Variant report

Variant	nsv1050076
Chromosome Location	chr12:40813295-40831595
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	chr12:40830307-40830707	GM12878	blood:	n/a	n/a
2	CEBPB	chr12:40826439-40826590	A549	lung:	n/a	n/a
3	CEBPB	chr12:40818598-40818846	IMR90	lung:	n/a	chr12:40818717-40818728
4	CEBPB	chr12:40818440-40818807	HepG2	liver:	n/a	chr12:40818529-40818540 chr12:40818717-40818728
5	CEBPB	chr12:40818440-40818848	A549	lung:	n/a	chr12:40818529-40818540 chr12:40818717-40818728
6	CTCF	chr12:40823200-40823350	HPAF	blood vessel:	n/a	n/a
7	E2F4	chr12:40818494-40818875	MCF10A-Er-Src	breast:	n/a	n/a
8	E2F4	chr12:40815772-40816219	MCF10A-Er-Src	breast:	n/a	n/a
9	E2F4	chr12:40821967-40822010	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr12:40826282-40826397	GM12878	blood:	n/a	n/a
11	GATA3	chr12:40827754-40827880	SH-SY5Y	brain:	n/a	n/a
12	GATA3	chr12:40826604-40826634	SH-SY5Y	brain:	n/a	n/a
13	MAFF	chr12:40829073-40829416	K562	blood:	n/a	chr12:40829244-40829262
14	MAFF	chr12:40829071-40829418	HepG2	liver:	n/a	chr12:40829244-40829262
15	MAFF	chr12:40825007-40825334	HepG2	liver:	n/a	chr12:40825154-40825172
16	MAFF	chr12:40825060-40825300	K562	blood:	n/a	chr12:40825154-40825172
17	MAFK	chr12:40825018-40825291	IMR90	lung:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
18	MAFK	chr12:40825051-40825231	K562	blood:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
19	MAFK	chr12:40825055-40825278	Hela-S3	cervix:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
20	MAFK	chr12:40829075-40829415	K562	blood:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
21	MAFK	chr12:40829111-40829402	Hela-S3	cervix:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
22	MAFK	chr12:40829066-40829429	HepG2	liver:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
23	MAFK	chr12:40829066-40829422	IMR90	lung:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
24	MAFK	chr12:40829069-40829372	HepG2	liver:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
25	MAFK	chr12:40824998-40825331	HepG2	liver:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
26	MAFK	chr12:40825008-40825332	HepG2	liver:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
27	MYC	chr12:40821207-40821299	K562	blood:	n/a	n/a
28	MYC	chr12:40821112-40821194	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr12:40827509-40827614	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:40825910-40825952	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr12:40822654-40822775	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr12:40825175-40825405	K562	blood:	n/a	n/a
33	POLR2A	chr12:40818255-40818307	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:40831588-40831799	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr12:40823652-40823772	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr12:40818471-40818628	MCF10A-Er-Src	breast:	n/a	n/a
37	RUNX3	chr12:40830405-40830692	GM12878	blood:	n/a	n/a
38	RUNX3	chr12:40830374-40830689	GM12878	blood:	n/a	n/a
39	STAT3	chr12:40813810-40814010	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr12:40826151-40826567	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC19-1	chr12:40830419-40830545	NONHSAT027728
2	lnc-MUC19-1	chr12:40821772-40821895	NONHSAT027728
3	lnc-SLC2A13-3	chr12:40814022-40814113	XLOC_010054
4	lnc-MUC19-1	chr12:40827566-40827715	NONHSAT027728
5	lnc-MUC19-1	chr12:40826180-40826264	NONHSAT027728
6	lnc-SLC2A13-3	chr12:40814022-40814118	XLOC_010054
7	lnc-SLC2A13-3	chr12:40814022-40814113	ENSG00000258167.1
8	lnc-MUC19-1	chr12:40825428-40825520	NONHSAT027728
9	lnc-MUC19-1	chr12:40829899-40829993	NONHSAT027728
10	lnc-MUC19-1	chr12:40815015-40815125	NONHSAT027728
11	lnc-MUC19-1	chr12:40820209-40820419	NONHSAT027728
12	lnc-MUC19-1	chr12:40821176-40821298	NONHSAT027728
13	lnc-SLC2A13-3	chr12:40814022-40814118	XLOC_010054
14	lnc-MUC19-1	chr12:40823344-40823479	NONHSAT027728
15	lnc-MUC19-1	chr12:40815906-40816003	NONHSAT027728
16	lnc-MUC19-1	chr12:40815642-40815702	NONHSAT027728
17	lnc-MUC19-1	chr12:40814009-40814237	NONHSAT027728
18	lnc-MUC19-1	chr12:40826429-40826566	NONHSAT027728

Variant related genes	Relation type
MUC19	TF binding region
MORF4L1	miRNA target sites
BLOC1S3	miRNA target sites

Extended variants
information (count: 165 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:165 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs551313124	chr12:40813297-40813298	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs569574992	chr12:40813323-40813324	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs541730490	chr12:40813333-40813334	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs186634539	chr12:40813342-40813343	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs573478140	chr12:40813380-40813381	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs534551108	chr12:40813399-40813400	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs140513418	chr12:40813400-40813401	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs563087340	chr12:40814023-40814024	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs17492201	chr12:40814026-40814027	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs528596253	chr12:40814035-40814036	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs566923437	chr12:40814053-40814054	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs190930617	chr12:40814099-40814100	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs2114566	chr12:40814107-40814108	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs372704493	chr12:40814162-40814163	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs17467164	chr12:40814197-40814198	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs184068670	chr12:40814219-40814220	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs556307997	chr12:40815028-40815029	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs367958333	chr12:40815043-40815044	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs542297711	chr12:40815050-40815051	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs149221842	chr12:40815060-40815061	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs528976982	chr12:40815077-40815078	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs572792330	chr12:40815078-40815079	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs544257810	chr12:40815094-40815095	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs183507530	chr12:40815099-40815100	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs188236516	chr12:40815124-40815125	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs572804855	chr12:40815648-40815649	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs540346078	chr12:40815652-40815653	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs199895088	chr12:40815657-40815658	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs141247415	chr12:40815774-40815775	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs562821398	chr12:40815775-40815776	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs540368061	chr12:40815797-40815798	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs368799486	chr12:40815817-40815818	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs559321359	chr12:40815821-40815822	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs542003169	chr12:40815838-40815839	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs190541850	chr12:40815883-40815884	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs571571656	chr12:40815889-40815890	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs150780776	chr12:40815907-40815908	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs552652826	chr12:40815911-40815912	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs570739634	chr12:40815912-40815913	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs531623183	chr12:40815963-40815964	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs369996871	chr12:40816000-40816001	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs539361912	chr12:40816068-40816069	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs568454786	chr12:40816076-40816077	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs535750547	chr12:40816083-40816084	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs17444805	chr12:40816096-40816097	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs181849016	chr12:40816109-40816110	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs186925390	chr12:40816137-40816138	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs112031457	chr12:40816143-40816144	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs12370083	chr12:40816185-40816186	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs200610116	chr12:40816212-40816213	Inactive region	TF binding region	1 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:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40813200-40813400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:40830000-40830600	Enhancers	Fetal Heart	heart
3	chr12:40830000-40830800	Enhancers	Primary neutrophils fromperipheralblood	blood

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