Variant report

Variant	nsv582079
Chromosome Location	chr2:57406771-57441853
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	chr2:57425380-57425788	ENSG00000255922
3	lnc-VRK2-4	chr2:57422543-57422644	ENSG00000255922

Variant related genes	Relation type
ENSG00000055813	chromatin interactions

Extended variants
information (count: 1163 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:1163 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1364524	chr2:57406771-57406772	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs10204630	chr2:57406775-57406776	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs565033433	chr2:57406822-57406823	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs527627054	chr2:57406862-57406863	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs547225753	chr2:57406874-57406875	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs567488362	chr2:57406902-57406903	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs536317238	chr2:57406968-57406969	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs376568372	chr2:57406983-57406984	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs11901735	chr2:57406993-57406994	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs76123059	chr2:57407001-57407002	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs200535840	chr2:57407004-57407005	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs142885516	chr2:57407005-57407006	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs143057248	chr2:57407007-57407008	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs547174914	chr2:57407008-57407009	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs67381551	chr2:57407009-57407010	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs200584249	chr2:57407011-57407012	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs11891117	chr2:57407012-57407013	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs201471264	chr2:57407013-57407014	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs28643491	chr2:57407014-57407015	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs9677977	chr2:57407015-57407016	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs373594957	chr2:57407016-57407017	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs77672198	chr2:57407017-57407018	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs578152916	chr2:57407020-57407021	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs199776956	chr2:57407023-57407024	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs200575762	chr2:57407024-57407025	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs534509707	chr2:57407026-57407027	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs193032095	chr2:57407029-57407030	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs7564223	chr2:57407052-57407053	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs542848236	chr2:57407057-57407058	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs143660756	chr2:57407064-57407065	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs576178496	chr2:57407104-57407105	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs112784428	chr2:57407126-57407127	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs565281117	chr2:57407134-57407135	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs569045890	chr2:57407243-57407244	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs527561311	chr2:57407269-57407270	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs547683959	chr2:57407309-57407310	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs185192524	chr2:57407315-57407316	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs529892092	chr2:57407327-57407328	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs549258080	chr2:57407336-57407337	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs573918342	chr2:57407339-57407340	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs187753185	chr2:57407354-57407355	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs569757772	chr2:57407379-57407380	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs79905380	chr2:57407382-57407383	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs141109203	chr2:57407433-57407434	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs565693105	chr2:57407453-57407454	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs575183938	chr2:57407478-57407479	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs72940754	chr2:57407497-57407498	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs554030529	chr2:57407501-57407502	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs574024155	chr2:57407509-57407510	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs114294448	chr2:57407510-57407511	Weak transcription Enhancers Flanking Active TSS	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:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57405600-57406800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:57406000-57406800	Enhancers	HUVEC	blood vessel
3	chr2:57406600-57407600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:57406600-57410000	Enhancers	HMEC	breast
5	chr2:57406600-57410200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:57406600-57410400	Enhancers	NHEK	skin
7	chr2:57406600-57410800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:57406800-57407200	Enhancers	NHDF-Ad	bronchial
9	chr2:57406800-57407400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:57406800-57407400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:57406800-57407600	Enhancers	HSMMtube	muscle
12	chr2:57406800-57407600	Flanking Active TSS	HUVEC	blood vessel
13	chr2:57406800-57407800	Enhancers	NH-A	brain
14	chr2:57406800-57411400	Enhancers	HSMM	muscle
15	chr2:57407000-57409000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:57407200-57409800	Weak transcription	NHDF-Ad	bronchial
17	chr2:57407400-57408000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:57407400-57408400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:57407400-57409400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:57407600-57408600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:57407600-57409800	Weak transcription	HSMMtube	muscle
22	chr2:57407600-57410200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:57407600-57410600	Enhancers	HUVEC	blood vessel
24	chr2:57407800-57408400	Weak transcription	NH-A	brain
25	chr2:57408000-57408400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:57408200-57409000	Enhancers	Fetal Heart	heart
27	chr2:57408400-57409800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:57408400-57410000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:57408400-57410000	Enhancers	NH-A	brain
30	chr2:57408400-57410400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:57408600-57409600	Enhancers	Hela-S3	cervix
32	chr2:57408600-57410000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:57409000-57409400	Weak transcription	Fetal Heart	heart
34	chr2:57409400-57410200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:57409400-57410400	Enhancers	Fetal Heart	heart
36	chr2:57409800-57410200	Enhancers	NHDF-Ad	bronchial
37	chr2:57409800-57410400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:57409800-57411400	Enhancers	HSMMtube	muscle
39	chr2:57410000-57410200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr2:57410400-57411600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:57411600-57412600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:57411800-57412600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr2:57412000-57412800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr2:57412000-57412800	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr2:57412000-57413400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr2:57412400-57412800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:57412600-57413000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr2:57412600-57413000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:57412600-57413200	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr2:57422800-57423000	Active TSS	ES-I3 Cell Line	embryonic stem cell

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