Variant report

Variant	nsv1044910
Chromosome Location	chr12:41778831-41813198
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	CEBPB	chr12:41793682-41794026	IMR90	lung:	n/a	chr12:41793843-41793852 chr12:41793842-41793853
2	CEBPB	chr12:41811200-41811531	HepG2	liver:	n/a	chr12:41811371-41811382
3	CEBPB	chr12:41788187-41788427	HepG2	liver:	n/a	chr12:41788258-41788269
4	CEBPB	chr12:41778988-41779077	A549	lung:	n/a	n/a
5	CEBPB	chr12:41793798-41793998	H1-hESC	embryonic stem cell:	n/a	chr12:41793843-41793852 chr12:41793842-41793853
6	CEBPB	chr12:41793716-41794026	Hela-S3	cervix:	n/a	chr12:41793843-41793852 chr12:41793842-41793853
7	CEBPB	chr12:41804428-41804688	A549	lung:	n/a	n/a
8	CEBPB	chr12:41811221-41811487	IMR90	lung:	n/a	chr12:41811371-41811382
9	CEBPB	chr12:41811273-41811516	A549	lung:	n/a	chr12:41811371-41811382
10	CEBPB	chr12:41793677-41794018	A549	lung:	n/a	chr12:41793843-41793852 chr12:41793842-41793853
11	CEBPB	chr12:41793794-41793971	K562	blood:	n/a	chr12:41793843-41793852 chr12:41793842-41793853
12	CEBPB	chr12:41793692-41794032	HepG2	liver:	n/a	chr12:41793843-41793852 chr12:41793842-41793853
13	CREB1	chr12:41799994-41800397	GM12878	blood:	n/a	n/a
14	CTCF	chr12:41803500-41803650	HCT-116	colon:	n/a	n/a
15	CTCF	chr12:41803460-41803610	HL-60	blood:	n/a	n/a
16	CTCF	chr12:41803560-41803710	GM12873	blood:	n/a	n/a
17	CTCF	chr12:41803520-41803670	RPTEC	kidney:	n/a	n/a
18	CTCF	chr12:41804540-41804690	HRE	kidney:	n/a	n/a
19	CTCF	chr12:41803560-41803710	HEK293	kidney:	n/a	n/a
20	CTCF	chr12:41803520-41803670	GM12874	blood:	n/a	n/a
21	CTCF	chr12:41803520-41803670	GM12871	blood:	n/a	n/a
22	CTCF	chr12:41803460-41803610	RPTEC	kidney:	n/a	n/a
23	CTCF	chr12:41803500-41803650	HepG2	liver:	n/a	n/a
24	CTCF	chr12:41793426-41793498	Fibrobl	skin:	n/a	n/a
25	E2F4	chr12:41807109-41807353	MCF10A-Er-Src	breast:	n/a	n/a
26	EBF1	chr12:41783444-41783535	GM12878	blood:	n/a	n/a
27	ELK1	chr12:41795423-41795483	Hela-S3	cervix:	n/a	n/a
28	FOS	chr12:41796620-41796960	MCF10A-Er-Src	breast:	n/a	chr12:41796783-41796795 chr12:41796783-41796794 chr12:41796785-41796794 chr12:41796784-41796794 chr12:41796784-41796793
29	FOS	chr12:41796626-41796908	MCF10A-Er-Src	breast:	n/a	chr12:41796783-41796795 chr12:41796783-41796794 chr12:41796785-41796794 chr12:41796784-41796794 chr12:41796784-41796793
30	FOS	chr12:41796596-41796986	HUVEC	blood vessel:	n/a	chr12:41796783-41796795 chr12:41796783-41796794 chr12:41796785-41796794 chr12:41796784-41796794 chr12:41796784-41796793
31	FOS	chr12:41796631-41796894	MCF10A-Er-Src	breast:	n/a	chr12:41796783-41796795 chr12:41796783-41796794 chr12:41796785-41796794 chr12:41796784-41796794 chr12:41796784-41796793
32	FOS	chr12:41796681-41796931	MCF10A-Er-Src	breast:	n/a	chr12:41796783-41796795 chr12:41796783-41796794 chr12:41796785-41796794 chr12:41796784-41796794 chr12:41796784-41796793
33	GATA3	chr12:41786387-41786508	SH-SY5Y	brain:	n/a	n/a
34	JUN	chr12:41796615-41796937	HepG2	liver:	n/a	chr12:41796783-41796795 chr12:41796785-41796794 chr12:41796784-41796794 chr12:41796784-41796793
35	JUN	chr12:41783121-41783225	H1-hESC	embryonic stem cell:	n/a	n/a
36	JUND	chr12:41796587-41797116	SK-N-SH	brain:	n/a	chr12:41796783-41796794 chr12:41796783-41796795 chr12:41796785-41796794 chr12:41796784-41796794 chr12:41796784-41796793
37	JUND	chr12:41796617-41796960	HepG2	liver:	n/a	chr12:41796783-41796794 chr12:41796783-41796795 chr12:41796785-41796794 chr12:41796784-41796794 chr12:41796784-41796793
38	MAFK	chr12:41789234-41789347	HepG2	liver:	n/a	n/a
39	MAFK	chr12:41784986-41785223	HepG2	liver:	n/a	n/a
40	MAFK	chr12:41785071-41785206	HepG2	liver:	n/a	n/a
41	MAFK	chr12:41794680-41794681	IMR90	lung:	n/a	n/a
42	MAFK	chr12:41809691-41809703	HepG2	liver:	n/a	n/a
43	MAFK	chr12:41796670-41796700	HepG2	liver:	n/a	n/a
44	MAX	chr12:41808556-41808884	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr12:41808661-41808897	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr12:41801080-41801327	H1-hESC	embryonic stem cell:	n/a	chr12:41801206-41801215 chr12:41801202-41801211
47	MAX	chr12:41812622-41812628	NB4	blood:	n/a	n/a
48	MAZ	chr12:41803542-41803544	HepG2	liver:	n/a	n/a
49	MYC	chr12:41794748-41794844	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr12:41809230-41809366	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:41797234-41797284	IMR90	lung:	fetal
2	chr12:41797234-41797284	PANC-1	pancreas:	n/a
3	chr12:41797234-41797284	SK-N-SH_RA	brain:	n/a
4	chr12:41797234-41797284	BJ	skin:	n/a
5	chr12:41797234-41797284	SKMC	muscle:	n/a
6	chr12:41797234-41797284	AG04449	skin:	fetal
7	chr12:41797234-41797284	T-47D	breast:	n/a
8	chr12:41797234-41797284	BE2_C	brain:	n/a
9	chr12:41797234-41797284	A549	lung:	n/a
10	chr12:41797234-41797284	Jurkat	blood:	n/a
11	chr12:41797234-41797284	U87	brain:	n/a
12	chr12:41797234-41797284	CMK	blood:	n/a
13	chr12:41797234-41797284	NT2-D1	testis:	n/a
14	chr12:41797234-41797284	HL-60	blood:	n/a
15	chr12:41797234-41797284	K562	blood:	n/a
16	chr12:41797234-41797284	GM06990	blood:	n/a
17	chr12:41797234-41797284	ECC-1	luminal epithelium:	n/a
18	chr12:41797234-41797284	Hepatocyte	liver:	n/a
19	chr12:41797234-41797284	HEK293	kidney:	embryo
20	chr12:41797234-41797284	SK-N-MC	brain:	n/a
21	chr12:41797234-41797284	AG04450	lung:	fetal
22	chr12:41797234-41797284	NHBE	bronchial:	n/a
23	chr12:41797234-41797284	NB4	blood:	n/a
24	chr12:41797234-41797284	AG09309	skin:	n/a
25	chr12:41797234-41797284	HEEpiC	esophagus:	n/a
26	chr12:41797234-41797284	MCF-7	breast:	n/a
27	chr12:41797234-41797284	HAEpiC	amniotic membrane:	n/a
28	chr12:41797234-41797284	HMEC	breast:	n/a
29	chr12:41797234-41797284	H1-hESC	embryonic stem cell:	embryo
30	chr12:41797234-41797284	AG09319	gingival:	n/a
31	chr12:41797234-41797284	PFSK-1	brain:	n/a
32	chr12:41797234-41797284	HNPCEpiC	eye:	n/a
33	chr12:41797234-41797284	HUVEC	blood vessel:	n/a
34	chr12:41797234-41797284	GM12878	blood:	n/a
35	chr12:41797234-41797284	HepG2	liver:	n/a
36	chr12:41797234-41797284	ovcar-3	ovarian:	n/a
37	chr12:41797234-41797284	AoSMC	blood vessel:	n/a
38	chr12:41797234-41797284	HRE	kidney:	n/a
39	chr12:41797234-41797284	GM12891	blood:	n/a
40	chr12:41797234-41797284	SK-N-SH	brain:	n/a
41	chr12:41797234-41797284	HCM	heart:	n/a
42	chr12:41797234-41797284	HCF	heart:	n/a
43	chr12:41797234-41797284	ProgFib	skin:	n/a
44	chr12:41797234-41797284	NHDF-neo	bronchial:	n/a
45	chr12:41797234-41797284	HRPEpiC	eye:	n/a
46	chr12:41797234-41797284	RPTEC	kidney:	n/a
47	chr12:41797234-41797284	AG10803	skin:	n/a
48	chr12:41797234-41797284	HIPEpiC	eye:	n/a
49	chr12:41797234-41797284	NH-A	brain:	n/a
50	chr12:41797234-41797284	HCT-116	colon:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GXYLT1-2	chr12:41803269-41803764	ENSG00000257228.1
2	lnc-GXYLT1-2	chr12:41806203-41806338	ENSG00000257228.1
3	lnc-GXYLT1-2	chr12:41806016-41806086	ENSG00000257228.1
4	lnc-GXYLT1-2	chr12:41806815-41806888	ENSG00000257228.1
5	lnc-GXYLT1-2	chr12:41806203-41806279	ENSG00000257228.1
6	lnc-GXYLT1-2	chr12:41805327-41805677	ENSG00000257228.1
7	lnc-GXYLT1-2	chr12:41806016-41806086	ENSG00000257228.1

Variant related genes	Relation type
ENSG00000257228	TF binding region
ENSG00000257228	CpG island

Extended variants
information (count: 1313 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:1313 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs78455438	chr12:41778835-41778836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs573303029	chr12:41778841-41778842	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs1902909	chr12:41778897-41778898	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs546908365	chr12:41778911-41778912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs533005011	chr12:41778930-41778931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs559290749	chr12:41778941-41778942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs577709784	chr12:41778960-41778961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs545068329	chr12:41778963-41778964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs373573490	chr12:41778978-41778979	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs1902910	chr12:41778982-41778983	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs566509633	chr12:41778993-41778994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs531095503	chr12:41779099-41779100	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs527385613	chr12:41779119-41779120	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs549721317	chr12:41779125-41779126	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs140326676	chr12:41779140-41779141	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs528506192	chr12:41779149-41779150	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs547058930	chr12:41779154-41779155	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs571594275	chr12:41779193-41779194	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs562768504	chr12:41779201-41779202	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs548775795	chr12:41779280-41779281	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs78983908	chr12:41779303-41779304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs75394956	chr12:41779306-41779307	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs372132860	chr12:41779337-41779338	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs144105461	chr12:41779355-41779356	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs551018108	chr12:41779384-41779385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs145041082	chr12:41779399-41779400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs376440714	chr12:41779436-41779437	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs1902911	chr12:41779443-41779444	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs541969978	chr12:41779453-41779454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs534599417	chr12:41779460-41779461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs552723356	chr12:41779535-41779536	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs577551772	chr12:41779581-41779582	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs560094453	chr12:41779646-41779647	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs118114403	chr12:41779680-41779681	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs115449925	chr12:41779734-41779735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs191181186	chr12:41779812-41779813	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs12306958	chr12:41779816-41779817	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs528842886	chr12:41779831-41779832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs540904759	chr12:41779832-41779833	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs565149726	chr12:41779838-41779839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs550525512	chr12:41779883-41779884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs532508599	chr12:41779888-41779889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs57638447	chr12:41779901-41779902	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs374990626	chr12:41779915-41779916	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs569292069	chr12:41779926-41779927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs368496578	chr12:41779946-41779947	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs10785259	chr12:41779948-41779949	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs548810826	chr12:41779951-41779952	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs149124303	chr12:41779963-41779964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs550606014	chr12:41779978-41779979	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Cancer	20164919	CNVD

Chromatin state (count:135 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41776200-41787400	Weak transcription	Aorta	Aorta
2	chr12:41779000-41779200	Enhancers	Gastric	stomach
3	chr12:41784400-41785000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:41785400-41787000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:41787400-41787800	ZNF genes & repeats	Aorta	Aorta
6	chr12:41790400-41790600	Enhancers	Brain Germinal Matrix	brain
7	chr12:41790600-41791200	Weak transcription	Brain Germinal Matrix	brain
8	chr12:41791200-41792200	Enhancers	Brain Germinal Matrix	brain
9	chr12:41792200-41792400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:41792400-41792800	Enhancers	Brain Germinal Matrix	brain
11	chr12:41792800-41793600	Weak transcription	Brain Germinal Matrix	brain
12	chr12:41793600-41794200	Enhancers	Brain Substantia Nigra	brain
13	chr12:41793600-41794400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:41793600-41794400	Enhancers	Brain Germinal Matrix	brain
15	chr12:41793800-41794200	Enhancers	Brain Hippocampus Middle	brain
16	chr12:41793800-41794400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr12:41794200-41794400	Enhancers	Colon Smooth Muscle	Colon
18	chr12:41795400-41795600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr12:41795600-41796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:41796600-41797000	Active TSS	Brain Anterior Caudate	brain
21	chr12:41796600-41797200	Enhancers	HUVEC	blood vessel
22	chr12:41796600-41797800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr12:41796800-41797800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr12:41797000-41797600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr12:41797000-41797800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr12:41797000-41798000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr12:41797000-41798400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr12:41797000-41800600	Weak transcription	Brain Anterior Caudate	brain
29	chr12:41797200-41797800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:41797600-41798200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:41797800-41798400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:41798200-41798400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr12:41798400-41798600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr12:41798600-41799200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:41799200-41799600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
36	chr12:41799800-41800400	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:41800000-41800800	Enhancers	Fetal Brain Male	brain
38	chr12:41800600-41800800	Enhancers	Brain Angular Gyrus	brain
39	chr12:41800600-41800800	Enhancers	Brain Anterior Caudate	brain
40	chr12:41800600-41801200	Enhancers	Brain Substantia Nigra	brain
41	chr12:41800600-41801600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:41800600-41801800	Enhancers	Fetal Brain Female	brain
43	chr12:41800600-41802200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr12:41800800-41801000	Enhancers	Brain Cingulate Gyrus	brain
45	chr12:41800800-41801000	Enhancers	Brain Hippocampus Middle	brain
46	chr12:41800800-41801000	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr12:41800800-41801000	Flanking Active TSS	Fetal Brain Male	brain
48	chr12:41800800-41801200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:41800800-41801200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:41800800-41801200	Flanking Active TSS	Brain Anterior Caudate	brain

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