Variant report

Variant	nsv460958
Chromosome Location	chr3:162741452-162879873
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:633)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:633 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr3:162774855-162774871	HepG2	liver:	n/a	n/a
2	BRCA1	chr3:162774683-162774995	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr3:162856075-162856324	MCF-7	breast:	n/a	n/a
4	CEBPB	chr3:162774587-162774998	MCF-7	breast:	n/a	n/a
5	CEBPB	chr3:162815287-162815558	IMR90	lung:	n/a	chr3:162815435-162815446
6	CEBPB	chr3:162815303-162815572	A549	lung:	n/a	chr3:162815435-162815446
7	CEBPB	chr3:162774590-162774941	A549	lung:	n/a	n/a
8	CEBPB	chr3:162773968-162774176	HepG2	liver:	n/a	chr3:162774022-162774033
9	CEBPB	chr3:162815262-162815596	HepG2	liver:	n/a	chr3:162815435-162815446
10	CEBPB	chr3:162774571-162774995	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr3:162815267-162815649	MCF-7	breast:	n/a	chr3:162815435-162815446
12	CEBPB	chr3:162774594-162775003	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr3:162789480-162789977	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr3:162843760-162843910	BE2_C	brain:	n/a	n/a
15	CTCF	chr3:162774747-162774999	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr3:162761040-162761190	GM12864	blood:	n/a	n/a
17	CTCF	chr3:162774700-162774850	RPTEC	kidney:	n/a	n/a
18	CTCF	chr3:162774739-162774986	K562	blood:	n/a	n/a
19	CTCF	chr3:162774760-162774910	GM12870	blood:	n/a	n/a
20	CTCF	chr3:162761040-162761190	RPTEC	kidney:	n/a	n/a
21	CTCF	chr3:162774775-162775033	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr3:162774800-162774950	HA-sp	spinal cord:	n/a	n/a
23	CTCF	chr3:162774780-162774930	HRPEpiC	eye:	n/a	n/a
24	CTCF	chr3:162761020-162761170	HCM	heart:	n/a	n/a
25	CTCF	chr3:162774820-162774970	HAc	cerebellar:	n/a	n/a
26	CTCF	chr3:162760982-162761149	GM19238	blood:	n/a	n/a
27	CTCF	chr3:162774780-162774930	GM12873	blood:	n/a	n/a
28	CTCF	chr3:162761060-162761210	NB4	blood:	n/a	n/a
29	CTCF	chr3:162774800-162774950	NHEK	skin:	n/a	n/a
30	CTCF	chr3:162774660-162774810	HAc	cerebellar:	n/a	n/a
31	CTCF	chr3:162773960-162774110	GM06990	blood:	n/a	n/a
32	CTCF	chr3:162771680-162771830	A549	lung:	n/a	n/a
33	CTCF	chr3:162761020-162761170	HBMEC	blood vessel:	n/a	n/a
34	CTCF	chr3:162760929-162761264	IMR90	lung:	n/a	n/a
35	CTCF	chr3:162843540-162843690	BE2_C	brain:	n/a	n/a
36	CTCF	chr3:162774780-162774930	HMF	breast:	n/a	n/a
37	CTCF	chr3:162774788-162774907	GM19240	blood:	n/a	n/a
38	CTCF	chr3:162774360-162774510	HRE	kidney:	n/a	n/a
39	CTCF	chr3:162760940-162761090	HRPEpiC	eye:	n/a	n/a
40	CTCF	chr3:162774780-162774930	HVMF	connective:	n/a	n/a
41	CTCF	chr3:162761040-162761190	NHLF	lung:	n/a	n/a
42	CTCF	chr3:162774760-162774910	HFF-Myc	foreskin:	n/a	n/a
43	CTCF	chr3:162761000-162761150	Caco-2	colon:	n/a	n/a
44	CTCF	chr3:162753290-162753354	GM13976	blood:	n/a	n/a
45	CTCF	chr3:162760960-162761110	GM12872	blood:	n/a	n/a
46	CTCF	chr3:162774880-162775030	HFF-Myc	foreskin:	n/a	n/a
47	CTCF	chr3:162761000-162761150	HPAF	blood vessel:	n/a	n/a
48	CTCF	chr3:162760920-162761070	GM12875	blood:	n/a	n/a
49	CTCF	chr3:162760922-162761177	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr3:162774780-162774930	BJ	skin:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156892021..156894345-chr3:162787273..162789725,2	MCF-7	breast:
2	chr3:162754967..162757825-chr3:162758379..162760616,2	MCF-7	breast:
3	chr3:162781747..162783965-chr3:162788037..162790015,2	MCF-7	breast:
4	chr3:162494680..162495563-chr3:162760633..162761552,3	MCF-7	breast:
5	chr3:162774415..162775478-chr3:163207241..163208645,5	MCF-7	breast:
6	chr3:162755966..162757761-chr3:162760804..162762764,2	MCF-7	breast:
7	chr3:162754967..162757825-chr3:162758379..162760616,2	MCF-7	breast:
8	chr3:162821263..162822976-chr3:162826872..162828945,2	MCF-7	breast:
9	chr3:162755966..162757761-chr3:162760804..162762764,2	MCF-7	breast:
10	chr3:162776529..162777484-chr3:163340191..163340771,2	MCF-7	breast:
11	chr3:162774576..162775267-chr3:162991199..162992106,3	MCF-7	breast:
12	chr3:162829065..162831690-chr3:162831998..162834078,2	MCF-7	breast:
13	chr3:162821263..162822976-chr3:162826872..162828945,2	MCF-7	breast:
14	chr3:162781747..162783965-chr3:162788037..162790015,2	MCF-7	breast:
15	chr2:174218936..174220527-chr3:162835384..162836884,2	K562	blood:
16	chr3:162003324..162004086-chr3:162760294..162761113,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTOL1-9	chr3:162833217-162833974	NONHSAT093027
2	lnc-OTOL1-2	chr3:162744184-162744286	ENSG00000241168.1
3	lnc-SI-4	chr3:162845711-162845859	ENSG00000241369
4	lnc-OTOL1-2	chr3:162744184-162744286	NONHSAT093026

No data

Variant related genes	Relation type
ENSG00000244571	TF binding region
ENSG00000241168	TF binding region
ENSG00000144354	chromatin interactions
ENSG00000243176	chromatin interactions
ENSG00000244571	chromatin interactions

Extended variants
information (count: 2042 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:2042 , 50 per page) page: 1 2 3 4 5 6 7 ... 41

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2046696	chr3:162741452-162741453	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs537396098	chr3:162741457-162741458	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs148428443	chr3:162741479-162741480	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs570694096	chr3:162741491-162741492	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs376580443	chr3:162741537-162741538	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs539085973	chr3:162741562-162741563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs552914110	chr3:162741582-162741583	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs7630244	chr3:162741643-162741644	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs373584188	chr3:162741648-162741649	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs145135960	chr3:162741655-162741656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs79333176	chr3:162741663-162741664	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs7625906	chr3:162741691-162741692	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs182884402	chr3:162741696-162741697	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs187839222	chr3:162741700-162741701	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs533647354	chr3:162741704-162741705	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs10470485	chr3:162741705-162741706	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs397708149	chr3:162741712-162741713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs147604457	chr3:162741718-162741719	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs560096898	chr3:162741735-162741736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs74635276	chr3:162741743-162741744	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs549058950	chr3:162741748-162741749	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs142186552	chr3:162741749-162741750	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs7633057	chr3:162741755-162741756	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs9290195	chr3:162741786-162741787	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs570684867	chr3:162741803-162741804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs539706150	chr3:162741869-162741870	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs546660565	chr3:162741879-162741880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs192955676	chr3:162741923-162741924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs9290196	chr3:162741926-162741927	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs34920622	chr3:162741937-162741938	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs555510611	chr3:162742013-162742014	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs575375906	chr3:162742015-162742016	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs184257759	chr3:162742017-162742018	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs558308671	chr3:162742043-162742044	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs578211001	chr3:162742080-162742081	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs114165697	chr3:162742094-162742095	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs560158075	chr3:162742097-162742098	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs7630728	chr3:162742143-162742144	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs542580756	chr3:162742145-162742146	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs146104132	chr3:162742165-162742166	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs7619891	chr3:162742196-162742197	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs571538002	chr3:162742245-162742246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs189072821	chr3:162742249-162742250	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs151217135	chr3:162742255-162742256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs533123322	chr3:162742274-162742275	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs546919623	chr3:162742300-162742301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs538778831	chr3:162742354-162742355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs71635254	chr3:162742414-162742415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs386667738	chr3:162742421-162742422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs11712205	chr3:162742423-162742424	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162735400-162745200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:162741000-162765600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:162745200-162745600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr3:162745600-162746000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:162752200-162752800	Enhancers	Dnd41	blood
6	chr3:162752800-162753200	Weak transcription	Dnd41	blood
7	chr3:162753200-162753400	Enhancers	Dnd41	blood
8	chr3:162753400-162756000	Weak transcription	Dnd41	blood
9	chr3:162756000-162756800	Enhancers	Dnd41	blood
10	chr3:162756800-162757200	Weak transcription	Dnd41	blood
11	chr3:162757200-162758000	Enhancers	Dnd41	blood
12	chr3:162762000-162763200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:162762600-162763400	Enhancers	Adipose Nuclei	Adipose
14	chr3:162762600-162764000	Enhancers	Dnd41	blood
15	chr3:162764000-162764400	Flanking Active TSS	Dnd41	blood
16	chr3:162764400-162765000	Enhancers	Dnd41	blood
17	chr3:162765000-162769000	Weak transcription	Dnd41	blood
18	chr3:162765600-162766000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:162769000-162770200	Enhancers	Dnd41	blood
20	chr3:162771600-162772000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:162775000-162776400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:162775400-162775800	Enhancers	Colon Smooth Muscle	Colon
23	chr3:162775400-162776000	Enhancers	Stomach Smooth Muscle	stomach
24	chr3:162775600-162776200	Enhancers	Adipose Nuclei	Adipose
25	chr3:162775600-162776400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:162775600-162776600	Enhancers	Fetal Stomach	stomach
27	chr3:162775600-162776600	Enhancers	Rectal Smooth Muscle	rectum
28	chr3:162775800-162776200	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr3:162776000-162776200	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr3:162776000-162776400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:162776000-162776600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:162776000-162776600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:162776200-162776600	Enhancers	Fetal Lung	lung
34	chr3:162776200-162776600	Enhancers	Fetal Muscle Leg	muscle
35	chr3:162776200-162776600	Active TSS	Stomach Smooth Muscle	stomach
36	chr3:162776200-162776800	Enhancers	Colon Smooth Muscle	Colon
37	chr3:162776600-162777600	Weak transcription	Fetal Stomach	stomach
38	chr3:162777600-162777800	Enhancers	Fetal Stomach	stomach
39	chr3:162789000-162789600	Enhancers	Hela-S3	cervix
40	chr3:162789400-162789600	Weak transcription	Aorta	Aorta
41	chr3:162789400-162789800	Enhancers	Fetal Lung	lung
42	chr3:162789600-162789800	Enhancers	Aorta	Aorta
43	chr3:162789800-162790800	Weak transcription	Aorta	Aorta
44	chr3:162790600-162792200	ZNF genes & repeats	Dnd41	blood
45	chr3:162790800-162792000	ZNF genes & repeats	Aorta	Aorta
46	chr3:162791000-162792000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:162791200-162792000	ZNF genes & repeats	Spleen	Spleen
48	chr3:162791800-162792000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:162791800-162792000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:162791800-162792000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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