Variant report

Variant	esv2763567
Chromosome Location	chr1:80555664-80596899
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	chr1:80579439-80579499	K562	blood:	n/a	n/a
2	CBX3	chr1:80576699-80576922	K562	blood:	n/a	n/a
3	CBX3	chr1:80576645-80576941	K562	blood:	n/a	n/a
4	CEBPB	chr1:80572688-80572902	IMR90	lung:	n/a	n/a
5	CEBPB	chr1:80578715-80578978	K562	blood:	n/a	n/a
6	CEBPB	chr1:80578699-80578996	IMR90	lung:	n/a	n/a
7	CEBPB	chr1:80578688-80579006	HepG2	liver:	n/a	n/a
8	CEBPB	chr1:80555874-80556156	IMR90	lung:	n/a	chr1:80555985-80555998 chr1:80555986-80555997
9	CEBPB	chr1:80578708-80578995	A549	lung:	n/a	n/a
10	CEBPB	chr1:80555874-80556123	HepG2	liver:	n/a	chr1:80555985-80555998 chr1:80555986-80555997
11	CTCF	chr1:80593120-80593270	HEK293	kidney:	n/a	n/a
12	CTCF	chr1:80581508-80581584	Fibrobl	skin:	n/a	n/a
13	CTCF	chr1:80593173-80593290	GM12878	blood:	n/a	n/a
14	CTCF	chr1:80593189-80593282	GM19239	blood:	n/a	n/a
15	CTCF	chr1:80593195-80593286	GM12892	blood:	n/a	n/a
16	CTCF	chr1:80593060-80593210	RPTEC	kidney:	n/a	n/a
17	CTCF	chr1:80593208-80593293	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:80593180-80593330	BE2_C	brain:	n/a	n/a
19	CTCF	chr1:80580987-80581042	LNCaP	prostate:	n/a	n/a
20	CTCF	chr1:80593140-80593290	GM12872	blood:	n/a	n/a
21	CTCF	chr1:80593160-80593310	WERI-Rb-1	eye:	n/a	n/a
22	CTCF	chr1:80570240-80570390	GM12869	blood:	n/a	n/a
23	CTCF	chr1:80593216-80593267	Gliobla	brain:	n/a	n/a
24	CTCF	chr1:80593080-80593230	GM12872	blood:	n/a	n/a
25	CTCF	chr1:80583020-80583033	LNCaP	prostate:	n/a	n/a
26	CUX1	chr1:80560706-80560736	GM12878	blood:	n/a	n/a
27	EP300	chr1:80596371-80596942	MCF-7	breast:	n/a	n/a
28	FOS	chr1:80586769-80587018	HUVEC	blood vessel:	n/a	chr1:80586881-80586892 chr1:80586883-80586890 chr1:80586882-80586891 chr1:80586883-80586891
29	FOXA1	chr1:80596486-80596842	T-47D	breast:	n/a	n/a
30	GATA3	chr1:80596252-80596994	MCF-7	breast:	n/a	n/a
31	GATA3	chr1:80579624-80579765	SH-SY5Y	brain:	n/a	n/a
32	GATA3	chr1:80596362-80596890	MCF-7	breast:	n/a	n/a
33	GATA3	chr1:80596383-80596846	T-47D	breast:	n/a	n/a
34	GATA3	chr1:80596193-80597045	MCF-7	breast:	n/a	n/a
35	GATA3	chr1:80596410-80596849	T-47D	breast:	n/a	n/a
36	GATA3	chr1:80565889-80565993	SH-SY5Y	brain:	n/a	n/a
37	GATA3	chr1:80596269-80596951	MCF-7	breast:	n/a	n/a
38	JUN	chr1:80561090-80561169	K562	blood:	n/a	n/a
39	JUND	chr1:80568437-80568702	HepG2	liver:	n/a	chr1:80568546-80568557
40	JUND	chr1:80578797-80578999	HepG2	liver:	n/a	n/a
41	JUND	chr1:80596529-80596877	MCF-7	breast:	n/a	n/a
42	KAP1	chr1:80566842-80567288	U2OS	brain:	n/a	n/a
43	KAP1	chr1:80566861-80567327	HEK293	kidney:	n/a	n/a
44	KAP1	chr1:80576498-80577031	HEK293	kidney:	n/a	n/a
45	KAP1	chr1:80576468-80576886	K562	blood:	n/a	n/a
46	MAFK	chr1:80571652-80571926	HepG2	liver:	n/a	chr1:80571780-80571800 chr1:80571789-80571800 chr1:80571782-80571798
47	MAFK	chr1:80595677-80595748	HepG2	liver:	n/a	n/a
48	MAFK	chr1:80571747-80571928	HepG2	liver:	n/a	chr1:80571780-80571800 chr1:80571789-80571800 chr1:80571782-80571798
49	MAFK	chr1:80571653-80571886	IMR90	lung:	n/a	chr1:80571780-80571800 chr1:80571789-80571800 chr1:80571782-80571798
50	NFYA	chr1:80566902-80567024	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:80568623..80571326-chr1:80577304..80579523,2	K562	blood:
2	chr1:80568623..80571326-chr1:80577304..80579523,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LPHN2-3	chr1:80580628-80582603	ENSG00000260322.1
2	lnc-ELTD1-11	chr1:80557788-80558922	NONHSAT004104

Variant related genes	Relation type
ENSG00000235756	TF binding region
ENSG00000260322	TF binding region

Extended variants
information (count: 499 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:499 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs139687959	chr1:80557793-80557794	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs145285045	chr1:80557818-80557819	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs549603389	chr1:80557821-80557822	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs187915918	chr1:80557822-80557823	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs542844579	chr1:80557839-80557840	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs560919691	chr1:80557868-80557869	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs528250955	chr1:80557895-80557896	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs114287900	chr1:80557900-80557901	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs541259292	chr1:80557934-80557935	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs532175631	chr1:80557935-80557936	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs550580546	chr1:80557949-80557950	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs570368796	chr1:80557964-80557965	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs564427594	chr1:80557970-80557971	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs549605633	chr1:80557976-80557977	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs567772279	chr1:80558048-80558049	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs535183615	chr1:80558093-80558094	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs553072000	chr1:80558130-80558131	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs115448432	chr1:80558201-80558202	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs58749981	chr1:80558215-80558216	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs193249774	chr1:80558257-80558258	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs11162920	chr1:80558259-80558260	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs542569186	chr1:80558278-80558279	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs116197394	chr1:80558329-80558330	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs12094648	chr1:80558382-80558383	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs367828789	chr1:80558391-80558392	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs34266545	chr1:80558401-80558402	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs182676124	chr1:80558433-80558434	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs552962729	chr1:80558459-80558460	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs573177477	chr1:80558483-80558484	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs187799566	chr1:80558587-80558588	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs147650544	chr1:80558590-80558591	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs192733431	chr1:80558627-80558628	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs577964186	chr1:80558637-80558638	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs541754498	chr1:80558690-80558691	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs528688568	chr1:80558728-80558729	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs546773828	chr1:80558778-80558779	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs571446496	chr1:80558780-80558781	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs538741533	chr1:80558785-80558786	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs4131985	chr1:80558788-80558789	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs569177102	chr1:80558799-80558800	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs200109676	chr1:80558810-80558811	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs397801040	chr1:80558816-80558817	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs200604341	chr1:80558817-80558818	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs141952773	chr1:80558879-80558880	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs554596680	chr1:80558888-80558889	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs149679061	chr1:80558907-80558908	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs534020978	chr1:80558918-80558919	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs565483426	chr1:80558920-80558921	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs530209424	chr1:80560107-80560108	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs548348739	chr1:80560178-80560179	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:100)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	17133270	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Ewing''s sarcoma	17952124	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Poland''s syndrome	22110015	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma multiforme	21922591	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Cancer	22429812	CNVD
Effusion lymphoma	18079361	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
small cell lung cancer	20016488	CNVD
Colorectal cancer	16774939	CNVD
Pancreatic endocrine tumor	17639061	CNVD

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:80563600-80568800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:80564600-80565600	Enhancers	Liver	Liver
3	chr1:80565600-80566000	Flanking Active TSS	Liver	Liver
4	chr1:80566000-80566200	Enhancers	Liver	Liver
5	chr1:80577800-80578400	Weak transcription	Liver	Liver
6	chr1:80578600-80579000	Enhancers	Liver	Liver
7	chr1:80579000-80579200	Flanking Active TSS	Liver	Liver
8	chr1:80579200-80579400	Enhancers	Liver	Liver
9	chr1:80579400-80579600	Flanking Active TSS	Liver	Liver
10	chr1:80579600-80580200	Enhancers	Liver	Liver

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