Variant report

Variant	nsv528440
Chromosome Location	chr1:56412081-56420193
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	CEBPB	chr1:56413288-56413390	HepG2	liver:	n/a	chr1:56413334-56413345
2	CEBPB	chr1:56413125-56413530	Hela-S3	cervix:	n/a	chr1:56413334-56413345
3	CTCF	chr1:56417200-56417350	GM12801	blood:	n/a	n/a
4	E2F4	chr1:56414714-56414993	MCF10A-Er-Src	breast:	n/a	n/a
5	E2F4	chr1:56413901-56413919	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr1:56413167-56413451	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr1:56414220-56414330	SH-SY5Y	brain:	n/a	n/a
8	POLR2A	chr1:56419116-56419149	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:56419583-56419829	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr1:56415331-56415421	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKAA2-6	chr1:56415505-56415792	NONHSAT003429
2	lnc-PRKAA2-6	chr1:56415506-56415792	XLOC_000209

Variant related genes	Relation type
ENSG00000230250	TF binding region

Extended variants
information (count: 345 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:345 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12081053	chr1:56412081-56412082	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs6656718	chr1:56412089-56412090	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs564487400	chr1:56412166-56412167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs533424731	chr1:56412170-56412171	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs550414841	chr1:56412178-56412179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs61777621	chr1:56412220-56412221	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs74434474	chr1:56412251-56412252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs181111143	chr1:56412302-56412303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs142370420	chr1:56412306-56412307	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs535063981	chr1:56412354-56412355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs551775602	chr1:56412363-56412364	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs559335332	chr1:56412366-56412367	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs570792000	chr1:56412415-56412416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571079593	chr1:56412431-56412432	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs150525969	chr1:56412518-56412519	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs576163040	chr1:56412610-56412611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs185344037	chr1:56412617-56412618	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs555084151	chr1:56412624-56412625	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs139512875	chr1:56412666-56412667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs540653910	chr1:56412687-56412688	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs189709349	chr1:56412712-56412713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs6660039	chr1:56412729-56412730	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs543761577	chr1:56412747-56412748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs181985636	chr1:56412789-56412790	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs562008500	chr1:56412791-56412792	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs545135981	chr1:56412793-56412794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs529500931	chr1:56412827-56412828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs186367702	chr1:56412845-56412846	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs11448683	chr1:56412864-56412865	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs397774493	chr1:56412871-56412872	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs398102732	chr1:56412872-56412873	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs563037102	chr1:56412897-56412898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs191715569	chr1:56412934-56412935	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs183611266	chr1:56412953-56412954	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs186520697	chr1:56412989-56412990	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs571692528	chr1:56412994-56412995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs78998732	chr1:56413026-56413027	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs562785923	chr1:56413027-56413028	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs75964560	chr1:56413117-56413118	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs34702909	chr1:56413125-56413126	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs535337939	chr1:56413154-56413155	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs72906393	chr1:56413185-56413186	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs6662998	chr1:56413260-56413261	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
44	rs55689401	chr1:56413269-56413270	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs557383630	chr1:56413305-56413306	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs72906399	chr1:56413337-56413338	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs75192525	chr1:56413372-56413373	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs149703104	chr1:56413380-56413381	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs574251574	chr1:56413385-56413386	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs12758651	chr1:56413408-56413409	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	mRNA abundance

Variant related diseases (count:92)

Disease	PMID	Source
Papillary thyroid carcinoma	21436994	CNVD
Adenoid cystic carcinoma	18698036	CNVD
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
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
Prostate cancer	18632612	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Meckel-Gruber syndrome	21572526	CNVD
Breast cancer	16620391	CNVD
Multiple myeloma	16616336	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	19490664	CNVD
Glioblastoma multiforme	22286061	CNVD
Ovarian cancer	21720365	CNVD

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56402000-56416800	Weak transcription	Aorta	Aorta
2	chr1:56404600-56416200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:56410600-56418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:56413000-56413800	Enhancers	Dnd41	blood
5	chr1:56413200-56413800	Enhancers	Hela-S3	cervix
6	chr1:56416200-56418200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:56416400-56417400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:56416400-56417600	Enhancers	NHDF-Ad	bronchial
9	chr1:56416800-56417200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:56416800-56417200	Enhancers	Aorta	Aorta
11	chr1:56416800-56417400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:56417200-56418600	Weak transcription	Aorta	Aorta
13	chr1:56417200-56420600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:56417400-56420400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:56417400-56420600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:56417600-56419400	Weak transcription	NHDF-Ad	bronchial
17	chr1:56418200-56419600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:56418600-56419400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:56419200-56419400	ZNF genes & repeats	Aorta	Aorta
20	chr1:56419400-56421400	Enhancers	NHDF-Ad	bronchial
21	chr1:56419400-56425200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:56419600-56421400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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