Variant report

Variant	nsv471009
Chromosome Location	chr5:29040955-29116706
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	chr5:29070987-29071060	K562	blood:	n/a	n/a
2	ATF1	chr5:29089739-29090287	K562	blood:	n/a	n/a
3	ATF1	chr5:29114649-29114850	K562	blood:	n/a	n/a
4	BATF	chr5:29099772-29100098	GM12878	blood:	n/a	n/a
5	BATF	chr5:29099732-29100010	GM12878	blood:	n/a	n/a
6	BHLHE40	chr5:29114706-29114820	K562	blood:	n/a	n/a
7	BHLHE40	chr5:29089838-29090224	K562	blood:	n/a	n/a
8	BRCA1	chr5:29077488-29077830	Hela-S3	cervix:	n/a	n/a
9	CCNT2	chr5:29089941-29090240	K562	blood:	n/a	n/a
10	CCNT2	chr5:29051731-29051997	K562	blood:	n/a	chr5:29051832-29051852
11	CCNT2	chr5:29079757-29080002	K562	blood:	n/a	n/a
12	CEBPB	chr5:29072750-29072805	HepG2	liver:	n/a	chr5:29072772-29072783
13	CEBPB	chr5:29096209-29096500	HepG2	liver:	n/a	chr5:29096332-29096343 chr5:29096327-29096344 chr5:29096330-29096343 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096330-29096341
14	CEBPB	chr5:29096282-29096449	H1-hESC	embryonic stem cell:	n/a	chr5:29096332-29096343 chr5:29096327-29096344 chr5:29096330-29096343 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096330-29096341
15	CEBPB	chr5:29085361-29085554	HepG2	liver:	n/a	n/a
16	CEBPB	chr5:29096184-29096509	IMR90	lung:	n/a	chr5:29096332-29096343 chr5:29096327-29096344 chr5:29096330-29096343 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096330-29096341
17	CEBPB	chr5:29077957-29078214	A549	lung:	n/a	n/a
18	CEBPB	chr5:29096172-29096477	K562	blood:	n/a	chr5:29096332-29096343 chr5:29096327-29096344 chr5:29096330-29096343 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096330-29096341
19	CEBPB	chr5:29077432-29078233	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr5:29096216-29096495	Hela-S3	cervix:	n/a	chr5:29096332-29096343 chr5:29096327-29096344 chr5:29096330-29096343 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096330-29096341
21	CEBPB	chr5:29096194-29096516	A549	lung:	n/a	chr5:29096332-29096343 chr5:29096327-29096344 chr5:29096330-29096343 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096332-29096341 chr5:29096330-29096341
22	CHD1	chr5:29095636-29095675	H1-hESC	embryonic stem cell:	n/a	n/a
23	CHD1	chr5:29048762-29048773	H1-hESC	embryonic stem cell:	n/a	n/a
24	CHD2	chr5:29077610-29077959	Hela-S3	cervix:	n/a	n/a
25	CHD2	chr5:29114366-29114830	Hela-S3	cervix:	n/a	n/a
26	CHD2	chr5:29079997-29080028	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr5:29079930-29080162	MCF-7	breast:	n/a	n/a
28	CTCF	chr5:29080011-29080049	GM13976	blood:	n/a	n/a
29	CTCF	chr5:29079950-29080147	MCF-7	breast:	n/a	n/a
30	CTCF	chr5:29079980-29080134	GM12878	blood:	n/a	n/a
31	CTCF	chr5:29079895-29080131	HepG2	liver:	n/a	n/a
32	CTCF	chr5:29079910-29080169	MCF-7	breast:	n/a	n/a
33	CTCF	chr5:29079960-29080110	SK-N-SH_RA	brain:	n/a	n/a
34	CTCF	chr5:29079960-29080110	A549	lung:	n/a	n/a
35	CTCF	chr5:29079968-29080103	LNCaP	prostate:	n/a	n/a
36	CTCF	chr5:29115472-29115646	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr5:29106085-29106127	GM10266	blood:	n/a	n/a
38	CTCF	chr5:29079881-29080161	K562	blood:	n/a	n/a
39	CTCF	chr5:29079960-29080110	GM12866	blood:	n/a	n/a
40	CTCF	chr5:29079949-29080141	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr5:29093430-29093630	K562	blood:	n/a	n/a
42	CTCF	chr5:29048280-29048430	HCM	heart:	n/a	n/a
43	CTCF	chr5:29079980-29080130	NHEK	skin:	n/a	n/a
44	CTCF	chr5:29079960-29080110	HRE	kidney:	n/a	n/a
45	CTCF	chr5:29079983-29080114	GM12891	blood:	n/a	n/a
46	CTCF	chr5:29079972-29080131	MCF-7	breast:	n/a	n/a
47	CTCF	chr5:29079988-29080113	A549	lung:	n/a	n/a
48	CTCF	chr5:29079960-29080110	BE2_C	brain:	n/a	n/a
49	CTCF	chr5:29079945-29080142	MCF-7	breast:	n/a	n/a
50	CTCF	chr5:29079964-29080105	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:28906947..28909506-chr5:29049292..29051622,2	K562	blood:
2	chr5:29026756..29028723-chr5:29043428..29045918,2	K562	blood:
3	chr5:29059482..29062466-chr5:29065874..29068673,2	MCF-7	breast:
4	chr5:29059482..29062466-chr5:29065874..29068673,2	MCF-7	breast:
5	chr5:29050111..29052926-chr5:29053158..29054737,2	MCF-7	breast:
6	chr5:29050111..29052926-chr5:29053158..29054737,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDH6-11	chr5:29106999-29107219	NONHSAT100835
2	lnc-CDH6-3	chr5:29073007-29073329	ENSG00000249322
3	lnc-CDH6-12	chr5:29105449-29105545	NONHSAT100833
4	lnc-CDH9-14	chr5:29105675-29106968	NONHSAT100834
5	lnc-CDH6-3	chr5:29065351-29065724	NR_109948
6	lnc-CDH6-3	chr5:29066381-29070363	NR_109948
7	lnc-CDH6-3	chr5:29065946-29066069	NR_109948
8	lnc-CDH6-3	chr5:29065946-29066069	ENSG00000249322
9	lnc-CDH6-12	chr5:29104987-29105152	NONHSAT100833
10	lnc-CDH6-3	chr5:29066381-29070363	ENSG00000249322
11	lnc-CDH6-3	chr5:29073007-29073330	NR_109948
12	lnc-CDH6-3	chr5:29065351-29065724	ENSG00000249322

Variant related genes	Relation type
ENSG00000252601	TF binding region
ENSG00000248687	TF binding region
ENSG00000270430	TF binding region
CBFB	miRNA target sites
FOXD1	miRNA target sites

Extended variants
information (count: 1179 )
Associated
traits (count: 98 )

Variant overlapped rSNPs/rCNVs (count:1179 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs180809952	chr5:29042269-29042270	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs516480	chr5:29042277-29042278	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs563120827	chr5:29042314-29042315	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs538539434	chr5:29042330-29042331	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs111518551	chr5:29042334-29042335	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs575785105	chr5:29042337-29042338	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs568686438	chr5:29042363-29042364	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs150576753	chr5:29042389-29042390	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs532708901	chr5:29042397-29042398	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs34428977	chr5:29042419-29042420	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs116553157	chr5:29042432-29042433	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs186267143	chr5:29042478-29042479	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs514676	chr5:29042479-29042480	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs569947610	chr5:29042485-29042486	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs607286	chr5:29042495-29042496	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs370851858	chr5:29042498-29042499	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs140556437	chr5:29042512-29042513	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs189716549	chr5:29042554-29042555	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs546032398	chr5:29042563-29042564	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs183086575	chr5:29042576-29042577	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs606408	chr5:29042679-29042680	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs33930524	chr5:29042680-29042681	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs201133205	chr5:29042694-29042695	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs72339919	chr5:29042695-29042696	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs375746880	chr5:29042696-29042697	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs200264010	chr5:29042698-29042699	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs11955509	chr5:29042718-29042719	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs541734285	chr5:29042724-29042725	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs190386743	chr5:29042862-29042863	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs595097	chr5:29042872-29042873	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs183777613	chr5:29042925-29042926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs545889956	chr5:29042926-29042927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs553887353	chr5:29042942-29042943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs115390563	chr5:29042948-29042949	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs79287210	chr5:29042954-29042955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs78715581	chr5:29042955-29042956	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs77371169	chr5:29042959-29042960	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs509431	chr5:29043018-29043019	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs594297	chr5:29043027-29043028	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs561850932	chr5:29043032-29043033	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs144401876	chr5:29043043-29043044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs570041451	chr5:29043067-29043068	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs509297	chr5:29043069-29043070	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs147279674	chr5:29043076-29043077	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs594211	chr5:29043091-29043092	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs534776802	chr5:29043093-29043094	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs72529135	chr5:29043126-29043127	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs35892462	chr5:29043127-29043128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs552775225	chr5:29043128-29043129	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs371161283	chr5:29043189-29043190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:98)

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
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
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:29042200-29042600	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr5:29042200-29042600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr5:29042200-29042800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr5:29042200-29045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:29042400-29042800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:29042400-29042800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:29042800-29045000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:29043600-29044000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:29044000-29045000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:29045000-29045200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:29045000-29045200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:29045000-29045400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:29045400-29045800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:29045800-29046400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:29051200-29052400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:29052400-29054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:29054200-29054400	Enhancers	Fetal Heart	heart
18	chr5:29054400-29054800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr5:29054400-29054800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:29054400-29054800	Flanking Active TSS	Fetal Heart	heart
21	chr5:29054400-29055000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:29054400-29055000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:29054600-29054800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:29054800-29055000	Enhancers	Fetal Heart	heart
25	chr5:29061400-29061800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:29067600-29067800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr5:29067800-29068200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr5:29067800-29068200	Enhancers	Stomach Mucosa	stomach
29	chr5:29068000-29068400	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr5:29068200-29068400	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr5:29068400-29068600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr5:29068400-29068600	Weak transcription	Stomach Mucosa	stomach
33	chr5:29068400-29068800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr5:29068400-29069200	Enhancers	Pancreas	Pancrea
35	chr5:29068400-29069200	Enhancers	HepG2	liver
36	chr5:29068400-29070200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr5:29068600-29069000	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr5:29068600-29069000	Active TSS	Stomach Mucosa	stomach
39	chr5:29069000-29069200	Flanking Active TSS	Stomach Mucosa	stomach
40	chr5:29069000-29069400	Active TSS	Rectal Smooth Muscle	rectum
41	chr5:29069000-29069600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr5:29069200-29069600	Enhancers	Stomach Mucosa	stomach
43	chr5:29069600-29070800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr5:29077400-29078000	Enhancers	A549	lung
45	chr5:29077400-29078400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:29077400-29078400	Enhancers	Hela-S3	cervix
47	chr5:29077600-29078000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:29079200-29080000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:29085000-29085800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr5:29090200-29090600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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