Variant report

Variant	nsv519956
Chromosome Location	chr2:78027298-78069474
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	chr17:56735169..56737848-chr2:78047828..78049670,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRTM4-3	chr2:78066895-78067016	NR_110288

Variant related genes	Relation type
ENSG00000202077	chromatin interactions

Extended variants
information (count: 1519 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:1519 , 50 per page) page: 1 2 3 4 5 6 7 ... 31

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs139975932	chr2:78031013-78031014	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs569421770	chr2:78031039-78031040	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs567321348	chr2:78031084-78031085	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs535122219	chr2:78031092-78031093	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs553010731	chr2:78031122-78031123	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs556576901	chr2:78031139-78031140	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs541061195	chr2:78031149-78031150	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs576410411	chr2:78031159-78031160	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs12478850	chr2:78031400-78031401	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs562029722	chr2:78031414-78031415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs149742789	chr2:78031415-78031416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs543902187	chr2:78031432-78031433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs13006532	chr2:78031448-78031449	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs561168497	chr2:78031449-78031450	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs1979564	chr2:78031481-78031482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs12474656	chr2:78031498-78031499	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs367962060	chr2:78031515-78031516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs564517075	chr2:78031527-78031528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs4853341	chr2:78031531-78031532	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs547080894	chr2:78031547-78031548	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs560339825	chr2:78031548-78031549	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs1979563	chr2:78031552-78031553	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs190825175	chr2:78031579-78031580	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs145589698	chr2:78031580-78031581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs538177728	chr2:78031584-78031585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs551657428	chr2:78031594-78031595	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs4853342	chr2:78031649-78031650	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs148870141	chr2:78031791-78031792	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs573312936	chr2:78031807-78031808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs183004704	chr2:78031826-78031827	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs553053056	chr2:78031829-78031830	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs566407359	chr2:78031831-78031832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs4853343	chr2:78031832-78031833	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs555300534	chr2:78031857-78031858	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs532350664	chr2:78031858-78031859	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs372596716	chr2:78031861-78031862	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs143306226	chr2:78031864-78031865	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs544556975	chr2:78031993-78031994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs558043883	chr2:78031994-78031995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs545058185	chr2:78032026-78032027	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs578073858	chr2:78032027-78032028	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs540237122	chr2:78032051-78032052	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs186554792	chr2:78032083-78032084	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs147906991	chr2:78032179-78032180	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs529404376	chr2:78032187-78032188	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs543089522	chr2:78032239-78032240	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs192209005	chr2:78032292-78032293	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs113628013	chr2:78032367-78032368	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs141618957	chr2:78032457-78032458	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs182666581	chr2:78032483-78032484	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	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
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Lung cancer	18438408	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Renal cell carcinoma	18765545	CNVD
Myxofibrosarcoma	16751306	CNVD
small cell lung cancer	20016488	CNVD
Acute myeloid leukemia	21251322	CNVD
Mental retardation	17124404	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Cancer	17440070	CNVD
Myelofibrosis	22110671	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Breast cancer	16272173	CNVD
Epilepsy	22083797	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:78031000-78031200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:78031400-78032000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:78031600-78031800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:78031800-78033000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:78032000-78033000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:78032800-78033000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:78033000-78033400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:78033000-78036000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:78033800-78036000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:78034800-78035000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr2:78035000-78035400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:78035200-78035800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:78035200-78035800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:78035600-78035800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr2:78035800-78040600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:78040000-78041000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:78040400-78041000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:78040600-78041000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:78040600-78041000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr2:78040600-78041000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:78040600-78041000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr2:78040600-78041200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr2:78040600-78041200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:78040600-78041200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:78040600-78041400	Enhancers	HepG2	liver
26	chr2:78040600-78042200	Enhancers	Fetal Intestine Large	intestine
27	chr2:78041000-78043600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:78041200-78048800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:78041400-78043600	Weak transcription	HepG2	liver
30	chr2:78043600-78044000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr2:78043600-78044000	Enhancers	HepG2	liver
32	chr2:78044000-78048800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:78044000-78050000	Weak transcription	HepG2	liver
34	chr2:78048800-78049600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr2:78048800-78049800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr2:78048800-78050000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:78048800-78050200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr2:78049600-78055600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:78050000-78050400	Enhancers	Fetal Intestine Large	intestine
40	chr2:78050000-78050800	Enhancers	HepG2	liver
41	chr2:78050400-78050800	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr2:78050800-78058000	Weak transcription	HepG2	liver
43	chr2:78051800-78052000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:78052000-78052400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:78052400-78058000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:78055400-78057000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:78055600-78056600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:78055600-78057600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:78055800-78056600	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr2:78055800-78057600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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