408444	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs558932985	chr2:57408448-57408449	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs987051	chr2:57408460-57408461	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs535133328	chr2:57408477-57408478	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs534421606	chr2:57408483-57408484	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs574908092	chr2:57408488-57408489	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs144248231	chr2:57408495-57408496	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs368152212	chr2:57408496-57408497	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs537470210	chr2:57408579-57408580	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs75327015	chr2:57408606-57408607	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57406600-57410000	Enhancers	HMEC	breast
2	chr2:57406600-57410200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:57406600-57410400	Enhancers	NHEK	skin
4	chr2:57406600-57410800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr2:57406800-57407800	Enhancers	NH-A	brain
6	chr2:57406800-57411400	Enhancers	HSMM	muscle
7	chr2:57407000-57409000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:57407200-57409800	Weak transcription	NHDF-Ad	bronchial
9	chr2:57407400-57408000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:57407400-57408400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:57407400-57409400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:57407600-57408600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:57407600-57409800	Weak transcription	HSMMtube	muscle
14	chr2:57407600-57410200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:57407600-57410600	Enhancers	HUVEC	blood vessel
16	chr2:57407800-57408400	Weak transcription	NH-A	brain
17	chr2:57408000-57408400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:57408200-57409000	Enhancers	Fetal Heart	heart
19	chr2:57408400-57409800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:57408400-57410000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:57408400-57410000	Enhancers	NH-A	brain
22	chr2:57408400-57410400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:57408600-57409600	Enhancers	Hela-S3	cervix
24	chr2:57408600-57410000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:57409000-57409400	Weak transcription	Fetal Heart	heart
26	chr2:57409400-57410200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:57409400-57410400	Enhancers	Fetal Heart	heart
28	chr2:57409800-57410200	Enhancers	NHDF-Ad	bronchial
29	chr2:57409800-57410400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr2:57409800-57411400	Enhancers	HSMMtube	muscle
31	chr2:57410000-57410200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr2:57410400-57411600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:57411600-57412600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr2:57411800-57412600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr2:57412000-57412800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr2:57412000-57412800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr2:57412000-57413400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr2:57412400-57412800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:57412600-57413000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr2:57412600-57413000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr2:57412600-57413200	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr2:57422800-57423000	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr2:57423000-57427600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:57426000-57427000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr2:57426000-57427800	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr2:57426200-57426800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr2:57426600-57427800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:57427600-57427800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr2:57431400-57432000	Enhancers	Fetal Kidney	kidney
50	chr2:57431400-57433000	Enhancers	Fetal Intestine Large	intestine

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