Variant report

Variant	nsv558604
Chromosome Location	chr12:40818260-40831569
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	chr12:40818440-40818848	A549	lung:	n/a	chr12:40818529-40818540 chr12:40818717-40818728
5	CEBPB	chr12:40818440-40818807	HepG2	liver:	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	chr12:40821967-40822010	MCF10A-Er-Src	breast:	n/a	n/a
9	EP300	chr12:40826282-40826397	GM12878	blood:	n/a	n/a
10	GATA3	chr12:40826604-40826634	SH-SY5Y	brain:	n/a	n/a
11	GATA3	chr12:40827754-40827880	SH-SY5Y	brain:	n/a	n/a
12	MAFF	chr12:40829071-40829418	HepG2	liver:	n/a	chr12:40829244-40829262
13	MAFF	chr12:40825060-40825300	K562	blood:	n/a	chr12:40825154-40825172
14	MAFF	chr12:40829073-40829416	K562	blood:	n/a	chr12:40829244-40829262
15	MAFF	chr12:40825007-40825334	HepG2	liver:	n/a	chr12:40825154-40825172
16	MAFK	chr12:40824998-40825331	HepG2	liver:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
17	MAFK	chr12:40829111-40829402	Hela-S3	cervix:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
18	MAFK	chr12:40829066-40829422	IMR90	lung:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
19	MAFK	chr12:40825008-40825332	HepG2	liver:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
20	MAFK	chr12:40829066-40829429	HepG2	liver:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
21	MAFK	chr12:40825018-40825291	IMR90	lung:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
22	MAFK	chr12:40829075-40829415	K562	blood:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
23	MAFK	chr12:40825055-40825278	Hela-S3	cervix:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
24	MAFK	chr12:40829069-40829372	HepG2	liver:	n/a	chr12:40829245-40829260 chr12:40829240-40829260
25	MAFK	chr12:40825051-40825231	K562	blood:	n/a	chr12:40825156-40825171 chr12:40825157-40825168 chr12:40825157-40825168 chr12:40825155-40825169
26	MYC	chr12:40821112-40821194	Hela-S3	cervix:	n/a	n/a
27	MYC	chr12:40821207-40821299	K562	blood:	n/a	n/a
28	POLR2A	chr12:40822654-40822775	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr12:40827509-40827614	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:40818255-40818307	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:40825910-40825952	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr12:40825175-40825405	K562	blood:	n/a	n/a
33	POLR2A	chr12:40818471-40818628	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr12:40823652-40823772	MCF10A-Er-Src	breast:	n/a	n/a
35	RUNX3	chr12:40830374-40830689	GM12878	blood:	n/a	n/a
36	RUNX3	chr12:40830405-40830692	GM12878	blood:	n/a	n/a
37	STAT3	chr12:40826151-40826567	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC19-1	chr12:40829899-40829993	NONHSAT027728
2	lnc-MUC19-1	chr12:40820209-40820419	NONHSAT027728
3	lnc-MUC19-1	chr12:40830419-40830545	NONHSAT027728
4	lnc-MUC19-1	chr12:40821772-40821895	NONHSAT027728
5	lnc-MUC19-1	chr12:40821176-40821298	NONHSAT027728
6	lnc-MUC19-1	chr12:40823344-40823479	NONHSAT027728
7	lnc-MUC19-1	chr12:40825428-40825520	NONHSAT027728
8	lnc-MUC19-1	chr12:40827566-40827715	NONHSAT027728
9	lnc-MUC19-1	chr12:40826429-40826566	NONHSAT027728
10	lnc-MUC19-1	chr12:40826180-40826264	NONHSAT027728

Variant related genes	Relation type
MUC19	TF binding region

Extended variants
information (count: 114 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:114 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7972535	chr12:40818260-40818261	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs531116611	chr12:40818282-40818283	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs182535445	chr12:40818296-40818297	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs12425677	chr12:40818450-40818451	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs532812534	chr12:40818457-40818458	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs12425678	chr12:40818462-40818463	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs74076504	chr12:40818481-40818482	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs146029406	chr12:40818496-40818497	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs555118526	chr12:40818551-40818552	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs139672245	chr12:40818659-40818660	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs567362228	chr12:40818672-40818673	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs549254684	chr12:40818712-40818713	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs551339971	chr12:40818724-40818725	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs553217697	chr12:40818765-40818766	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs10590770	chr12:40818766-40818767	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs398019205	chr12:40818769-40818770	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs577967292	chr12:40818772-40818773	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs545458136	chr12:40818774-40818775	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs538084109	chr12:40818786-40818787	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs138773151	chr12:40818787-40818788	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs556062218	chr12:40818792-40818793	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs575961490	chr12:40818853-40818854	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs565434385	chr12:40820239-40820240	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs144166248	chr12:40820240-40820241	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs75634075	chr12:40820245-40820246	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs371988285	chr12:40820247-40820248	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs140154105	chr12:40820253-40820254	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs554131026	chr12:40820268-40820269	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs548258640	chr12:40820295-40820296	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs566872046	chr12:40820347-40820348	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs550397578	chr12:40820354-40820355	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs558854000	chr12:40820396-40820397	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs11564249	chr12:40820403-40820404	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs28365245	chr12:40820406-40820407	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs7955308	chr12:40821176-40821177	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs572740906	chr12:40821177-40821178	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs540194750	chr12:40821200-40821201	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs558588008	chr12:40821218-40821219	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs577180882	chr12:40821221-40821222	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs17467263	chr12:40821278-40821279	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs186094107	chr12:40821282-40821283	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs61736852	chr12:40821795-40821796	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs11176584	chr12:40821839-40821840	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs11564170	chr12:40821847-40821848	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs7958987	chr12:40821867-40821868	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs143195891	chr12:40821870-40821871	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs17467284	chr12:40821871-40821872	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs529562667	chr12:40821876-40821877	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs73101540	chr12:40821881-40821882	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
50	rs11564245	chr12:40823354-40823355	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	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:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40830000-40830600	Enhancers	Fetal Heart	heart
2	chr12:40830000-40830800	Enhancers	Primary neutrophils fromperipheralblood	blood

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