Variant report

Variant	esv3379462
Chromosome Location	chr12:40539260-40541633
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	CTCF	chr12:40539620-40539770	HCT-116	colon:	n/a	n/a
2	CTCF	chr12:40539660-40539810	HPAF	blood vessel:	n/a	n/a
3	CTCF	chr12:40539740-40539890	A549	lung:	n/a	n/a
4	CTCF	chr12:40539546-40539674	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr12:40539612-40539661	MCF-7	breast:	n/a	n/a
6	CTCF	chr12:40539620-40539770	Caco-2	colon:	n/a	n/a
7	CTCF	chr12:40539700-40539850	HRE	kidney:	n/a	n/a
8	MYC	chr12:40540808-40540848	NB4	blood:	n/a	n/a
9	SPI1	chr12:40541064-40541566	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000260943	TF binding region

Extended variants
information (count: 204 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:204 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs201313685	chr12:40539269-40539270	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs71449749	chr12:40539276-40539277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs533345176	chr12:40539282-40539283	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs551498996	chr12:40539290-40539291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs570301053	chr12:40539293-40539294	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs572046223	chr12:40539298-40539299	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs180949673	chr12:40539313-40539314	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs186332458	chr12:40539326-40539327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs567509076	chr12:40539339-40539340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs534931736	chr12:40539352-40539353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs191080648	chr12:40539365-40539366	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs552884364	chr12:40539383-40539384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs181452333	chr12:40539398-40539399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs539394149	chr12:40539399-40539400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs71449750	chr12:40539402-40539403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs368081782	chr12:40539405-40539406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs557474398	chr12:40539415-40539416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs576247218	chr12:40539420-40539421	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs71449751	chr12:40539421-40539422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs17518805	chr12:40539422-40539423	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs542949087	chr12:40539430-40539431	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs113027337	chr12:40539435-40539436	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs562010960	chr12:40539441-40539442	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs573859605	chr12:40539445-40539446	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs17458752	chr12:40539447-40539448	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs17489951	chr12:40539451-40539452	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs140876311	chr12:40539457-40539458	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs71449752	chr12:40539463-40539464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs551706732	chr12:40539475-40539476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs563541302	chr12:40539507-40539508	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs71449753	chr12:40539514-40539515	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs530973484	chr12:40539531-40539532	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs549260989	chr12:40539552-40539553	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs186751292	chr12:40539587-40539588	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs534870415	chr12:40539592-40539593	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs113211197	chr12:40539648-40539649	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs546802853	chr12:40539659-40539660	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs144917126	chr12:40539677-40539678	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs147925542	chr12:40539689-40539690	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs376239858	chr12:40539693-40539694	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs200049887	chr12:40539702-40539703	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs374994717	chr12:40539703-40539704	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs28527769	chr12:40539709-40539710	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs11175324	chr12:40539711-40539712	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs28689900	chr12:40539713-40539714	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs71078214	chr12:40539714-40539715	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs372692579	chr12:40539717-40539718	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs375882922	chr12:40539723-40539724	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs200441407	chr12:40539729-40539730	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs71078215	chr12:40539730-40539731	Weak transcription	TF binding region	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:5 , 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	chr12:40540800-40541400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:40541000-40541800	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr12:40541200-40541400	Enhancers	Aorta	Aorta
5	chr12:40541400-40546600	Weak transcription	Primary monocytes fromperipheralblood	blood

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