Variant report

Variant	esv3398206
Chromosome Location	chr12:40556364-40581392
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	chr12:40561772-40562281	GM12878	blood:	n/a	n/a
2	ATF2	chr12:40561760-40562320	GM12878	blood:	n/a	n/a
3	ATF2	chr12:40562517-40563164	GM12878	blood:	n/a	n/a
4	ATF2	chr12:40562547-40563179	GM12878	blood:	n/a	n/a
5	BATF	chr12:40562763-40563054	GM12878	blood:	n/a	n/a
6	BATF	chr12:40561850-40562111	GM12878	blood:	n/a	chr12:40562020-40562031
7	BATF	chr12:40561861-40562191	GM12878	blood:	n/a	chr12:40562020-40562031
8	BATF	chr12:40562718-40563113	GM12878	blood:	n/a	n/a
9	BCL11A	chr12:40561855-40562181	GM12878	blood:	n/a	chr12:40562020-40562029 chr12:40562019-40562028
10	BCL11A	chr12:40562639-40563067	GM12878	blood:	n/a	chr12:40562817-40562826
11	BCL11A	chr12:40562744-40562991	GM12878	blood:	n/a	chr12:40562817-40562826
12	BCLAF1	chr12:40562599-40563097	GM12878	blood:	n/a	chr12:40562817-40562826
13	BHLHE40	chr12:40561787-40563459	GM12878	blood:	n/a	n/a
14	CEBPB	chr12:40565470-40565502	A549	lung:	n/a	n/a
15	CEBPB	chr12:40562546-40563162	GM12878	blood:	n/a	n/a
16	CEBPB	chr12:40564027-40564186	A549	lung:	n/a	chr12:40564105-40564116
17	CEBPB	chr12:40558987-40559278	HepG2	liver:	n/a	n/a
18	CEBPB	chr12:40558991-40559285	A549	lung:	n/a	n/a
19	CHD2	chr12:40570471-40570477	GM12878	blood:	n/a	n/a
20	CHD2	chr12:40562672-40563107	GM12878	blood:	n/a	n/a
21	CREB1	chr12:40562700-40563169	GM12878	blood:	n/a	n/a
22	CREB1	chr12:40561823-40562211	GM12878	blood:	n/a	n/a
23	CTCF	chr12:40557615-40557685	Lung_OC	lung:	n/a	n/a
24	CTCF	chr12:40562317-40562428	Spleen_OC	spleen:	n/a	n/a
25	CTCF	chr12:40568418-40568463	GM20000	blood:	n/a	n/a
26	CTCF	chr12:40577842-40577901	Kidney_OC	kidney:	n/a	n/a
27	CUX1	chr12:40561846-40562199	GM12878	blood:	n/a	chr12:40562154-40562165
28	CUX1	chr12:40562734-40563149	GM12878	blood:	n/a	n/a
29	E2F4	chr12:40567217-40567328	MCF10A-Er-Src	breast:	n/a	n/a
30	E2F4	chr12:40561249-40561449	MCF10A-Er-Src	breast:	n/a	n/a
31	EBF1	chr12:40561861-40562137	GM12878	blood:	n/a	n/a
32	EBF1	chr12:40562649-40563082	GM12878	blood:	n/a	n/a
33	EP300	chr12:40561858-40562146	GM12878	blood:	n/a	chr12:40562020-40562029 chr12:40562019-40562028 chr12:40562054-40562068
34	EP300	chr12:40562625-40563097	GM12878	blood:	n/a	chr12:40562956-40562970
35	EP300	chr12:40561844-40562232	GM12878	blood:	n/a	chr12:40562020-40562029 chr12:40562164-40562178 chr12:40562019-40562028 chr12:40562054-40562068
36	EP300	chr12:40562584-40563080	GM12878	blood:	n/a	chr12:40562956-40562970
37	EP300	chr12:40562712-40563079	GM12878	blood:	n/a	chr12:40562956-40562970
38	EP300	chr12:40561776-40562218	GM12878	blood:	n/a	chr12:40562020-40562029 chr12:40562164-40562178 chr12:40562019-40562028 chr12:40562054-40562068
39	FOS	chr12:40561956-40562156	MCF10A-Er-Src	breast:	n/a	chr12:40562020-40562029 chr12:40562020-40562028 chr12:40562019-40562028 chr12:40562020-40562027
40	FOS	chr12:40565446-40565640	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr12:40565372-40565589	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr12:40561956-40562055	MCF10A-Er-Src	breast:	n/a	chr12:40562020-40562029 chr12:40562020-40562028 chr12:40562019-40562028 chr12:40562020-40562027
43	FOS	chr12:40561916-40562126	MCF10A-Er-Src	breast:	n/a	chr12:40562020-40562029 chr12:40562020-40562028 chr12:40562019-40562028 chr12:40562020-40562027
44	FOXA1	chr12:40579631-40579900	T-47D	breast:	n/a	n/a
45	FOXA1	chr12:40579507-40579981	T-47D	breast:	n/a	n/a
46	FOXM1	chr12:40561830-40562189	GM12878	blood:	n/a	n/a
47	FOXM1	chr12:40562549-40563123	GM12878	blood:	n/a	n/a
48	GATA3	chr12:40579489-40579953	MCF-7	breast:	n/a	n/a
49	GATA3	chr12:40579498-40580051	T-47D	breast:	n/a	n/a
50	GATA3	chr12:40579572-40579935	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:125795379..125796137-chr12:40561478..40561982,2	MCF-7	breast:
2	12:40570708-40576790..12:40691796-40694737	K562	blood:
3	12:40570708-40576790..12:40703633-40711447	K562	blood:
4	12:40560427-40561510..12:40703633-40711447	GM12878	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A13-2	chr12:40579811-40579985	XLOC_010053
2	lnc-LRRK2-1	chr12:40560053-40560152	NONHSAT027720
3	lnc-LRRK2-1	chr12:40561050-40561414	XLOC_009712
4	lnc-LRRK2-1	chr12:40560054-40560152	XLOC_009712
5	lnc-LRRK2-1	chr12:40561050-40561509	XLOC_009712
6	lnc-LRRK2-1	chr12:40561049-40561678	NONHSAT027720

Variant related genes	Relation type
ENSG00000223914	TF binding region
ENSG00000188906	chromatin interactions
SDCBP	miRNA target sites
NR3C1	miRNA target sites

Extended variants
information (count: 814 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:814 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs552605408	chr12:40556386-40556387	ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs571115047	chr12:40556400-40556401	ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs532031595	chr12:40556413-40556414	ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs374322384	chr12:40556458-40556459	ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs184854127	chr12:40556483-40556484	ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs568538378	chr12:40556499-40556500	ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs536080792	chr12:40556520-40556521	ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs116730162	chr12:40556568-40556569	ZNF genes & repeats Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs376153767	chr12:40556599-40556600	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs11175401	chr12:40556601-40556602	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs188605243	chr12:40556611-40556612	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs558121921	chr12:40556621-40556622	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs576477612	chr12:40556650-40556651	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs192963470	chr12:40556702-40556703	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs184767466	chr12:40556705-40556706	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs189637182	chr12:40556767-40556768	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs150087671	chr12:40556848-40556849	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs374532384	chr12:40556850-40556851	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs138549653	chr12:40556854-40556855	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs180692697	chr12:40556859-40556860	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs2708473	chr12:40556860-40556861	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs531758715	chr12:40556892-40556893	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs550191905	chr12:40556901-40556902	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs376529297	chr12:40556966-40556967	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs371088760	chr12:40556967-40556968	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs71078219	chr12:40556968-40556969	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs200803347	chr12:40556978-40556979	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs568750688	chr12:40557001-40557002	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs7358699	chr12:40557035-40557036	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs73267627	chr12:40557124-40557125	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs547594305	chr12:40557161-40557162	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs111831356	chr12:40557210-40557211	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs2708474	chr12:40557238-40557239	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs533640104	chr12:40557294-40557295	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs112270295	chr12:40557330-40557331	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs2708475	chr12:40557334-40557335	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs141620147	chr12:40557342-40557343	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs181897916	chr12:40557347-40557348	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs79553162	chr12:40557355-40557356	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs368020222	chr12:40557366-40557367	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs553997774	chr12:40557389-40557390	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs569505541	chr12:40557424-40557425	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs191743662	chr12:40557469-40557470	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs546296741	chr12:40557504-40557505	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs75711313	chr12:40557539-40557540	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs386376246	chr12:40557552-40557553	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs60934970	chr12:40557553-40557554	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs564603712	chr12:40557557-40557558	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs531573183	chr12:40557559-40557560	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs543821026	chr12:40557563-40557564	ZNF genes & repeats Weak transcription	n/a	n/a	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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40547200-40558600	Weak transcription	Liver	Liver
2	chr12:40556200-40557400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:40556400-40557600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:40557400-40564600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:40558600-40559400	Enhancers	Liver	Liver
6	chr12:40561800-40562000	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr12:40561800-40563200	Enhancers	Primary B cells from cord blood	blood
8	chr12:40562000-40562200	Enhancers	GM12878-XiMat	blood
9	chr12:40562000-40562600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:40562000-40563000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr12:40562000-40563000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr12:40562000-40563200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:40562200-40562400	Flanking Active TSS	GM12878-XiMat	blood
14	chr12:40562200-40562600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr12:40562200-40562600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:40562200-40562800	Enhancers	Primary B cells from peripheral blood	blood
17	chr12:40562200-40563000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:40562400-40562600	Enhancers	GM12878-XiMat	blood
19	chr12:40562400-40562800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:40562400-40563000	Enhancers	Primary T cells from cord blood	blood
21	chr12:40562600-40562800	Flanking Active TSS	GM12878-XiMat	blood
22	chr12:40562600-40563000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr12:40562800-40564400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:40562800-40565600	Enhancers	GM12878-XiMat	blood
25	chr12:40563000-40564400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:40563000-40564400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:40563200-40564600	Weak transcription	Primary B cells from cord blood	blood
28	chr12:40564400-40564800	Enhancers	Primary B cells from peripheral blood	blood
29	chr12:40564400-40565200	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr12:40564400-40566600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr12:40564600-40564800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:40564600-40564800	Enhancers	Primary B cells from cord blood	blood
33	chr12:40564600-40566200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:40564800-40565200	Weak transcription	Primary B cells from cord blood	blood
35	chr12:40565200-40565600	Enhancers	Primary B cells from cord blood	blood
36	chr12:40565200-40565800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr12:40565800-40566400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr12:40566400-40568800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:40566600-40568800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr12:40568800-40569200	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr12:40568800-40569400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr12:40571200-40571600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:40575200-40575800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr12:40575200-40575800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr12:40575200-40575800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:40575200-40575800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr12:40575200-40576000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:40575200-40576000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:40575200-40576000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr12:40575200-40576000	Enhancers	HUVEC	blood vessel

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