Variant report

Variant	esv3350575
Chromosome Location	chr1:185580344-185614213
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	ATF1	chr1:185613768-185613774	K562	blood:	n/a	n/a
2	ATF2	chr1:185605765-185606613	GM12878	blood:	n/a	n/a
3	ATF2	chr1:185605815-185606537	GM12878	blood:	n/a	n/a
4	BATF	chr1:185605891-185606537	GM12878	blood:	n/a	n/a
5	BATF	chr1:185605962-185606403	GM12878	blood:	n/a	n/a
6	BCL11A	chr1:185606043-185606300	GM12878	blood:	n/a	n/a
7	BCL11A	chr1:185605910-185606453	GM12878	blood:	n/a	n/a
8	BCL3	chr1:185605988-185606319	GM12878	blood:	n/a	n/a
9	BCL3	chr1:185605972-185606348	GM12878	blood:	n/a	n/a
10	BCLAF1	chr1:185605861-185606467	GM12878	blood:	n/a	n/a
11	BCLAF1	chr1:185605835-185606338	GM12878	blood:	n/a	n/a
12	BHLHE40	chr1:185605941-185606390	GM12878	blood:	n/a	n/a
13	CEBPB	chr1:185580123-185580478	Hela-S3	cervix:	n/a	chr1:185580286-185580299 chr1:185580286-185580299 chr1:185580286-185580297 chr1:185580286-185580299
14	CEBPB	chr1:185614212-185614571	MCF-7	breast:	n/a	n/a
15	CEBPB	chr1:185580123-185580481	IMR90	lung:	n/a	chr1:185580286-185580299 chr1:185580286-185580299 chr1:185580286-185580297 chr1:185580286-185580299
16	CEBPB	chr1:185614171-185614497	IMR90	lung:	n/a	n/a
17	CEBPB	chr1:185613567-185614941	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr1:185605858-185606430	GM12878	blood:	n/a	n/a
19	CEBPB	chr1:185606030-185606304	GM12878	blood:	n/a	n/a
20	CEBPB	chr1:185586138-185586203	A549	lung:	n/a	n/a
21	CEBPB	chr1:185580054-185580554	A549	lung:	n/a	chr1:185580286-185580299 chr1:185580286-185580299 chr1:185580286-185580297 chr1:185580286-185580299
22	CEBPB	chr1:185614197-185614488	H1-hESC	embryonic stem cell:	n/a	n/a
23	CEBPB	chr1:185614082-185614773	MCF-7	breast:	n/a	n/a
24	CEBPB	chr1:185580133-185580474	K562	blood:	n/a	chr1:185580286-185580299 chr1:185580286-185580299 chr1:185580286-185580297 chr1:185580286-185580299
25	CEBPB	chr1:185580150-185580470	HepG2	liver:	n/a	chr1:185580286-185580299 chr1:185580286-185580299 chr1:185580286-185580297 chr1:185580286-185580299
26	CEBPB	chr1:185585997-185586235	IMR90	lung:	n/a	n/a
27	CEBPB	chr1:185580130-185580473	A549	lung:	n/a	chr1:185580286-185580299 chr1:185580286-185580299 chr1:185580286-185580297 chr1:185580286-185580299
28	CHD1	chr1:185605520-185605720	GM12878	blood:	n/a	n/a
29	CHD2	chr1:185605980-185606392	GM12878	blood:	n/a	n/a
30	CREB1	chr1:185605752-185606452	GM12878	blood:	n/a	n/a
31	CREB1	chr1:185605851-185606406	GM12878	blood:	n/a	n/a
32	CTCF	chr1:185604040-185604190	GM12874	blood:	n/a	n/a
33	CTCF	chr1:185603458-185603555	Fibrobl	skin:	n/a	n/a
34	CTCF	chr1:185606148-185606277	GM12878	blood:	n/a	n/a
35	CUX1	chr1:185606146-185606508	GM12878	blood:	n/a	n/a
36	CUX1	chr1:185605584-185605683	GM12878	blood:	n/a	n/a
37	CUX1	chr1:185594214-185594262	GM12878	blood:	n/a	n/a
38	E2F4	chr1:185601933-185602133	MCF10A-Er-Src	breast:	n/a	n/a
39	EBF1	chr1:185605980-185606441	GM12878	blood:	n/a	n/a
40	EBF1	chr1:185606002-185606382	GM12878	blood:	n/a	n/a
41	EBF1	chr1:185606017-185606382	GM12878	blood:	n/a	n/a
42	EGR1	chr1:185606025-185606291	GM12878	blood:	n/a	n/a
43	EGR1	chr1:185606079-185606238	GM12878	blood:	n/a	n/a
44	ELF1	chr1:185605860-185606508	GM12878	blood:	n/a	n/a
45	ELK1	chr1:185606150-185606330	GM12878	blood:	n/a	n/a
46	EP300	chr1:185605960-185606482	GM12878	blood:	n/a	n/a
47	EP300	chr1:185605890-185606376	GM12878	blood:	n/a	n/a
48	EP300	chr1:185605878-185606430	GM12878	blood:	n/a	n/a
49	EP300	chr1:185613756-185614796	Hela-S3	cervix:	n/a	n/a
50	EP300	chr1:185605974-185606290	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:121485050..121485934-chr1:185593425..185594410,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IVNS1ABP-2	chr1:185595624-185595687	XLOC_001126
2	lnc-IVNS1ABP-2	chr1:185595624-185595687	XLOC_001126
3	lnc-IVNS1ABP-2	chr1:185591745-185591971	XLOC_001126
4	lnc-IVNS1ABP-2	chr1:185595624-185595687	XLOC_001126
5	lnc-IVNS1ABP-2	chr1:185597539-185597648	XLOC_001126
6	lnc-IVNS1ABP-2	chr1:185595624-185595687	XLOC_001126
7	lnc-SWT1-5	chr1:185595470-185596078	NONHSAT008420
8	lnc-IVNS1ABP-2	chr1:185597539-185597648	XLOC_001126
9	lnc-IVNS1ABP-2	chr1:185595624-185595687	XLOC_001126
10	lnc-IVNS1ABP-2	chr1:185597539-185597659	XLOC_001126
11	lnc-IVNS1ABP-2	chr1:185591859-185591914	XLOC_001126
12	lnc-IVNS1ABP-2	chr1:185595624-185595687	XLOC_001126
13	lnc-IVNS1ABP-2	chr1:185597539-185597648	XLOC_001126
14	lnc-IVNS1ABP-2	chr1:185597539-185597648	XLOC_001126
15	lnc-IVNS1ABP-2	chr1:185597539-185597620	XLOC_001126
16	lnc-HMCN1-2	chr1:185590089-185590112	XLOC_000495
17	lnc-IVNS1ABP-2	chr1:185591859-185591971	XLOC_001126
18	lnc-IVNS1ABP-2	chr1:185590593-185590718	XLOC_001126
19	lnc-IVNS1ABP-2	chr1:185590593-185590718	XLOC_001126

Variant related genes	Relation type
ENSG00000207108	TF binding region
ENSG00000201596	TF binding region
ENSG00000228309	TF binding region
MTMR9	miRNA target sites
FOXJ3	miRNA target sites
PLEKHA1	miRNA target sites
MBNL2	miRNA target sites
WEE1	miRNA target sites
LIN28B	miRNA target sites
SPG20	miRNA target sites
ARHGAP12	miRNA target sites
VEGFA	miRNA target sites
GPR137C	miRNA target sites

Extended variants
information (count: 1466 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:1466 , 50 per page) page: 1 2 3 4 5 6 7 ... 30

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs565148597	chr1:185580358-185580359	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs532552541	chr1:185580380-185580381	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs181044359	chr1:185580435-185580436	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs185465604	chr1:185580447-185580448	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs370858053	chr1:185580529-185580530	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs548227871	chr1:185580540-185580541	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs59772563	chr1:185580554-185580555	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs534088032	chr1:185580569-185580570	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs558841033	chr1:185580616-185580617	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs190951501	chr1:185580646-185580647	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs142222350	chr1:185580672-185580673	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs537634399	chr1:185580727-185580728	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs566331790	chr1:185580769-185580770	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs76227946	chr1:185580823-185580824	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs12081525	chr1:185580932-185580933	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs4651281	chr1:185580951-185580952	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs150472643	chr1:185580956-185580957	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs375350157	chr1:185580965-185580966	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs554560297	chr1:185580973-185580974	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs572863124	chr1:185580978-185580979	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs146399500	chr1:185580979-185580980	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs565438958	chr1:185580990-185580991	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs373651235	chr1:185581007-185581008	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs532784844	chr1:185581035-185581036	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs57929036	chr1:185581038-185581039	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs187323427	chr1:185581050-185581051	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs192175136	chr1:185581065-185581066	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs183501180	chr1:185581081-185581082	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs187387866	chr1:185581096-185581097	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs59739768	chr1:185581131-185581132	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs74901446	chr1:185581171-185581172	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs139478592	chr1:185581212-185581213	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs114003772	chr1:185581222-185581223	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs11811612	chr1:185581225-185581226	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs191787579	chr1:185581248-185581249	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs182835554	chr1:185581253-185581254	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs58210626	chr1:185581263-185581264	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs553756433	chr1:185581325-185581326	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs142773834	chr1:185581327-185581328	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs572940578	chr1:185581351-185581352	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs540227154	chr1:185581358-185581359	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs10911762	chr1:185581395-185581396	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs577485716	chr1:185581411-185581412	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs544864342	chr1:185581437-185581438	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs577501678	chr1:185581474-185581475	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs199930791	chr1:185581509-185581510	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs562946020	chr1:185581517-185581518	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs187122845	chr1:185581528-185581529	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs115053291	chr1:185581553-185581554	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs537354746	chr1:185581564-185581565	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Glioblastoma multiforme	17369134	CNVD
Cancer	17440070	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Metanephric adenoma	20802469	CNVD
Renal cell carcinoma	18765545	CNVD
Nephroblastoma	17189400	CNVD
Melanoma	20688739	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21611746	CNVD
Myelofibrosis	22110671	CNVD
primary effusion lymphomas	17116491	CNVD
Breast cancer	17393978	CNVD
Barrett''s syndrome	19417022	CNVD
Schizophrenia	19197363	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:136 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185580000-185581800	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr1:185580200-185580600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr1:185582000-185588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:185588000-185588400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:185588400-185601400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:185593000-185593200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:185593200-185594600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:185593800-185596000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:185593800-185596000	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:185594000-185595000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:185594000-185596600	Enhancers	Placenta	Placenta
12	chr1:185594200-185594800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:185594200-185594800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:185594200-185595000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:185594600-185595400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr1:185594800-185596400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:185595000-185597000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:185595400-185597000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:185596200-185597600	Enhancers	Fetal Brain Male	brain
20	chr1:185596400-185601800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:185596600-185601600	Weak transcription	Placenta	Placenta
22	chr1:185597000-185597600	Enhancers	Fetal Lung	lung
23	chr1:185597000-185597800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:185597000-185598000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:185597600-185597800	Enhancers	H9 Cell Line	embryonic stem cell
26	chr1:185597800-185600800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:185598000-185599200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr1:185598200-185598600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr1:185598600-185601400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:185599200-185601200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:185600800-185602200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:185601000-185602600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:185601200-185602200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr1:185601200-185603400	Enhancers	HMEC	breast
35	chr1:185601200-185603800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:185601400-185602000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr1:185601400-185602600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:185601400-185603000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:185601400-185603000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:185601600-185602800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:185601600-185603600	Enhancers	Placenta	Placenta
42	chr1:185601800-185602000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:185601800-185602200	Enhancers	HSMMtube	muscle
44	chr1:185601800-185602600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:185601800-185602800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:185601800-185602800	Enhancers	Primary B cells from cord blood	blood
47	chr1:185602000-185602600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:185602000-185602600	Enhancers	NHEK	skin
49	chr1:185602000-185602800	Enhancers	Primary B cells from peripheral blood	blood
50	chr1:185602000-185603000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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