Variant report

Variant	nsv3060
Chromosome Location	chr2:179990791-180035511
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	chr2:179994512-179994681	HepG2	liver:	n/a	n/a
2	BACH1	chr2:180022603-180022624	H1-hESC	embryonic stem cell:	n/a	n/a
3	BATF	chr2:179994289-179994529	GM12878	blood:	n/a	chr2:179994389-179994400
4	CEBPB	chr2:180015456-180015582	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr2:179999259-179999503	HepG2	liver:	n/a	chr2:179999417-179999428
6	CEBPB	chr2:179999279-179999554	IMR90	lung:	n/a	chr2:179999417-179999428
7	CEBPB	chr2:180023664-180023714	HepG2	liver:	n/a	n/a
8	CTCF	chr2:179994480-179994630	SK-N-SH_RA	brain:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
9	CTCF	chr2:179994480-179994630	AG09309	skin:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
10	CTCF	chr2:179994463-179994667	HepG2	liver:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
11	CTCF	chr2:179994460-179994610	RPTEC	kidney:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
12	CTCF	chr2:179994600-179994750	BE2_C	brain:	n/a	n/a
13	CTCF	chr2:179994520-179994670	SAEC	small airway:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
14	CTCF	chr2:179994462-179994680	GM13976	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
15	CTCF	chr2:179994480-179994630	NHLF	lung:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
16	CTCF	chr2:179994500-179994650	NHDF-neo	bronchial:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
17	CTCF	chr2:179994500-179994650	HBMEC	blood vessel:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
18	CTCF	chr2:179994460-179994610	HVMF	connective:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
19	CTCF	chr2:179994380-179994530	HAc	cerebellar:	n/a	n/a
20	CTCF	chr2:179994460-179994610	AG09319	gingival:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
21	CTCF	chr2:179994430-179994602	A549	lung:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
22	CTCF	chr2:179994470-179994696	K562	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
23	CTCF	chr2:179994540-179994690	GM12878	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
24	CTCF	chr2:179994460-179994610	HCT-116	colon:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
25	CTCF	chr2:179994500-179994650	AG09309	skin:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
26	CTCF	chr2:179994480-179994630	AG10803	skin:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
27	CTCF	chr2:179994400-179994550	A549	lung:	n/a	n/a
28	CTCF	chr2:179994460-179994610	GM12869	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
29	CTCF	chr2:179994520-179994670	WERI-Rb-1	eye:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
30	CTCF	chr2:179994500-179994650	GM12866	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
31	CTCF	chr2:179994480-179994630	HCFaa	heart:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
32	CTCF	chr2:179994457-179994669	A549	lung:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
33	CTCF	chr2:179994520-179994670	K562	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
34	CTCF	chr2:179994500-179994650	HRPEpiC	eye:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
35	CTCF	chr2:179994440-179994590	GM12869	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
36	CTCF	chr2:179994480-179994630	RPTEC	kidney:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
37	CTCF	chr2:179994437-179994707	Spleen_OC	spleen:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
38	CTCF	chr2:179994448-179994738	Medullo	brain:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
39	CTCF	chr2:179994460-179994699	MCF-7	breast:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
40	CTCF	chr2:179994310-179994708	HCT-116	colon:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
41	CTCF	chr2:179994520-179994670	GM12864	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
42	CTCF	chr2:179994480-179994630	AG09319	gingival:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
43	CTCF	chr2:179994460-179994610	HEEpiC	esophagus:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
44	CTCF	chr2:179994456-179994816	MCF-7	breast:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
45	CTCF	chr2:179994480-179994630	HFF	foreskin:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
46	CTCF	chr2:179994460-179994610	HFF-Myc	foreskin:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
47	CTCF	chr2:179994460-179994610	HBMEC	blood vessel:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
48	CTCF	chr2:179994480-179994630	GM12875	blood:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
49	CTCF	chr2:179994514-179994617	A549	lung:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572
50	CTCF	chr2:179994480-179994630	HEK293	kidney:	n/a	chr2:179994557-179994573 chr2:179994556-179994574 chr2:179994551-179994572

No.	Distal block	Cell Line	Cell type
1	chr2:180005469..180007805-chr2:180127766..180130374,2	MCF-7	breast:
2	chr2:180027947..180030148-chr2:180031681..180034023,3	MCF-7	breast:
3	chr2:179756153..179756818-chr2:179994138..179995053,3	MCF-7	breast:
4	chr2:179990644..179992721-chr2:180003873..180005520,2	K562	blood:
5	chr2:179660489..179661428-chr2:179994042..179994549,2	K562	blood:
6	chr2:179628215..179630011-chr2:180014131..180016832,2	MCF-7	breast:
7	chr2:179988043..179990926-chr2:179994238..179996343,2	K562	blood:
8	chr2:179990644..179992721-chr2:180003873..180005520,2	K562	blood:
9	chr2:180005225..180008035-chr2:180008843..180011202,2	K562	blood:
10	chr2:179660514..179661453-chr2:179994101..179994985,3	MCF-7	breast:
11	chr2:180027947..180030148-chr2:180031681..180034023,3	MCF-7	breast:

Variant related genes	Relation type
SESTD1	TF binding region
ENSG00000238339	TF binding region
ENSG00000187231	chromatin interactions
ENSG00000238339	chromatin interactions

Extended variants
information (count: 1674 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:1674 , 50 per page) page: 1 2 3 4 5 6 7 ... 34

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs183337802	chr2:179990796-179990797	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
2	rs562400639	chr2:179990831-179990832	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
3	rs56109193	chr2:179990847-179990848	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs541605693	chr2:179990868-179990869	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
5	rs561933992	chr2:179990874-179990875	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
6	rs186835426	chr2:179990875-179990876	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
7	rs547661195	chr2:179990876-179990877	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
8	rs75601525	chr2:179990905-179990906	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
9	rs74552817	chr2:179990932-179990933	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
10	rs530705146	chr2:179990992-179990993	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
11	rs191663625	chr2:179991000-179991001	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
12	rs550152347	chr2:179991002-179991003	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
13	rs146467499	chr2:179991004-179991005	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
14	rs75463178	chr2:179991065-179991066	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
15	rs549245333	chr2:179991079-179991080	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
16	rs568241252	chr2:179991114-179991115	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
17	rs34660861	chr2:179991213-179991214	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs534001070	chr2:179991214-179991215	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs554076844	chr2:179991231-179991232	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs183762675	chr2:179991306-179991307	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs188079527	chr2:179991309-179991310	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs550285844	chr2:179991321-179991322	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs564825249	chr2:179991343-179991344	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs556120091	chr2:179991345-179991346	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs138801493	chr2:179991359-179991360	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
26	rs569570383	chr2:179991375-179991376	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
27	rs544101886	chr2:179991409-179991410	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs79877384	chr2:179991433-179991434	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs34919547	chr2:179991497-179991498	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
30	rs555069673	chr2:179991553-179991554	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
31	rs572277882	chr2:179991562-179991563	Weak transcription Enhancers Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
32	rs193278597	chr2:179991667-179991668	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
33	rs78495393	chr2:179991669-179991670	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
34	rs367997744	chr2:179991684-179991685	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
35	rs533674199	chr2:179991700-179991701	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
36	rs544456569	chr2:179991738-179991739	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
37	rs543803935	chr2:179991812-179991813	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
38	rs185440261	chr2:179991881-179991882	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
39	rs75064448	chr2:179991945-179991946	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
40	rs529301016	chr2:179991999-179992000	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
41	rs34549467	chr2:179992014-179992015	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
42	rs75851023	chr2:179992041-179992042	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
43	rs76426605	chr2:179992045-179992046	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
44	rs144776937	chr2:179992047-179992048	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
45	rs577231828	chr2:179992061-179992062	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
46	rs148147168	chr2:179992078-179992079	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
47	rs558378743	chr2:179992079-179992080	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
48	rs547615012	chr2:179992119-179992120	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
49	rs533706823	chr2:179992125-179992126	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
50	rs17363260	chr2:179992164-179992165	Weak transcription Strong transcription Enhancers	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:55)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	16272173	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
Colorectal cancer	16272173	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Glioblastoma	21080181	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Prostate cancer	18632612	CNVD
Sudden cardiac death	19188705	CNVD
Acute myeloid leukemia	20729466	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	18923514	CNVD
Schizophrenia	22241247	CNVD
Mental retardation	21062444	CNVD
Facial dysmorphism	20548289	CNVD
Mental retardation	20548289	CNVD
Schizophrenia	19348701	CNVD
Muscular dystrophy	17160897	CNVD
Cardiomyopathy	17576883	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:659 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
2	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
4	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:179972600-180001800	Weak transcription	NHEK	skin
9	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
11	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
12	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
13	chr2:179973400-180012600	Weak transcription	NHLF	lung
14	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:179974400-179994200	Strong transcription	HepG2	liver
16	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:179976000-180004400	Weak transcription	Aorta	Aorta
18	chr2:179977400-180004400	Weak transcription	Lung	lung
19	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
20	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
21	chr2:179977600-180002000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:179978800-180004400	Weak transcription	Spleen	Spleen
24	chr2:179980000-180038800	Weak transcription	HMEC	breast
25	chr2:179980000-180056800	Weak transcription	HSMM	muscle
26	chr2:179980400-180005200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:179980400-180005600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:179981000-179991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:179981400-180001800	Weak transcription	Placenta	Placenta
30	chr2:179981400-180005000	Weak transcription	Ovary	ovary
31	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:179981600-179991000	Weak transcription	Brain Anterior Caudate	brain
33	chr2:179981600-179997600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:179981600-180004400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:179981600-180005000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:179981800-180005400	Weak transcription	Osteobl	bone
37	chr2:179982400-180004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:179982800-180004400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:179982800-180004600	Weak transcription	Fetal Brain Male	brain
40	chr2:179983600-180005000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:179984600-180003000	Weak transcription	Fetal Lung	lung
42	chr2:179984600-180004600	Weak transcription	HUVEC	blood vessel
43	chr2:179984800-180002000	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:179984800-180004200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:179984800-180005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
47	chr2:179985200-180004400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:179985200-180004400	Weak transcription	Fetal Stomach	stomach
49	chr2:179985400-180004000	Weak transcription	Dnd41	blood
50	chr2:179985600-179996200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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