Variant report

Variant	nsv1016558
Chromosome Location	chr5:59729770-59771723
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	chr5:59759049-59759883	HepG2	liver:	n/a	n/a
2	ARID3A	chr5:59769493-59769923	HepG2	liver:	n/a	n/a
3	ARID3A	chr5:59742744-59743990	HepG2	liver:	n/a	chr5:59743535-59743551
4	ATF3	chr5:59758895-59759556	A549	lung:	n/a	n/a
5	BCL3	chr5:59758832-59759533	A549	lung:	n/a	n/a
6	BCL3	chr5:59758809-59759695	A549	lung:	n/a	chr5:59759578-59759587
7	BHLHE40	chr5:59742844-59743730	HepG2	liver:	n/a	n/a
8	BHLHE40	chr5:59743228-59743638	HepG2	liver:	n/a	n/a
9	BHLHE40	chr5:59758956-59759660	HepG2	liver:	n/a	n/a
10	BHLHE40	chr5:59758972-59759353	A549	lung:	n/a	n/a
11	BHLHE40	chr5:59743262-59743636	HepG2	liver:	n/a	n/a
12	BRCA1	chr5:59758918-59759295	Hela-S3	cervix:	n/a	n/a
13	CCNT2	chr5:59747083-59747168	K562	blood:	n/a	n/a
14	CEBPB	chr5:59758981-59759376	K562	blood:	n/a	chr5:59759173-59759184
15	CEBPB	chr5:59759016-59759277	HepG2	liver:	n/a	chr5:59759173-59759184
16	CEBPB	chr5:59758780-59759728	A549	lung:	n/a	chr5:59759173-59759184 chr5:59758810-59758822 chr5:59758883-59758895
17	CEBPB	chr5:59744444-59744829	Hela-S3	cervix:	n/a	chr5:59744753-59744765
18	CEBPB	chr5:59758995-59759301	K562	blood:	n/a	chr5:59759173-59759184
19	CEBPB	chr5:59740891-59741112	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr5:59758954-59759375	A549	lung:	n/a	chr5:59759173-59759184
21	CEBPB	chr5:59758865-59759496	A549	lung:	n/a	chr5:59759173-59759184 chr5:59758883-59758895
22	CEBPB	chr5:59759094-59759253	H1-hESC	embryonic stem cell:	n/a	chr5:59759173-59759184
23	CEBPB	chr5:59758972-59759399	MCF-7	breast:	n/a	chr5:59759173-59759184
24	CEBPB	chr5:59758926-59759470	Hela-S3	cervix:	n/a	chr5:59759173-59759184
25	CEBPB	chr5:59758997-59759365	IMR90	lung:	n/a	chr5:59759173-59759184
26	CEBPB	chr5:59761806-59762009	A549	lung:	n/a	n/a
27	CEBPB	chr5:59758957-59759712	HepG2	liver:	n/a	chr5:59759173-59759184
28	CEBPB	chr5:59744195-59744769	A549	lung:	n/a	chr5:59744753-59744765
29	CEBPB	chr5:59758902-59759356	HepG2	liver:	n/a	chr5:59759173-59759184
30	CEBPB	chr5:59738481-59738678	HepG2	liver:	n/a	chr5:59738605-59738616
31	CEBPB	chr5:59758952-59759391	HepG2	liver:	n/a	chr5:59759173-59759184
32	CEBPB	chr5:59759013-59759326	MCF-7	breast:	n/a	chr5:59759173-59759184
33	CHD2	chr5:59759045-59759296	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr5:59732400-59732550	GM12873	blood:	n/a	n/a
35	CTCF	chr5:59754640-59754790	AoAF	blood vessel:	n/a	n/a
36	CTCF	chr5:59732560-59732710	GM12866	blood:	n/a	n/a
37	CTCF	chr5:59754583-59754809	MCF-7	breast:	n/a	n/a
38	CTCF	chr5:59754600-59754750	K562	blood:	n/a	n/a
39	CTCF	chr5:59754600-59754750	A549	lung:	n/a	n/a
40	CTCF	chr5:59754620-59754770	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr5:59737560-59737622	GM13976	blood:	n/a	n/a
42	CTCF	chr5:59732460-59732610	RPTEC	kidney:	n/a	n/a
43	CTCF	chr5:59732480-59732630	GM12873	blood:	n/a	n/a
44	CTCF	chr5:59754660-59754810	BE2_C	brain:	n/a	n/a
45	CTCF	chr5:59754620-59754770	HAc	cerebellar:	n/a	n/a
46	CTCF	chr5:59754497-59754924	MCF-7	breast:	n/a	n/a
47	CTCF	chr5:59754643-59754772	K562	blood:	n/a	n/a
48	CTCF	chr5:59754640-59754790	HEEpiC	esophagus:	n/a	n/a
49	CTCF	chr5:59754600-59754750	SAEC	small airway:	n/a	n/a
50	CTCF	chr5:59742760-59743050	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:59750546..59752966-chr5:59754525..59756849,2	K562	blood:

Variant related genes	Relation type
ENSG00000213896	TF binding region
SETP21	TF binding region
PDE4D	TF binding region
ENSG00000214244	chromatin interactions

Extended variants
information (count: 1424 )
Associated
traits (count: 95 )

Variant overlapped rSNPs/rCNVs (count:1424 , 50 per page) page: 1 2 3 4 5 6 7 ... 29

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs542987804	chr5:59729787-59729788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs186351057	chr5:59729800-59729801	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs553491095	chr5:59729801-59729802	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs190804004	chr5:59729805-59729806	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs182477321	chr5:59729820-59729821	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs563128610	chr5:59729830-59729831	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs530217412	chr5:59729841-59729842	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs548941520	chr5:59729853-59729854	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs566500250	chr5:59729904-59729905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs530727147	chr5:59730033-59730034	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs185277612	chr5:59730056-59730057	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs372774868	chr5:59730070-59730071	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs549045644	chr5:59730087-59730088	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs569029728	chr5:59730094-59730095	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs537597336	chr5:59730104-59730105	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs557537489	chr5:59730108-59730109	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs577679983	chr5:59730153-59730154	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs9291691	chr5:59730184-59730185	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs33916352	chr5:59730264-59730265	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs553736708	chr5:59730266-59730267	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs397962464	chr5:59730274-59730275	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs573990658	chr5:59730314-59730315	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs543303761	chr5:59730350-59730351	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs562995907	chr5:59730361-59730362	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs576686819	chr5:59730418-59730419	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs545239427	chr5:59730419-59730420	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs565503585	chr5:59730549-59730550	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs570711825	chr5:59730613-59730614	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs533035680	chr5:59730646-59730647	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs370174219	chr5:59730655-59730656	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs148713309	chr5:59730715-59730716	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs560178971	chr5:59730721-59730722	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs144648220	chr5:59730736-59730737	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs367634374	chr5:59730817-59730818	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs569015903	chr5:59730936-59730937	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs538157010	chr5:59730962-59730963	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs191175753	chr5:59730964-59730965	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs571143344	chr5:59730965-59730966	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs565432352	chr5:59730966-59730967	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs202009766	chr5:59730968-59730969	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs183303224	chr5:59731018-59731019	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs574082953	chr5:59731070-59731071	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs552209712	chr5:59731095-59731096	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs539420464	chr5:59731154-59731155	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs556539750	chr5:59731157-59731158	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs557425559	chr5:59731167-59731168	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs116258058	chr5:59731177-59731178	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs565461704	chr5:59731190-59731191	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs11745404	chr5:59731191-59731192	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs188457941	chr5:59731194-59731195	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:95)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	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
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	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
Cancer	16751803	CNVD
Autism	22495311	CNVD
Intellectual disability	22102821	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Prostate cancer	21965145	CNVD
Esophageal cancer	20955586	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Ovarian cancer	20844748	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
adenomatous polyposis	22470819	CNVD
Acute myeloid leukemia	20729466	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Hepatocellular carcinoma	16750200	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	21251322	CNVD
Oral cancer	21386901	CNVD
Bladder cancer	21909424	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	17133270	CNVD
Breast cancer	19602461	CNVD
Renal cell carcinoma	18194544	CNVD
abnormal development	18461090	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Retinoblastoma	22278416	CNVD
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16774939	CNVD
Myelofibrosis	22110671	CNVD
Neuroticism	17667963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59717000-59730000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:59727200-59766600	Weak transcription	Primary B cells from cord blood	blood
3	chr5:59730000-59730400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:59730400-59731000	Enhancers	Colon Smooth Muscle	Colon
5	chr5:59730400-59731800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:59730400-59733200	Enhancers	HepG2	liver
7	chr5:59731800-59732000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:59732000-59732400	Enhancers	GM12878-XiMat	blood
9	chr5:59732400-59733000	Enhancers	Primary B cells from peripheral blood	blood
10	chr5:59732400-59733400	Flanking Active TSS	GM12878-XiMat	blood
11	chr5:59732800-59733000	Enhancers	Aorta	Aorta
12	chr5:59733000-59742600	Weak transcription	Aorta	Aorta
13	chr5:59733200-59738800	Weak transcription	HepG2	liver
14	chr5:59733400-59733800	Enhancers	GM12878-XiMat	blood
15	chr5:59734000-59734400	Enhancers	Fetal Kidney	kidney
16	chr5:59738800-59742800	Enhancers	HepG2	liver
17	chr5:59740000-59741200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:59740000-59741600	Enhancers	Fetal Brain Male	brain
19	chr5:59740200-59740600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:59740400-59741000	Enhancers	Fetal Brain Female	brain
21	chr5:59740400-59741000	Enhancers	Hela-S3	cervix
22	chr5:59740600-59740800	Enhancers	Gastric	stomach
23	chr5:59741000-59744200	Weak transcription	Hela-S3	cervix
24	chr5:59741200-59741600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:59741600-59741800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:59741600-59743200	Enhancers	Stomach Mucosa	stomach
27	chr5:59741600-59744800	Weak transcription	Fetal Brain Male	brain
28	chr5:59741800-59783200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:59742600-59743000	Enhancers	Aorta	Aorta
30	chr5:59742600-59743000	Enhancers	A549	lung
31	chr5:59742600-59744400	Enhancers	Gastric	stomach
32	chr5:59742800-59743200	Flanking Active TSS	HepG2	liver
33	chr5:59743000-59743600	Flanking Active TSS	A549	lung
34	chr5:59743000-59743800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:59743200-59744400	Weak transcription	Stomach Mucosa	stomach
36	chr5:59743200-59745200	Enhancers	HepG2	liver
37	chr5:59743400-59743800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr5:59743600-59744000	Active TSS	A549	lung
39	chr5:59743800-59747600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:59744000-59744200	Enhancers	A549	lung
41	chr5:59744200-59744400	Flanking Active TSS	A549	lung
42	chr5:59744200-59744600	Enhancers	Brain Angular Gyrus	brain
43	chr5:59744200-59744600	Active TSS	Hela-S3	cervix
44	chr5:59744400-59744600	Enhancers	Stomach Mucosa	stomach
45	chr5:59744400-59744800	Enhancers	A549	lung
46	chr5:59745200-59747400	Weak transcription	HepG2	liver
47	chr5:59747400-59750000	Enhancers	HepG2	liver
48	chr5:59747600-59748800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:59749200-59749400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:59749400-59751400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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