Variant report

Variant	esv3351748
Chromosome Location	chr12:40905885-40909783
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	chr12:40908726-40909128	GM12878	blood:	n/a	n/a
2	ATF2	chr12:40908630-40909221	GM12878	blood:	n/a	n/a
3	BATF	chr12:40908736-40909168	GM12878	blood:	n/a	n/a
4	BCL3	chr12:40908726-40909151	GM12878	blood:	n/a	chr12:40909008-40909017
5	EBF1	chr12:40908877-40909077	GM12878	blood:	n/a	n/a
6	EP300	chr12:40908979-40909091	GM12878	blood:	n/a	n/a
7	FOXM1	chr12:40908723-40909229	GM12878	blood:	n/a	n/a
8	GATA3	chr12:40907380-40907518	SH-SY5Y	brain:	n/a	n/a
9	IKZF1	chr12:40908802-40909562	GM12878	blood:	n/a	n/a
10	IRF4	chr12:40908732-40909220	GM12878	blood:	n/a	chr12:40909006-40909020
11	MEF2A	chr12:40908641-40909112	GM12878	blood:	n/a	n/a
12	NFATC1	chr12:40908747-40909190	GM12878	blood:	n/a	n/a
13	NFIC	chr12:40908578-40909672	GM12878	blood:	n/a	n/a
14	NFIC	chr12:40908686-40909278	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:40909127-40909689	HL-60	blood:	n/a	n/a
16	POLR2A	chr12:40908152-40908329	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr12:40907816-40907819	MCF10A-Er-Src	breast:	n/a	n/a
18	RAD21	chr12:40909316-40909527	GM12878	blood:	n/a	n/a
19	RCOR1	chr12:40909264-40909285	GM12878	blood:	n/a	n/a
20	RFX5	chr12:40907502-40907608	GM12878	blood:	n/a	n/a
21	RUNX3	chr12:40908708-40909585	GM12878	blood:	n/a	n/a
22	RUNX3	chr12:40908578-40909613	GM12878	blood:	n/a	n/a
23	SMC3	chr12:40908923-40909005	GM12878	blood:	n/a	n/a
24	SPI1	chr12:40909049-40909750	GM12878	blood:	n/a	chr12:40909420-40909427
25	SPI1	chr12:40909197-40909634	HL-60	blood:	n/a	chr12:40909420-40909427
26	SPI1	chr12:40909183-40909613	GM12891	blood:	n/a	chr12:40909420-40909427
27	SPI1	chr12:40909329-40909523	GM12878	blood:	n/a	chr12:40909420-40909427
28	SPI1	chr12:40909118-40909756	HL-60	blood:	n/a	chr12:40909420-40909427
29	SPI1	chr12:40909285-40909547	GM12878	blood:	n/a	chr12:40909420-40909427
30	SPI1	chr12:40909256-40909560	GM12891	blood:	n/a	chr12:40909420-40909427
31	TBL1XR1	chr12:40909042-40909053	GM12878	blood:	n/a	n/a
32	UBTF	chr12:40907485-40907534	K562	blood:	n/a	n/a
33	WRNIP1	chr12:40908918-40908932	GM12878	blood:	n/a	n/a
34	ZNF143	chr12:40908423-40908429	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40882994..40885029-chr12:40904694..40907438,2	K562	blood:
2	chr12:40902352..40904327-chr12:40904757..40907254,2	K562	blood:

Variant related genes	Relation type
MUC19	TF binding region

Extended variants
information (count: 358 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:358 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs530666854	chr12:40905911-40905912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs143329232	chr12:40905925-40905926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs548893974	chr12:40905975-40905976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs192318184	chr12:40905990-40905991	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs570930404	chr12:40906004-40906005	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs59095251	chr12:40906005-40906006	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs11307440	chr12:40906046-40906047	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs77866141	chr12:40906073-40906074	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs200872246	chr12:40906087-40906088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs200677561	chr12:40906096-40906097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs369303711	chr12:40906138-40906139	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs146729410	chr12:40906179-40906180	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs184158420	chr12:40906190-40906191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs539348707	chr12:40906210-40906211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs111510971	chr12:40906219-40906220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs557640522	chr12:40906221-40906222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs113831664	chr12:40906222-40906223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs189963326	chr12:40906246-40906247	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs192259828	chr12:40906265-40906266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs184546221	chr12:40906271-40906272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs4768283	chr12:40906287-40906288	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs562558632	chr12:40906288-40906289	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs5797674	chr12:40906328-40906329	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs374544899	chr12:40906373-40906374	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs190281724	chr12:40906415-40906416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs139352204	chr12:40906432-40906433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs181896368	chr12:40906449-40906450	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs540735670	chr12:40906528-40906529	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs552560578	chr12:40906529-40906530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs577173640	chr12:40906544-40906545	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs544604301	chr12:40906561-40906562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs563281864	chr12:40906636-40906637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs142666497	chr12:40906650-40906651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs115088416	chr12:40906672-40906673	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs151018653	chr12:40906706-40906707	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs374614892	chr12:40906726-40906727	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs140916172	chr12:40906756-40906757	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs560889087	chr12:40906759-40906760	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs185716557	chr12:40906773-40906774	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs188892773	chr12:40906778-40906779	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs150198534	chr12:40906788-40906789	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs113309005	chr12:40906799-40906800	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs550978724	chr12:40906818-40906819	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs569599868	chr12:40906867-40906868	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs562604664	chr12:40906869-40906870	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs375722458	chr12:40906895-40906896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs200701638	chr12:40906911-40906912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs555160726	chr12:40906959-40906960	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs566913432	chr12:40906977-40906978	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs56778408	chr12:40906994-40906995	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:58)

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
Pancreatic cancer	17952125	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40894800-40908600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40905800-40908000	Weak transcription	GM12878-XiMat	blood
3	chr12:40906800-40908000	Weak transcription	HMEC	breast
4	chr12:40907800-40908400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
5	chr12:40908000-40909800	Enhancers	GM12878-XiMat	blood
6	chr12:40908000-40910400	Enhancers	HMEC	breast
7	chr12:40908200-40910200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr12:40908400-40910200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr12:40908400-40910800	Enhancers	Dnd41	blood
10	chr12:40908600-40910000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr12:40908600-40910000	Enhancers	NHEK	skin
12	chr12:40908600-40910400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:40908800-40909800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:40908800-40909800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr12:40908800-40910000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:40908800-40910000	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:40909000-40909600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:40909000-40910200	Enhancers	Colon Smooth Muscle	Colon
19	chr12:40909400-40909800	Enhancers	Fetal Thymus	thymus
20	chr12:40909400-40911800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:40909600-40910000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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