Variant report

Variant	nsv520570
Chromosome Location	chr12:4929787-4954591
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	ATF2	chr12:4938411-4939170	GM12878	blood:	n/a	n/a
2	ATF2	chr12:4938544-4938986	GM12878	blood:	n/a	n/a
3	BACH1	chr12:4933648-4933872	H1-hESC	embryonic stem cell:	n/a	n/a
4	BATF	chr12:4949429-4949630	GM12878	blood:	n/a	n/a
5	CEBPB	chr12:4942228-4942429	HepG2	liver:	n/a	n/a
6	CHD2	chr12:4937906-4939356	GM12878	blood:	n/a	n/a
7	CHD2	chr12:4934303-4934415	GM12878	blood:	n/a	n/a
8	CTCF	chr12:4953640-4953790	A549	lung:	n/a	n/a
9	CTCF	chr12:4953640-4953790	HEK293	kidney:	n/a	n/a
10	CTCF	chr12:4951748-4951848	LNCaP	prostate:	n/a	n/a
11	CTCF	chr12:4940200-4940350	GM12865	blood:	n/a	n/a
12	CUX1	chr12:4938367-4939017	GM12878	blood:	n/a	n/a
13	E2F4	chr12:4933645-4933916	MCF10A-Er-Src	breast:	n/a	chr12:4933863-4933877
14	EBF1	chr12:4937668-4939281	GM12878	blood:	n/a	chr12:4939175-4939188 chr12:4938006-4938015 chr12:4939176-4939186
15	EBF1	chr12:4938731-4939255	GM12878	blood:	n/a	chr12:4939175-4939188 chr12:4939176-4939186
16	EBF1	chr12:4938673-4939046	GM12878	blood:	n/a	n/a
17	EGR1	chr12:4931762-4932002	K562	blood:	n/a	chr12:4931891-4931904 chr12:4931893-4931903 chr12:4931892-4931903 chr12:4931891-4931905 chr12:4931890-4931905
18	ELF1	chr12:4939027-4939772	GM12878	blood:	n/a	n/a
19	EP300	chr12:4938461-4939373	GM12878	blood:	n/a	chr12:4939236-4939250
20	EP300	chr12:4938512-4938989	GM12878	blood:	n/a	n/a
21	EP300	chr12:4938299-4939084	GM12878	blood:	n/a	chr12:4938361-4938368
22	EP300	chr12:4938676-4938986	GM12878	blood:	n/a	n/a
23	EP300	chr12:4937757-4938115	GM12878	blood:	n/a	n/a
24	ETS1	chr12:4938503-4939044	GM12878	blood:	n/a	n/a
25	FOS	chr12:4933446-4934083	HUVEC	blood vessel:	n/a	chr12:4933824-4933832 chr12:4933824-4933832 chr12:4933824-4933831 chr12:4933823-4933833
26	FOS	chr12:4933705-4933907	MCF10A-Er-Src	breast:	n/a	chr12:4933824-4933832 chr12:4933824-4933832 chr12:4933824-4933831 chr12:4933823-4933833
27	FOS	chr12:4933520-4933977	MCF10A-Er-Src	breast:	n/a	chr12:4933824-4933832 chr12:4933824-4933832 chr12:4933824-4933831 chr12:4933823-4933833
28	FOS	chr12:4934601-4934949	HUVEC	blood vessel:	n/a	n/a
29	FOS	chr12:4933554-4933989	MCF10A-Er-Src	breast:	n/a	chr12:4933824-4933832 chr12:4933824-4933832 chr12:4933824-4933831 chr12:4933823-4933833
30	FOS	chr12:4933590-4933967	MCF10A-Er-Src	breast:	n/a	chr12:4933824-4933832 chr12:4933824-4933832 chr12:4933824-4933831 chr12:4933823-4933833
31	FOSL2	chr12:4933586-4934072	SK-N-SH	brain:	n/a	chr12:4933824-4933832 chr12:4933824-4933832 chr12:4933824-4933831 chr12:4933823-4933833
32	FOXM1	chr12:4938330-4939075	GM12878	blood:	n/a	n/a
33	FOXM1	chr12:4938314-4939151	GM12878	blood:	n/a	n/a
34	GATA2	chr12:4934512-4934971	HUVEC	blood vessel:	n/a	chr12:4934765-4934781
35	IRF1	chr12:4934744-4934802	K562	blood:	n/a	n/a
36	JUND	chr12:4947978-4948091	HepG2	liver:	n/a	n/a
37	JUND	chr12:4933672-4934059	SK-N-SH	brain:	n/a	chr12:4933824-4933832 chr12:4933824-4933832 chr12:4933824-4933831 chr12:4933823-4933833
38	KAP1	chr12:4937535-4938220	U2OS	brain:	n/a	n/a
39	KAP1	chr12:4942293-4942643	HEK293	kidney:	n/a	n/a
40	KAP1	chr12:4947906-4948168	U2OS	brain:	n/a	n/a
41	MAFF	chr12:4933738-4933952	HepG2	liver:	n/a	chr12:4933822-4933840
42	MAFF	chr12:4953102-4953430	HepG2	liver:	n/a	n/a
43	MAFF	chr12:4942287-4942503	HepG2	liver:	n/a	n/a
44	MAFK	chr12:4953117-4953425	IMR90	lung:	n/a	n/a
45	MAFK	chr12:4933676-4933984	HepG2	liver:	n/a	chr12:4933823-4933838 chr12:4933824-4933834
46	MAFK	chr12:4933705-4933903	HepG2	liver:	n/a	chr12:4933823-4933838 chr12:4933824-4933834
47	MAFK	chr12:4953216-4953334	K562	blood:	n/a	n/a
48	MAFK	chr12:4942272-4942526	HepG2	liver:	n/a	chr12:4942389-4942404
49	MAFK	chr12:4933699-4933899	K562	blood:	n/a	chr12:4933823-4933838 chr12:4933824-4933834
50	MAFK	chr12:4953093-4953440	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNA1-2	chr12:4948121-4948527	ENSG00000255608.1
2	lnc-KCNA1-2	chr12:4951689-4951841	ENSG00000255608.1

Variant related genes	Relation type
ENSG00000255608	TF binding region

Extended variants
information (count: 975 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:975 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17702448	chr12:4929787-4929788	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs548533875	chr12:4930001-4930002	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs555346644	chr12:4930063-4930064	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs6489568	chr12:4930100-4930101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs371892774	chr12:4930137-4930138	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
6	rs374086527	chr12:4930161-4930162	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
7	rs567171226	chr12:4930170-4930171	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs551651746	chr12:4930186-4930187	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs13377683	chr12:4930202-4930203	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs7963542	chr12:4930235-4930236	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs567223734	chr12:4930257-4930258	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs547896740	chr12:4930295-4930296	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs567625751	chr12:4930298-4930299	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs371858702	chr12:4930341-4930342	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs12423234	chr12:4930360-4930361	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs570422563	chr12:4930439-4930440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs142327523	chr12:4930510-4930511	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs576502464	chr12:4930517-4930518	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs556224225	chr12:4930536-4930537	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs75230097	chr12:4930583-4930584	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs367670255	chr12:4930585-4930586	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs57032622	chr12:4930588-4930589	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs375453555	chr12:4930606-4930607	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs374462901	chr12:4930612-4930613	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs201402385	chr12:4930627-4930628	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs10849146	chr12:4930755-4930756	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs558070420	chr12:4930855-4930856	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs16931710	chr12:4930882-4930883	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs540026913	chr12:4930984-4930985	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs560210433	chr12:4931000-4931001	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs188269167	chr12:4931010-4931011	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs550049608	chr12:4931037-4931038	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs542218244	chr12:4931071-4931072	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs534500556	chr12:4931079-4931080	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs57945693	chr12:4931169-4931170	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs571929231	chr12:4931243-4931244	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs145982765	chr12:4931290-4931291	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs61907140	chr12:4931291-4931292	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs180811227	chr12:4931292-4931293	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs186626638	chr12:4931296-4931297	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs374106798	chr12:4931301-4931302	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs376915620	chr12:4931308-4931309	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs530266167	chr12:4931322-4931323	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs564047124	chr12:4931348-4931349	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs138584803	chr12:4931350-4931351	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs570102046	chr12:4931354-4931355	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs371770984	chr12:4931442-4931443	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs577921888	chr12:4931471-4931472	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs141757292	chr12:4931490-4931491	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs34101690	chr12:4931495-4931496	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:75)

Disease	PMID	Source
Ovarian cancer	20844748	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Hepatocellular carcinoma	16750200	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	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
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164919	CNVD
lymphocytic leukemia	21291569	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Epilepsy	21858020	CNVD
Colorectal cancer	19359472	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Breast cancer	21509527	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21364760	CNVD
Glioma	20126413	CNVD

Chromatin state (count:272 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4925200-4932000	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:4925600-4934600	Enhancers	Primary B cells from cord blood	blood
3	chr12:4926000-4929800	Enhancers	Fetal Thymus	thymus
4	chr12:4926000-4930000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:4926400-4939000	Weak transcription	Spleen	Spleen
6	chr12:4927400-4929800	Weak transcription	Fetal Stomach	stomach
7	chr12:4927400-4934400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:4927400-4935400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:4927600-4929800	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:4927600-4930800	Enhancers	Fetal Brain Male	brain
11	chr12:4927800-4933200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:4927800-4933200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:4927800-4938800	Weak transcription	Brain Germinal Matrix	brain
14	chr12:4928000-4935800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:4928200-4930400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:4928200-4932400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:4928200-4933400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:4928400-4929800	Enhancers	GM12878-XiMat	blood
19	chr12:4928400-4931400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:4928400-4932000	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:4928400-4933200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:4928600-4930200	Weak transcription	Right Atrium	heart
23	chr12:4928600-4930600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:4928600-4931000	Enhancers	Rectal Smooth Muscle	rectum
25	chr12:4928600-4931600	Enhancers	Colon Smooth Muscle	Colon
26	chr12:4928800-4930000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:4928800-4930600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr12:4929000-4930400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:4929000-4934800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:4929000-4939200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:4929200-4930200	Weak transcription	Placenta	Placenta
32	chr12:4929200-4933200	Weak transcription	Thymus	Thymus
33	chr12:4929200-4934000	Weak transcription	Primary T cells from cord blood	blood
34	chr12:4929200-4966600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:4929400-4930600	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr12:4929400-4930800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr12:4929400-4933200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:4929400-4934000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:4929400-4937800	Weak transcription	Fetal Brain Female	brain
40	chr12:4929400-4966600	Weak transcription	Brain Angular Gyrus	brain
41	chr12:4929600-4930800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:4929800-4930200	Weak transcription	GM12878-XiMat	blood
43	chr12:4929800-4930400	Enhancers	Fetal Muscle Leg	muscle
44	chr12:4929800-4930600	Enhancers	Fetal Stomach	stomach
45	chr12:4929800-4933800	Weak transcription	Fetal Thymus	thymus
46	chr12:4930000-4930800	Enhancers	Fetal Kidney	kidney
47	chr12:4930000-4931000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:4930200-4930400	Bivalent Enhancer	Fetal Lung	lung
49	chr12:4930200-4930400	Enhancers	Placenta	Placenta
50	chr12:4930200-4930400	Enhancers	GM12878-XiMat	blood

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