Variant report

Variant	esv3505007
Chromosome Location	chr12:45249908-45251699
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	chr12:45245058..45246783-chr12:45249459..45251550,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM117-4	chr12:45251306-45251369	l_632_chr12:45063675-45150311_ovary

Variant related genes	Relation type
ENSG00000184613	chromatin interactions

Extended variants
information (count: 74 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:74 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs537576734	chr12:45249914-45249915	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs555810449	chr12:45249938-45249939	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs1876240	chr12:45249956-45249957	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs534835333	chr12:45249984-45249985	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs142254884	chr12:45249988-45249989	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs541871260	chr12:45249994-45249995	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs2710457	chr12:45250001-45250002	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs544902271	chr12:45250023-45250024	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs556576957	chr12:45250034-45250035	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs181302102	chr12:45250062-45250063	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs71459271	chr12:45250073-45250074	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs561057730	chr12:45250074-45250075	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs375301076	chr12:45250107-45250108	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs1605298	chr12:45250112-45250113	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs541621629	chr12:45250259-45250260	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs559643520	chr12:45250283-45250284	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs369577139	chr12:45250304-45250305	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs533716064	chr12:45250309-45250310	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs552472139	chr12:45250353-45250354	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs139027487	chr12:45250372-45250373	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs570093967	chr12:45250375-45250376	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs73279180	chr12:45250405-45250406	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs549075445	chr12:45250420-45250421	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs1605297	chr12:45250429-45250430	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs534764482	chr12:45250503-45250504	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs2658968	chr12:45250528-45250529	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs571103395	chr12:45250536-45250537	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs149389160	chr12:45250538-45250539	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs568012338	chr12:45250570-45250571	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs184799175	chr12:45250617-45250618	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs567871205	chr12:45250620-45250621	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs1605296	chr12:45250626-45250627	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs189367773	chr12:45250649-45250650	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs80342904	chr12:45250670-45250671	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs75656843	chr12:45250764-45250765	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs539949609	chr12:45250866-45250867	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs11182715	chr12:45250868-45250869	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs578200939	chr12:45250892-45250893	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs545589168	chr12:45250896-45250897	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs180862693	chr12:45250931-45250932	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs531069497	chr12:45250938-45250939	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs11182716	chr12:45250951-45250952	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs549360136	chr12:45251000-45251001	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs185803292	chr12:45251049-45251050	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs73279183	chr12:45251056-45251057	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs551241315	chr12:45251078-45251079	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs2710459	chr12:45251110-45251111	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs571139146	chr12:45251136-45251137	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs573005731	chr12:45251196-45251197	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs538469942	chr12:45251202-45251203	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Cancer	20164919	CNVD
Adenoid cystic carcinoma	18332873	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Gastric cancer	18160780	CNVD
Myelofibrosis	22110671	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Hodgkin''s lymphoma	18641027	CNVD

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45242800-45252200	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr12:45243800-45250600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:45243800-45251600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:45246600-45250200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:45247400-45253600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:45247800-45250200	Weak transcription	Fetal Brain Female	brain
7	chr12:45247800-45251400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr12:45248400-45250400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:45248400-45252400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:45248600-45259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:45248800-45255800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:45249000-45250400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:45249000-45252400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:45249000-45255400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:45249200-45251000	Weak transcription	Fetal Brain Male	brain
16	chr12:45249200-45252400	Enhancers	Primary T cells from cord blood	blood
17	chr12:45250200-45250600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr12:45250400-45250800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr12:45250400-45251200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:45250600-45251600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:45250600-45253800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:45250800-45255400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:45251000-45251200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:45251000-45252400	Enhancers	Fetal Brain Male	brain
25	chr12:45251200-45252400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:45251400-45253600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:45251600-45252800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:45251600-45253600	Enhancers	Primary T cells fromperipheralblood	blood

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