Variant report

Variant	nsv526485
Chromosome Location	chr12:59412802-59422668
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:59422466-59422666	A549	lung:	n/a	chr12:59422524-59422533 chr12:59422524-59422533 chr12:59422524-59422533 chr12:59422522-59422533 chr12:59422524-59422533 chr12:59422524-59422535
2	CEBPB	chr12:59420905-59421451	MCF-7	breast:	n/a	chr12:59421183-59421194
3	CEBPB	chr12:59421021-59421369	MCF-7	breast:	n/a	chr12:59421183-59421194
4	CEBPB	chr12:59422407-59422651	HepG2	liver:	n/a	chr12:59422524-59422533 chr12:59422524-59422533 chr12:59422524-59422533 chr12:59422522-59422533 chr12:59422524-59422533 chr12:59422524-59422535
5	CTCF	chr12:59414340-59414490	AG10803	skin:	n/a	n/a
6	CTCF	chr12:59414340-59414490	AG04449	skin:	n/a	n/a
7	E2F4	chr12:59413124-59413281	MCF10A-Er-Src	breast:	n/a	n/a
8	E2F4	chr12:59417159-59417354	MCF10A-Er-Src	breast:	n/a	n/a
9	E2F4	chr12:59419610-59419688	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr12:59420891-59421500	T-47D	breast:	n/a	n/a
11	ESR1	chr12:59418488-59418914	T-47D	breast:	n/a	chr12:59418694-59418711
12	ESR1	chr12:59418522-59418815	T-47D	breast:	n/a	chr12:59418694-59418711
13	ESR1	chr12:59418475-59418843	T-47D	breast:	n/a	chr12:59418694-59418711
14	FOXA1	chr12:59420987-59421379	T-47D	breast:	n/a	n/a
15	FOXA1	chr12:59420872-59421431	T-47D	breast:	n/a	n/a
16	GATA3	chr12:59414056-59414501	T-47D	breast:	n/a	n/a
17	GATA3	chr12:59420971-59421515	MCF-7	breast:	n/a	chr12:59421456-59421464
18	GATA3	chr12:59421114-59421345	MCF-7	breast:	n/a	n/a
19	GATA3	chr12:59420907-59421506	T-47D	breast:	n/a	chr12:59421456-59421464
20	GATA3	chr12:59420217-59420709	MCF-7	breast:	n/a	n/a
21	GATA3	chr12:59420896-59421470	T-47D	breast:	n/a	chr12:59421456-59421464
22	GATA3	chr12:59413913-59414619	T-47D	breast:	n/a	n/a
23	GATA3	chr12:59420965-59421640	MCF-7	breast:	n/a	chr12:59421456-59421464
24	HDAC2	chr12:59420980-59421455	MCF-7	breast:	n/a	n/a
25	JUND	chr12:59420847-59421532	T-47D	breast:	n/a	chr12:59420849-59420861
26	KAP1	chr12:59418547-59419441	HEK293	kidney:	n/a	n/a
27	POLR2A	chr12:59422584-59422636	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:59417007-59417175	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr12:59421339-59421343	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr12:59414089-59414255	GM12878	blood:	n/a	n/a
31	REST	chr12:59416265-59416648	H1-neurons	neurons:	n/a	n/a
32	REST	chr12:59416106-59416650	H1-neurons	neurons:	n/a	n/a
33	STAT3	chr12:59413235-59413474	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr12:59419568-59419592	MCF10A-Er-Src	breast:	n/a	n/a
35	TBP	chr12:59417838-59417883	Hela-S3	cervix:	n/a	n/a
36	ZNF217	chr12:59420955-59421424	MCF-7	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-362K2.2.1-3	chr12:59413950-59414675	NONHSAT029040

Variant related genes	Relation type
RPS6P22	TF binding region

Extended variants
information (count: 362 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:362 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7974440	chr12:59412802-59412803	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs563981813	chr12:59412814-59412815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs566265734	chr12:59412856-59412857	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs113666427	chr12:59412884-59412885	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs536308708	chr12:59412895-59412896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs533309131	chr12:59412896-59412897	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs143792879	chr12:59412919-59412920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs78119326	chr12:59412971-59412972	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs577413662	chr12:59412984-59412985	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs1444102	chr12:59413022-59413023	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs151274716	chr12:59413044-59413045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs577171908	chr12:59413109-59413110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs191040686	chr12:59413129-59413130	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs547414275	chr12:59413133-59413134	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs140475675	chr12:59413181-59413182	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs150406226	chr12:59413225-59413226	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs546925315	chr12:59413252-59413253	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs76938125	chr12:59413260-59413261	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs535888100	chr12:59413261-59413262	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs371633868	chr12:59413262-59413263	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs75320985	chr12:59413308-59413309	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs563073528	chr12:59413341-59413342	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs574878753	chr12:59413342-59413343	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs545361463	chr12:59413358-59413359	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs183404714	chr12:59413411-59413412	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs532649246	chr12:59413427-59413428	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs186653132	chr12:59413535-59413536	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs528188321	chr12:59413539-59413540	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs373632260	chr12:59413676-59413677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs559681253	chr12:59413681-59413682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs192070838	chr12:59413698-59413699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs549110575	chr12:59413725-59413726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs138129323	chr12:59413828-59413829	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs570196536	chr12:59413835-59413836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs74397303	chr12:59413836-59413837	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs74091469	chr12:59413838-59413839	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs570836629	chr12:59413847-59413848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs183478823	chr12:59413855-59413856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs187705504	chr12:59413870-59413871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs192586416	chr12:59413925-59413926	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs182147067	chr12:59413933-59413934	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs199907266	chr12:59413963-59413964	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs79953325	chr12:59413966-59413967	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs574966753	chr12:59413984-59413985	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs74091470	chr12:59413992-59413993	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs550855977	chr12:59414032-59414033	Weak transcription Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
47	rs537628974	chr12:59414041-59414042	Weak transcription Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
48	rs551164479	chr12:59414046-59414047	Weak transcription Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
49	rs557289481	chr12:59414047-59414048	Weak transcription Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
50	rs17121854	chr12:59414066-59414067	Weak transcription Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:82)

Disease	PMID	Source
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
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	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
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
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	18632612	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Urothelial cell carcinoma	18451213	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Leukemia	18628472	CNVD
Glioblastoma multiforme	22291905	CNVD
Glioblastoma multiforme	19435819	CNVD
Myelofibrosis	22110671	CNVD
Phyllodes tumor	17334353	CNVD
Glaucoma	21310917	CNVD
Breast cancer	16272173	CNVD
Mental retardation	19951919	CNVD
Glaucoma	21447600	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Developmental delay	21267005	CNVD
12q14 microdeletion syndrome	21267005	CNVD
Developmental delay	19277063	CNVD
Dwarfism	19277063	CNVD
Fibroblasts	20926602	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Glioblastoma multiforme	20080666	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	17133270	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Glioblastoma	17090523	CNVD
Multiple myeloma	16616336	CNVD
Lung cancer	16773561	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59408600-59420800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:59414000-59414800	Active TSS	NHDF-Ad	bronchial
3	chr12:59416000-59418800	Weak transcription	Aorta	Aorta
4	chr12:59417000-59417400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:59417200-59418800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:59417400-59417800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:59417400-59418200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:59417400-59418200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:59417400-59418200	Enhancers	Osteobl	bone
10	chr12:59417400-59418600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:59417400-59419200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:59417600-59430200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:59417800-59418400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:59419200-59426400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:59419800-59420000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:59420000-59420200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:59420600-59421400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:59421400-59425200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links