Variant report

Variant	nsv519063
Chromosome Location	chr12:40536061-40538858
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	chr12:40535738-40536586	Hela-S3	cervix:	n/a	n/a
2	ELK4	chr12:40535775-40536082	Hela-S3	cervix:	n/a	n/a
3	EP300	chr12:40535760-40536514	Hela-S3	cervix:	n/a	n/a
4	FOS	chr12:40535878-40536234	MCF10A-Er-Src	breast:	n/a	chr12:40536080-40536090 chr12:40536080-40536090 chr12:40536080-40536090
5	FOS	chr12:40535923-40536440	MCF10A-Er-Src	breast:	n/a	chr12:40536080-40536090 chr12:40536080-40536090 chr12:40536080-40536090
6	FOS	chr12:40535923-40536458	MCF10A-Er-Src	breast:	n/a	chr12:40536080-40536090 chr12:40536080-40536090 chr12:40536080-40536090
7	FOSL2	chr12:40535957-40536483	A549	lung:	n/a	chr12:40536080-40536090 chr12:40536080-40536090 chr12:40536080-40536090
8	MAX	chr12:40535776-40536501	Hela-S3	cervix:	n/a	n/a
9	MAX	chr12:40538008-40538106	Hela-S3	cervix:	n/a	chr12:40538038-40538048
10	MAX	chr12:40537893-40538124	NB4	blood:	n/a	chr12:40537980-40537990 chr12:40538038-40538048
11	RCOR1	chr12:40535838-40536465	Hela-S3	cervix:	n/a	n/a
12	SPI1	chr12:40537924-40538060	K562	blood:	n/a	n/a
13	SPI1	chr12:40537766-40538271	HL-60	blood:	n/a	n/a
14	STAT3	chr12:40535900-40536502	Hela-S3	cervix:	n/a	chr12:40536151-40536158
15	STAT3	chr12:40536256-40536289	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF7L2	chr12:40535934-40536502	Hela-S3	cervix:	n/a	chr12:40536081-40536090
17	TCF7L2	chr12:40535875-40536436	Hela-S3	cervix:	n/a	chr12:40536081-40536090
18	USF2	chr12:40535835-40536102	Hela-S3	cervix:	n/a	n/a
19	ZKSCAN1	chr12:40535779-40536654	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40536767..40538493-chr12:40545018..40546756,2	K562	blood:
2	chr1:169315069..169315689-chr12:40537506..40538182,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A13-1	chr12:40534259-40536436	XLOC_010052
2	lnc-SLC2A13-1	chr12:40537983-40538106	XLOC_010052
3	lnc-SLC2A13-1	chr12:40534728-40536678	ENSG00000260943.1
4	lnc-SLC2A13-1	chr12:40537621-40538106	XLOC_010052

Variant related genes	Relation type
ENSG00000260943	TF binding region
BRMS1L	miRNA target sites

Extended variants
information (count: 91 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:91 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs726330	chr12:40536061-40536062	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs566321432	chr12:40536079-40536080	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs533783619	chr12:40536128-40536129	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs190526186	chr12:40536222-40536223	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs577301257	chr12:40536267-40536268	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs138130630	chr12:40536274-40536275	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs535780666	chr12:40536314-40536315	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs535972418	chr12:40536315-40536316	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs373924727	chr12:40536317-40536318	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs556541773	chr12:40536329-40536330	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs370090731	chr12:40536333-40536334	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs574984389	chr12:40536408-40536409	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs183096480	chr12:40536452-40536453	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs17442735	chr12:40536470-40536471	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs372511036	chr12:40536482-40536483	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs572671291	chr12:40536505-40536506	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs75881506	chr12:40536506-40536507	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs7306099	chr12:40536513-40536514	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs2638223	chr12:40536581-40536582	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs142022962	chr12:40536612-40536613	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs562514776	chr12:40536638-40536639	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs529681839	chr12:40536640-40536641	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs188110851	chr12:40536643-40536644	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs7294643	chr12:40536678-40536679	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs2708460	chr12:40536689-40536690	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs551967903	chr12:40536760-40536761	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs570827523	chr12:40536826-40536827	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs192718140	chr12:40536843-40536844	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs17442742	chr12:40536845-40536846	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs530733332	chr12:40536916-40536917	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs556241885	chr12:40536936-40536937	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs183444198	chr12:40536939-40536940	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs554277048	chr12:40536973-40536974	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs146340499	chr12:40537040-40537041	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs17442749	chr12:40537046-40537047	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs572795159	chr12:40537060-40537061	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs546393053	chr12:40537089-40537090	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs12228200	chr12:40537144-40537145	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs113986209	chr12:40537163-40537164	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs2638222	chr12:40537203-40537204	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs187560355	chr12:40537377-40537378	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs7484475	chr12:40537450-40537451	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs562490600	chr12:40537460-40537461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs141954302	chr12:40537506-40537507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs7306718	chr12:40537656-40537657	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs200172435	chr12:40537705-40537706	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs75408137	chr12:40537706-40537707	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs559980511	chr12:40537718-40537719	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs2253171	chr12:40537828-40537829	Weak transcription	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs552038335	chr12:40537834-40537835	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:56)

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

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40532800-40543800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40535000-40537200	Enhancers	Hela-S3	cervix
3	chr12:40535600-40536600	Enhancers	HMEC	breast
4	chr12:40535600-40536600	Enhancers	NHEK	skin
5	chr12:40535800-40536400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:40535800-40536400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:40536000-40536600	Enhancers	Placenta Amnion	Placenta Amnion

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