Variant report

Variant	nsv558601
Chromosome Location	chr12:40802840-40824917
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:20)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:40818598-40818846	IMR90	lung:	n/a	chr12:40818717-40818728
2	CEBPB	chr12:40818440-40818807	HepG2	liver:	n/a	chr12:40818529-40818540 chr12:40818717-40818728
3	CEBPB	chr12:40818440-40818848	A549	lung:	n/a	chr12:40818529-40818540 chr12:40818717-40818728
4	CTCF	chr12:40823200-40823350	HPAF	blood vessel:	n/a	n/a
5	CTCF	chr12:40805024-40805091	LNCaP	prostate:	n/a	n/a
6	E2F4	chr12:40815772-40816219	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F4	chr12:40818494-40818875	MCF10A-Er-Src	breast:	n/a	n/a
8	E2F4	chr12:40821967-40822010	MCF10A-Er-Src	breast:	n/a	n/a
9	GATA3	chr12:40810161-40810625	MCF-7	breast:	n/a	n/a
10	MAFK	chr12:40811655-40811801	HepG2	liver:	n/a	n/a
11	MYC	chr12:40821207-40821299	K562	blood:	n/a	n/a
12	MYC	chr12:40821112-40821194	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr12:40818471-40818628	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr12:40806369-40806465	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr12:40803385-40803422	A549	lung:	n/a	n/a
16	POLR2A	chr12:40823652-40823772	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr12:40818255-40818307	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:40822654-40822775	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:40803454-40803476	A549	lung:	n/a	n/a
20	STAT3	chr12:40808552-40808706	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr12:40813810-40814010	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT3	chr12:40806038-40806113	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT3	chr12:40809708-40809713	MCF10A-Er-Src	breast:	n/a	n/a
24	USF2	chr12:40808250-40808281	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40802735..40804254-chr12:40811941..40814562,2	K562	blood:
2	chr12:40802843..40805068-chr12:40806902..40808859,2	K562	blood:
3	chr12:40803393..40806032-chr12:40844478..40846629,2	K562	blood:
4	chr12:40802843..40805068-chr12:40806902..40808859,2	K562	blood:
5	12:40793507-40812339..12:40836437-40839614	H1-hESC	embryonic stem cell:	embryo

(count:20 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A13-3	chr12:40814022-40814118	XLOC_010054
2	lnc-SLC2A13-3	chr12:40814022-40814113	ENSG00000258167.1
3	lnc-SLC2A13-3	chr12:40814022-40814118	XLOC_010054
4	lnc-MUC19-1	chr12:40815015-40815125	NONHSAT027728
5	lnc-MUC19-1	chr12:40812976-40813035	NONHSAT027728
6	lnc-MUC19-1	chr12:40821176-40821298	NONHSAT027728
7	lnc-SLC2A13-3	chr12:40807837-40807921	XLOC_010054
8	lnc-MUC19-1	chr12:40815642-40815702	NONHSAT027728
9	lnc-SLC2A13-3	chr12:40810105-40810240	XLOC_010054
10	lnc-SLC2A13-3	chr12:40814022-40814113	XLOC_010054
11	lnc-MUC19-1	chr12:40814009-40814237	NONHSAT027728
12	lnc-MUC19-1	chr12:40805835-40805984	NONHSAT027728
13	lnc-MUC19-1	chr12:40815906-40816003	NONHSAT027728
14	lnc-SLC2A13-3	chr12:40810103-40810240	XLOC_010054
15	lnc-MUC19-1	chr12:40823344-40823479	NONHSAT027728
16	lnc-MUC19-1	chr12:40821772-40821895	NONHSAT027728
17	lnc-SLC2A13-3	chr12:40810105-40810240	XLOC_010054
18	lnc-MUC19-1	chr12:40820209-40820419	NONHSAT027728
19	lnc-MUC19-1	chr12:40811932-40811982	NONHSAT027728
20	lnc-MUC19-1	chr12:40805409-40805429	NONHSAT027728

No data

Variant related genes	Relation type
MUC19	TF binding region
ENSG00000258167	chromatin interactions
ENSG00000205592	chromatin interactions
STXBP3	miRNA target sites
BLOC1S3	miRNA target sites
SEC23IP	miRNA target sites
MORF4L1	miRNA target sites

Extended variants
information (count: 561 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:561 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10784599	chr12:40802840-40802841	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs544792263	chr12:40802868-40802869	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs182539809	chr12:40802885-40802886	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs369143162	chr12:40802945-40802946	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs542724252	chr12:40802953-40802954	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs146759849	chr12:40802964-40802965	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs367756476	chr12:40802965-40802966	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs561468991	chr12:40803029-40803030	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs74966781	chr12:40803038-40803039	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs35944596	chr12:40803041-40803042	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs539510131	chr12:40803044-40803045	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs555593648	chr12:40803046-40803047	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs144010270	chr12:40803059-40803060	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs565570523	chr12:40803095-40803096	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs532814865	chr12:40803098-40803099	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs76962234	chr12:40803112-40803113	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs186496149	chr12:40803117-40803118	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs12422390	chr12:40803129-40803130	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs12423986	chr12:40803194-40803195	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs370216664	chr12:40803222-40803223	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs534313795	chr12:40803223-40803224	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs374529325	chr12:40803243-40803244	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs73279557	chr12:40803246-40803247	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs149710327	chr12:40803285-40803286	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs34251471	chr12:40803301-40803302	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs74640981	chr12:40803399-40803400	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs398019204	chr12:40803400-40803401	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs145577334	chr12:40803429-40803430	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs17492138	chr12:40803486-40803487	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs192281212	chr12:40803515-40803516	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs184667653	chr12:40803556-40803557	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs536477192	chr12:40803560-40803561	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs148891216	chr12:40803562-40803563	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs113112112	chr12:40803586-40803587	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs190297574	chr12:40803704-40803705	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs565233270	chr12:40803722-40803723	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs577330968	chr12:40803771-40803772	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs2404840	chr12:40803788-40803789	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs527244087	chr12:40803796-40803797	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs193286562	chr12:40803820-40803821	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs184392877	chr12:40803869-40803870	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs530209963	chr12:40803931-40803932	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs548808054	chr12:40803951-40803952	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs560809662	chr12:40803962-40803963	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs17444681	chr12:40803965-40803966	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs538473372	chr12:40803973-40803974	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs371946266	chr12:40803978-40803979	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs546290111	chr12:40803995-40803996	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs570878140	chr12:40804004-40804005	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs561771367	chr12:40804041-40804042	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Acute lymphoblastic leukemia	21390130	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
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40799600-40813200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:40803400-40805600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:40805600-40806200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:40806200-40807600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:40807800-40808000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:40813200-40813400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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