Variant report

Variant	nsv1015344
Chromosome Location	chr5:28986059-29062414
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	ARID3A	chr5:28990432-28990436	K562	blood:	n/a	n/a
2	ATF1	chr5:29005496-29006030	K562	blood:	n/a	n/a
3	CCNT2	chr5:29017623-29017823	K562	blood:	n/a	n/a
4	CCNT2	chr5:29051731-29051997	K562	blood:	n/a	chr5:29051832-29051852
5	CEBPB	chr5:29005648-29005964	A549	lung:	n/a	chr5:29005787-29005798
6	CEBPB	chr5:29040534-29040845	A549	lung:	n/a	chr5:29040710-29040721
7	CEBPB	chr5:28996802-28996842	K562	blood:	n/a	n/a
8	CEBPB	chr5:29040539-29040883	HepG2	liver:	n/a	chr5:29040710-29040721
9	CEBPB	chr5:29005633-29005968	IMR90	lung:	n/a	chr5:29005787-29005798
10	CEBPB	chr5:29040539-29040883	IMR90	lung:	n/a	chr5:29040710-29040721
11	CEBPB	chr5:29005532-29005991	Hela-S3	cervix:	n/a	chr5:29005787-29005798
12	CEBPB	chr5:28996799-28997003	HepG2	liver:	n/a	n/a
13	CEBPB	chr5:29025866-29026131	HepG2	liver:	n/a	chr5:29026021-29026032
14	CEBPB	chr5:29037785-29038205	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr5:29005619-29005973	HepG2	liver:	n/a	chr5:29005787-29005798
16	CEBPB	chr5:28996795-28996999	A549	lung:	n/a	n/a
17	CEBPB	chr5:29005612-29005970	K562	blood:	n/a	chr5:29005787-29005798
18	CEBPB	chr5:29040551-29040876	K562	blood:	n/a	chr5:29040710-29040721
19	CEBPB	chr5:28996805-28996847	Hela-S3	cervix:	n/a	n/a
20	CHD1	chr5:29048762-29048773	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr5:29001860-29002010	Caco-2	colon:	n/a	n/a
22	CTCF	chr5:29021060-29021210	NHEK	skin:	n/a	n/a
23	CTCF	chr5:29024764-29024789	GM13976	blood:	n/a	n/a
24	CTCF	chr5:29005558-29005604	H1-hESC	embryonic stem cell:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
25	CTCF	chr5:29005560-29005577	GM10248	blood:	n/a	n/a
26	CTCF	chr5:29005480-29005630	HA-sp	spinal cord:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
27	CTCF	chr5:29005500-29005650	Caco-2	colon:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
28	CTCF	chr5:29005480-29005630	Caco-2	colon:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
29	CTCF	chr5:29005500-29005650	HepG2	liver:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
30	CTCF	chr5:29001889-29002008	MCF-7	breast:	n/a	n/a
31	CTCF	chr5:29001840-29001990	HEK293	kidney:	n/a	n/a
32	CTCF	chr5:29001813-29002111	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr5:29001911-29001964	A549	lung:	n/a	n/a
34	CTCF	chr5:29005560-29005710	MCF-7	breast:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
35	CTCF	chr5:29036907-29036942	Lung_OC	lung:	n/a	n/a
36	CTCF	chr5:29005520-29005670	WERI-Rb-1	eye:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
37	CTCF	chr5:29005520-29005670	HRPEpiC	eye:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
38	CTCF	chr5:29016180-29016330	BE2_C	brain:	n/a	n/a
39	CTCF	chr5:29001900-29002050	BE2_C	brain:	n/a	n/a
40	CTCF	chr5:29005518-29005661	MCF-7	breast:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
41	CTCF	chr5:29005480-29005630	HVMF	connective:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
42	CTCF	chr5:29016300-29016450	A549	lung:	n/a	n/a
43	CTCF	chr5:29016120-29016270	MCF-7	breast:	n/a	n/a
44	CTCF	chr5:29016151-29016501	MCF-7	breast:	n/a	n/a
45	CTCF	chr5:29025601-29025721	LNCaP	prostate:	n/a	n/a
46	CTCF	chr5:29001901-29002009	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr5:29001860-29002010	HBMEC	blood vessel:	n/a	n/a
48	CTCF	chr5:29005620-29005770	RPTEC	kidney:	n/a	n/a
49	CTCF	chr5:29005520-29005670	HBMEC	blood vessel:	n/a	chr5:29005574-29005583 chr5:29005573-29005594 chr5:29005571-29005589
50	CTCF	chr5:29005533-29005585	GM13977	blood:	n/a	chr5:29005574-29005583

No.	Distal block	Cell Line	Cell type
1	chr5:28996102..28998420-chr5:29007454..29009412,2	K562	blood:
2	chr5:29005255..29006082-chr5:29217591..29218623,4	MCF-7	breast:
3	chr5:29003141..29005545-chr5:29008862..29010410,2	K562	blood:
4	chr5:29026756..29028723-chr5:29043428..29045918,2	K562	blood:
5	chr5:28986098..28988611-chr5:28988993..28991455,2	MCF-7	breast:
6	chr5:29050111..29052926-chr5:29053158..29054737,2	MCF-7	breast:
7	chr5:28996102..28998420-chr5:29007454..29009412,2	K562	blood:
8	chr5:29005476..29006055-chr5:29218041..29218711,2	MCF-7	breast:
9	chr5:29059482..29062466-chr5:29065874..29068673,2	MCF-7	breast:
10	chr5:29003141..29005545-chr5:29008862..29010410,2	K562	blood:
11	chr5:29026756..29028723-chr5:29043428..29045918,2	K562	blood:
12	chr5:28906947..28909506-chr5:29049292..29051622,2	K562	blood:
13	chr20:55853010..55855279-chr5:29022487..29024544,2	MCF-7	breast:
14	chr5:28986098..28988611-chr5:28988993..28991455,2	MCF-7	breast:
15	chr5:28999555..29001892-chr5:29014306..29015830,2	K562	blood:
16	chr5:29050111..29052926-chr5:29053158..29054737,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDH6-13	chr5:29001867-29002148	NONHSAT100830
2	lnc-CDH6-13	chr5:29002720-29003464	NONHSAT100830

Variant related genes	Relation type
SUCLG2P4	TF binding region
ENSG00000249226	chromatin interactions

Extended variants
information (count: 970 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:970 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs569670168	chr5:28991025-28991026	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs537090008	chr5:28991048-28991049	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs552141476	chr5:28991066-28991067	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs570486141	chr5:28991165-28991166	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs74555478	chr5:28991168-28991169	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs554095413	chr5:28991185-28991186	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs572567271	chr5:28991199-28991200	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs536558534	chr5:28991200-28991201	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs554795463	chr5:28991231-28991232	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs60041854	chr5:28991282-28991283	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs543454734	chr5:28991294-28991295	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs374878902	chr5:28991305-28991306	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs147806829	chr5:28991306-28991307	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs541478700	chr5:28991342-28991343	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs559291396	chr5:28991353-28991354	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs529865574	chr5:28991404-28991405	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs115225729	chr5:28991413-28991414	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs372865438	chr5:28991419-28991420	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs192907208	chr5:28991443-28991444	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs530810754	chr5:28991470-28991471	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs561926052	chr5:28991502-28991503	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs148423438	chr5:28991503-28991504	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs534436253	chr5:28991505-28991506	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs530951384	chr5:28991537-28991538	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs546634866	chr5:28991538-28991539	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs565938403	chr5:28991541-28991542	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs369418060	chr5:28991559-28991560	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs142547837	chr5:28991566-28991567	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs550793555	chr5:28991567-28991568	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs2329918	chr5:28991572-28991573	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs184717211	chr5:28991578-28991579	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs140661625	chr5:28991579-28991580	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs190484223	chr5:28996878-28996879	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs563918546	chr5:28996902-28996903	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs138321786	chr5:28996984-28996985	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs546375688	chr5:28996996-28996997	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs564636460	chr5:28997306-28997307	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs528816439	chr5:28997313-28997314	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs139613637	chr5:28997324-28997325	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs183094775	chr5:28997380-28997381	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs562073011	chr5:28997411-28997412	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs529309247	chr5:28997440-28997441	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs560520571	chr5:28997447-28997448	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs16898399	chr5:28997461-28997462	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs76727180	chr5:28997494-28997495	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs529260624	chr5:28997503-28997504	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs533447706	chr5:28997516-28997517	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs551174207	chr5:28997547-28997548	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs566286617	chr5:28997561-28997562	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs568097505	chr5:28997586-28997587	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:97)

Disease	PMID	Source
Kartagener syndrome	16639409	CNVD
Medulloblastoma	21979893	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Cervical squamous cell carcinoma	21590768	CNVD
Non-small cell lung cancer	20864512	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	16783165	CNVD
Thyroid cancer	19087340	CNVD
Liposarcoma	21253554	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cervical Cancer	21857958	CNVD
Cervical cancer	21062161	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Oral cancer	21386901	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Ewing''s sarcoma	17952124	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Cervical cancer	18559093	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Multiple myeloma	17550852	CNVD
prenatal diagnosis	22389664	CNVD
Bladder cancer	21909424	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Breast cancer	21858162	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Cancer	16751803	CNVD
Breast cancer	16608533	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Intellectual disability	22102821	CNVD
Renal cell carcinoma	18194544	CNVD
Prostate cancer	21965145	CNVD
Cancer	21183584	CNVD
Ovarian cancer	20844748	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Non-small cell lung cancer	19010865	CNVD
Glioblastoma multiforme	22286061	CNVD
Compulsive disorder	18923513	CNVD
Epilepsy	18923513	CNVD
Prader-willi syndrome	18923513	CNVD
small cell lung cancer	20016488	CNVD
Ovarian cancer	21720365	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Esophageal cancer	20955586	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21364760	CNVD
Breast cancer	20409316	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	19553991	CNVD
Lung cancer	19553991	CNVD
Melanoma	19553991	CNVD
Ovarian cancer	19553991	CNVD
Prostate cancer	19553991	CNVD
Non-small cell lung cancer	17156491	CNVD
Breast cancer	17133270	CNVD
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:28991000-28991600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:28998600-28999000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:28999000-29002200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:29002000-29002400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:29002200-29002400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:29002400-29003200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:29016400-29016600	Enhancers	Pancreas	Pancrea
8	chr5:29016400-29017800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:29017400-29017800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:29017600-29018200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:29017800-29021000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:29021000-29021200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:29021200-29023200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:29023200-29023600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:29036000-29036800	Enhancers	Fetal Heart	heart
16	chr5:29037400-29038200	Enhancers	Hela-S3	cervix
17	chr5:29037400-29038400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:29042200-29042600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:29042200-29042600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:29042200-29042800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:29042200-29045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:29042400-29042800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr5:29042400-29042800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:29042800-29045000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:29043600-29044000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:29044000-29045000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:29045000-29045200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:29045000-29045200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:29045000-29045400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:29045400-29045800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:29045800-29046400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:29051200-29052400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:29052400-29054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:29054200-29054400	Enhancers	Fetal Heart	heart
35	chr5:29054400-29054800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr5:29054400-29054800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:29054400-29054800	Flanking Active TSS	Fetal Heart	heart
38	chr5:29054400-29055000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:29054400-29055000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:29054600-29054800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:29054800-29055000	Enhancers	Fetal Heart	heart
42	chr5:29061400-29061800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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