Variant report

Variant	nsv877795
Chromosome Location	chr3:162789059-162873933
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:220)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:220 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:162856075-162856324	MCF-7	breast:	n/a	n/a
2	CEBPB	chr3:162815303-162815572	A549	lung:	n/a	chr3:162815435-162815446
3	CEBPB	chr3:162815287-162815558	IMR90	lung:	n/a	chr3:162815435-162815446
4	CEBPB	chr3:162815262-162815596	HepG2	liver:	n/a	chr3:162815435-162815446
5	CEBPB	chr3:162815267-162815649	MCF-7	breast:	n/a	chr3:162815435-162815446
6	CEBPB	chr3:162789480-162789977	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr3:162825020-162825170	BE2_C	brain:	n/a	n/a
8	CTCF	chr3:162825060-162825210	HEK293	kidney:	n/a	n/a
9	CTCF	chr3:162791873-162791967	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:162804847-162804880	MCF-7	breast:	n/a	n/a
11	CTCF	chr3:162843680-162843830	WERI-Rb-1	eye:	n/a	n/a
12	CTCF	chr3:162790988-162790989	MCF-7	breast:	n/a	n/a
13	CTCF	chr3:162791855-162791872	MCF-7	breast:	n/a	n/a
14	CTCF	chr3:162850580-162850730	HCT-116	colon:	n/a	n/a
15	CTCF	chr3:162791861-162791922	MCF-7	breast:	n/a	n/a
16	CTCF	chr3:162843640-162843790	HEK293	kidney:	n/a	n/a
17	CTCF	chr3:162804858-162804924	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:162843720-162843870	A549	lung:	n/a	n/a
19	CTCF	chr3:162791899-162791917	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:162825100-162825250	HepG2	liver:	n/a	n/a
21	CTCF	chr3:162791888-162791898	MCF-7	breast:	n/a	n/a
22	CTCF	chr3:162870820-162870854	GM20000	blood:	n/a	n/a
23	CTCF	chr3:162790990-162791000	MCF-7	breast:	n/a	n/a
24	CTCF	chr3:162825582-162825613	Lung_OC	lung:	n/a	n/a
25	CTCF	chr3:162824920-162825070	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:162857527-162857550	MCF-7	breast:	n/a	n/a
27	CTCF	chr3:162849313-162849338	Fibrobl	skin:	n/a	n/a
28	CTCF	chr3:162843760-162843910	BE2_C	brain:	n/a	n/a
29	CTCF	chr3:162843540-162843690	BE2_C	brain:	n/a	n/a
30	CTCF	chr3:162825066-162825159	MCF-7	breast:	n/a	n/a
31	CTCF	chr3:162843696-162843728	K562	blood:	n/a	n/a
32	CTCF	chr3:162825040-162825190	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:162825049-162825156	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:162825085-162825127	MCF-7	breast:	n/a	n/a
35	CTCF	chr3:162843700-162843850	HBMEC	blood vessel:	n/a	n/a
36	E2F4	chr3:162853012-162853212	MCF10A-Er-Src	breast:	n/a	n/a
37	E2F4	chr3:162863651-162863841	MCF10A-Er-Src	breast:	n/a	n/a
38	E2F4	chr3:162839868-162840221	MCF10A-Er-Src	breast:	n/a	n/a
39	E2F4	chr3:162831163-162831234	MCF10A-Er-Src	breast:	n/a	n/a
40	E2F4	chr3:162817683-162817853	MCF10A-Er-Src	breast:	n/a	n/a
41	E2F4	chr3:162862212-162862415	MCF10A-Er-Src	breast:	n/a	n/a
42	ELK1	chr3:162790946-162790979	Hela-S3	cervix:	n/a	n/a
43	EP300	chr3:162789430-162789879	SK-N-SH_RA	brain:	n/a	n/a
44	EP300	chr3:162789446-162789994	SK-N-SH	brain:	n/a	n/a
45	EP300	chr3:162855997-162856485	MCF-7	breast:	n/a	n/a
46	EP300	chr3:162789409-162789957	MCF-7	breast:	n/a	n/a
47	EP300	chr3:162789491-162789945	MCF-7	breast:	n/a	n/a
48	EP300	chr3:162789511-162789880	SK-N-SH_RA	brain:	n/a	n/a
49	EP300	chr3:162789604-162789927	Hela-S3	cervix:	n/a	n/a
50	FOS	chr3:162856047-162856291	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:174218936..174220527-chr3:162835384..162836884,2	K562	blood:
2	chr3:156892021..156894345-chr3:162787273..162789725,2	MCF-7	breast:
3	chr3:162821263..162822976-chr3:162826872..162828945,2	MCF-7	breast:
4	chr3:162781747..162783965-chr3:162788037..162790015,2	MCF-7	breast:
5	chr3:162821263..162822976-chr3:162826872..162828945,2	MCF-7	breast:
6	chr3:162829065..162831690-chr3:162831998..162834078,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTOL1-9	chr3:162833217-162833974	NONHSAT093027
2	lnc-SI-4	chr3:162845711-162845859	ENSG00000241369

No data

Variant related genes	Relation type
ENSG00000244571	TF binding region
ENSG00000243176	chromatin interactions
ENSG00000244571	chromatin interactions
ENSG00000144354	chromatin interactions

Extended variants
information (count: 695 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:695 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13089621	chr3:162789059-162789060	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs139770591	chr3:162789069-162789070	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs560873234	chr3:162789094-162789095	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs529764500	chr3:162789223-162789224	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs550443308	chr3:162789261-162789262	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs149808977	chr3:162789294-162789295	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs573920448	chr3:162789346-162789347	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs73018935	chr3:162789358-162789359	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs145803928	chr3:162789364-162789365	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs566131712	chr3:162789405-162789406	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs13067606	chr3:162789431-162789432	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs548132138	chr3:162789432-162789433	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs568110458	chr3:162789441-162789442	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs537087453	chr3:162789458-162789459	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs141778750	chr3:162789460-162789461	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs556406812	chr3:162789505-162789506	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs576285282	chr3:162789516-162789517	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs538796486	chr3:162789549-162789550	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs190061746	chr3:162789585-162789586	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs147093122	chr3:162789591-162789592	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs13090583	chr3:162789598-162789599	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs143289834	chr3:162789616-162789617	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs554749482	chr3:162789623-162789624	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs181719121	chr3:162789637-162789638	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs543081850	chr3:162789683-162789684	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs147735736	chr3:162789685-162789686	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs142644236	chr3:162789770-162789771	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs546338711	chr3:162789780-162789781	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs187648247	chr3:162789838-162789839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs386667744	chr3:162789878-162789879	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs190328680	chr3:162789879-162789880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs568249696	chr3:162789952-162789953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs544386245	chr3:162789956-162789957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs201941270	chr3:162789957-162789958	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs550719886	chr3:162789973-162789974	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs76222310	chr3:162790040-162790041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs538562912	chr3:162790044-162790045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs549584108	chr3:162790061-162790062	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs73154861	chr3:162790092-162790093	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs180946546	chr3:162790104-162790105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs143027131	chr3:162790112-162790113	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs184966844	chr3:162790127-162790128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs554684511	chr3:162790140-162790141	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs549006082	chr3:162790151-162790152	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs574609550	chr3:162790160-162790161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs148204935	chr3:162790194-162790195	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs201164608	chr3:162790212-162790213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs375443015	chr3:162790217-162790218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs556693957	chr3:162790238-162790239	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs542084865	chr3:162790305-162790306	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Breast cancer	21364760	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Sudden cardiac death	19188705	CNVD
Mantle cell lymphoma	19029149	CNVD
Malformation	19546859	CNVD
Schizophrenia	19546859	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Bladder cancer	21909424	CNVD

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162789000-162789600	Enhancers	Hela-S3	cervix
2	chr3:162789400-162789600	Weak transcription	Aorta	Aorta
3	chr3:162789400-162789800	Enhancers	Fetal Lung	lung
4	chr3:162789600-162789800	Enhancers	Aorta	Aorta
5	chr3:162789800-162790800	Weak transcription	Aorta	Aorta
6	chr3:162790600-162792200	ZNF genes & repeats	Dnd41	blood
7	chr3:162790800-162792000	ZNF genes & repeats	Aorta	Aorta
8	chr3:162791000-162792000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:162791200-162792000	ZNF genes & repeats	Spleen	Spleen
10	chr3:162791800-162792000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:162791800-162792000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:162791800-162792000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:162825000-162825200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:162825200-162825800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:162825200-162825800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:162825200-162825800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:162825200-162826000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:162825200-162826000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:162825800-162826000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:162825800-162828800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:162841000-162841600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:162841600-162844400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:162841800-162842200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:162842200-162843000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:162843000-162843800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
26	chr3:162843000-162845000	ZNF genes & repeats	Dnd41	blood
27	chr3:162843400-162844400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:162844000-162844600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
29	chr3:162844000-162845000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
30	chr3:162847000-162847400	ZNF genes & repeats	Dnd41	blood
31	chr3:162847200-162847400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:162858000-162858800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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