Variant report

Variant	nsv895081
Chromosome Location	chr10:43474694-43506861
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	ATF1	chr10:43474747-43475125	K562	blood:	n/a	n/a
2	BHLHE40	chr10:43476829-43477169	K562	blood:	n/a	chr10:43476970-43476986
3	BHLHE40	chr10:43484487-43484837	K562	blood:	n/a	n/a
4	CCNT2	chr10:43476863-43477053	K562	blood:	n/a	n/a
5	CEBPB	chr10:43477134-43477208	K562	blood:	n/a	n/a
6	CEBPB	chr10:43474862-43474980	K562	blood:	n/a	n/a
7	CTCF	chr10:43475960-43476110	WERI-Rb-1	eye:	n/a	n/a
8	CTCF	chr10:43506000-43506150	GM12865	blood:	n/a	n/a
9	CTCF	chr10:43483840-43483990	GM12866	blood:	n/a	n/a
10	CTCF	chr10:43475360-43475510	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr10:43475300-43475530	BE2_C	brain:	n/a	n/a
12	CTCF	chr10:43494840-43494900	K562	blood:	n/a	n/a
13	CTCF	chr10:43490594-43490694	GM20000	blood:	n/a	n/a
14	CTCF	chr10:43505980-43506130	GM12878	blood:	n/a	n/a
15	CUX1	chr10:43476952-43477062	K562	blood:	n/a	n/a
16	E2F6	chr10:43484567-43484805	K562	blood:	n/a	n/a
17	E2F6	chr10:43484578-43484756	K562	blood:	n/a	n/a
18	E2F6	chr10:43478358-43478780	H1-hESC	embryonic stem cell:	n/a	n/a
19	EGR1	chr10:43484493-43484835	K562	blood:	n/a	chr10:43484693-43484704 chr10:43484660-43484669 chr10:43484659-43484672 chr10:43484691-43484705 chr10:43484660-43484670 chr10:43484659-43484669 chr10:43484693-43484704 chr10:43484659-43484672 chr10:43484692-43484705 chr10:43484659-43484672 chr10:43484659-43484672
20	EGR1	chr10:43484431-43484901	K562	blood:	n/a	chr10:43484693-43484704 chr10:43484660-43484669 chr10:43484659-43484672 chr10:43484691-43484705 chr10:43484660-43484670 chr10:43484659-43484669 chr10:43484693-43484704 chr10:43484659-43484672 chr10:43484692-43484705 chr10:43484659-43484672 chr10:43484659-43484672
21	ELF1	chr10:43484513-43484792	K562	blood:	n/a	n/a
22	EP300	chr10:43485843-43488472	SK-N-SH	brain:	n/a	chr10:43487845-43487861 chr10:43486353-43486369 chr10:43487362-43487378
23	EP300	chr10:43476532-43477685	SK-N-SH_RA	brain:	n/a	n/a
24	EP300	chr10:43476929-43477282	K562	blood:	n/a	n/a
25	EP300	chr10:43484600-43484758	K562	blood:	n/a	n/a
26	EP300	chr10:43476568-43477666	SK-N-SH_RA	brain:	n/a	n/a
27	EP300	chr10:43474569-43475003	SK-N-SH_RA	brain:	n/a	n/a
28	EP300	chr10:43475096-43475410	SK-N-SH_RA	brain:	n/a	n/a
29	EP300	chr10:43486591-43487378	SK-N-SH_RA	brain:	n/a	chr10:43487362-43487378
30	EP300	chr10:43476840-43477339	SK-N-SH	brain:	n/a	n/a
31	EP300	chr10:43473513-43475864	SK-N-SH	brain:	n/a	n/a
32	EP300	chr10:43475036-43475379	SK-N-SH_RA	brain:	n/a	n/a
33	EP300	chr10:43486685-43487394	SK-N-SH_RA	brain:	n/a	chr10:43487362-43487378
34	EP300	chr10:43475897-43478281	SK-N-SH	brain:	n/a	n/a
35	GATA1	chr10:43476687-43477887	K562	blood:	n/a	chr10:43476963-43476973 chr10:43477139-43477146 chr10:43477139-43477146 chr10:43477118-43477126 chr10:43476964-43476973 chr10:43477139-43477149 chr10:43477139-43477146 chr10:43476962-43476974
36	GATA2	chr10:43476504-43477595	SH-SY5Y	brain:	n/a	chr10:43476963-43476973 chr10:43477139-43477146 chr10:43477139-43477146 chr10:43477118-43477126 chr10:43476964-43476973 chr10:43477139-43477149 chr10:43477139-43477146 chr10:43476962-43476974
37	GATA2	chr10:43486723-43487405	SH-SY5Y	brain:	n/a	chr10:43487351-43487360
38	GATA2	chr10:43474698-43475483	SH-SY5Y	brain:	n/a	chr10:43474859-43474876
39	GATA3	chr10:43476721-43477552	SK-N-SH	brain:	n/a	chr10:43476963-43476973 chr10:43477139-43477146 chr10:43477139-43477146 chr10:43477118-43477126 chr10:43476964-43476973 chr10:43477139-43477149 chr10:43477139-43477146 chr10:43476962-43476974
40	GATA3	chr10:43486757-43487335	SK-N-SH	brain:	n/a	n/a
41	GATA3	chr10:43476664-43477427	SK-N-SH	brain:	n/a	chr10:43476963-43476973 chr10:43477139-43477146 chr10:43477139-43477146 chr10:43477118-43477126 chr10:43476964-43476973 chr10:43477139-43477149 chr10:43477139-43477146 chr10:43476962-43476974
42	GATA3	chr10:43476612-43477348	SH-SY5Y	brain:	n/a	chr10:43476963-43476973 chr10:43477139-43477146 chr10:43477139-43477146 chr10:43477118-43477126 chr10:43476964-43476973 chr10:43477139-43477149 chr10:43477139-43477146 chr10:43476962-43476974
43	GATA3	chr10:43474771-43475223	SH-SY5Y	brain:	n/a	chr10:43474859-43474876
44	GATA3	chr10:43486798-43487178	SH-SY5Y	brain:	n/a	n/a
45	GATA3	chr10:43486781-43487345	SK-N-SH	brain:	n/a	n/a
46	GATA3	chr10:43506704-43506904	SH-SY5Y	brain:	n/a	chr10:43506847-43506854
47	HMGN3	chr10:43484588-43484761	K562	blood:	n/a	n/a
48	HMGN3	chr10:43496188-43496220	K562	blood:	n/a	n/a
49	JUN	chr10:43474770-43475110	HepG2	liver:	n/a	chr10:43474945-43474958 chr10:43474949-43474958
50	JUN	chr10:43474550-43475213	K562	blood:	n/a	chr10:43474945-43474958 chr10:43474949-43474958

No.	Distal block	Cell Line	Cell type
1	chr10:43482866..43485744-chr10:43490374..43493373,2	K562	blood:
2	chr10:43474227..43476529-chr10:43479652..43481353,2	MCF-7	breast:
3	chr10:43477135..43480872-chr10:43482623..43485089,4	MCF-7	breast:
4	chr10:43486095..43489357-chr10:43490017..43492485,3	MCF-7	breast:
5	chr10:43472744..43475645-chr10:43482853..43485433,2	K562	blood:
6	chr10:43474536..43476774-chr10:43520389..43522895,3	MCF-7	breast:
7	chr10:43484291..43485932-chr10:43488466..43491187,2	MCF-7	breast:
8	chr10:43477135..43480872-chr10:43482623..43485089,4	MCF-7	breast:
9	chr10:43442278..43444933-chr10:43480874..43482921,2	K562	blood:
10	chr10:43496061..43498951-chr10:43575386..43576961,2	MCF-7	breast:
11	chr10:43472744..43475645-chr10:43482853..43485433,2	K562	blood:
12	chr10:43481086..43483555-chr10:43520776..43523098,2	MCF-7	breast:
13	chr10:43484291..43485932-chr10:43488466..43491187,2	MCF-7	breast:
14	chr10:43494956..43496475-chr10:43498262..43500423,2	K562	blood:
15	chr10:43494122..43496846-chr10:43520768..43523139,2	MCF-7	breast:
16	chr10:43487519..43490099-chr10:43491819..43493663,2	MCF-7	breast:
17	chr10:43495233..43497382-chr10:43502437..43504369,2	MCF-7	breast:
18	chr10:43495233..43497382-chr10:43502437..43504369,2	MCF-7	breast:
19	chr10:43486095..43489357-chr10:43490017..43492485,3	MCF-7	breast:
20	chr10:43494956..43496475-chr10:43498262..43500423,2	K562	blood:
21	chr10:43450408..43453024-chr10:43497080..43499917,2	K562	blood:
22	chr10:43474227..43476529-chr10:43479652..43481353,2	MCF-7	breast:
23	chr10:43472378..43475581-chr10:43520718..43522410,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RET-3	chr10:43487762-43487899	ucscGeneNc_uc001jba_2
2	lnc-RASGEF1A-1	chr10:43475731-43476007	XLOC_008790
3	lnc-RET-3	chr10:43487172-43487532	ucscGeneNc_uc001jba_2
4	lnc-RASGEF1A-1	chr10:43476816-43476955	XLOC_008790
5	lnc-RET-3	chr10:43489288-43490153	ucscGeneNc_uc001jba_2
6	lnc-RET-2	chr10:43481122-43481247	NONHSAT012938
7	lnc-RET-2	chr10:43482124-43482459	NONHSAT012938
8	lnc-RET-3	chr10:43486575-43486975	ucscGeneNc_uc001jba_2

miRNA name	Chromosome Location	mirBase accession
hsa-miR-5100	chr10:43493078-43493099	MIMAT0022259

Variant related genes	Relation type
MIR5100	TF binding region
ENSG00000229630	TF binding region
ENSG00000263795	chromatin interactions

Extended variants
information (count: 1372 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:1372 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10900291	chr10:43474694-43474695	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs573788405	chr10:43474746-43474747	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs76000027	chr10:43474788-43474789	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs559242760	chr10:43474791-43474792	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs533083684	chr10:43474874-43474875	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs544884443	chr10:43474947-43474948	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs563751231	chr10:43474954-43474955	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs530767960	chr10:43474958-43474959	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs573366864	chr10:43474985-43474986	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs549468372	chr10:43475013-43475014	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs528948314	chr10:43475032-43475033	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs567621711	chr10:43475040-43475041	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs528718622	chr10:43475042-43475043	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs73262104	chr10:43475059-43475060	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs142150090	chr10:43475061-43475062	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs184810390	chr10:43475062-43475063	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs557366671	chr10:43475087-43475088	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs548810756	chr10:43475115-43475116	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs536601181	chr10:43475143-43475144	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs190208165	chr10:43475152-43475153	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs151222091	chr10:43475165-43475166	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs192340017	chr10:43475208-43475209	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs552781152	chr10:43475209-43475210	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs577415744	chr10:43475267-43475268	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs184834064	chr10:43475274-43475275	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs544908429	chr10:43475275-43475276	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs531360286	chr10:43475281-43475282	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs189607619	chr10:43475306-43475307	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs78190284	chr10:43475383-43475384	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs2488279	chr10:43475416-43475417	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs542628523	chr10:43475480-43475481	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs73262106	chr10:43475483-43475484	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs528631982	chr10:43475490-43475491	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
34	rs181976677	chr10:43475505-43475506	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs375517706	chr10:43475516-43475517	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs1541225	chr10:43475568-43475569	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs532704843	chr10:43475601-43475602	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs551264343	chr10:43475610-43475611	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs56677915	chr10:43475648-43475649	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs537070170	chr10:43475649-43475650	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs58032110	chr10:43475651-43475652	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs79164303	chr10:43475653-43475654	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs534449284	chr10:43475679-43475680	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs41295811	chr10:43475699-43475700	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs41295813	chr10:43475719-43475720	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs141393534	chr10:43475750-43475751	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs557246060	chr10:43475757-43475758	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs532703856	chr10:43475759-43475760	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs11239851	chr10:43475778-43475779	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs185980665	chr10:43475791-43475792	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Pancreatic endocrine tumor	17639061	CNVD
Gastric cancer	17908304	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Melanoma	18172304	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Lung cancer	18438408	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	20724749	CNVD
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	18632612	CNVD
Autism	18414403	CNVD
Cockayne syndrome	18421352	CNVD
Glioblastoma	16823260	CNVD
Medulloblastoma	16968546	CNVD
Neuroblastoma	17533364	CNVD
Mental retardation	21062444	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Testicular germ cell tumor	18059402	CNVD
Squamous cell cancer	21044232	CNVD
Glioma	21971842	CNVD
Cancer	21637783	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	22241247	CNVD
Intellectual disability	21811512	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Obesity	21956041	CNVD
Renal cell carcinoma	18765545	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21948486	CNVD
Dysmorphic features	21948486	CNVD
Epilepsy	21948486	CNVD
Breast cancer	21509527	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43471000-43474800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:43471200-43474800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr10:43474200-43475000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr10:43474400-43475000	Enhancers	Fetal Brain Male	brain
5	chr10:43474600-43474800	Enhancers	Gastric	stomach
6	chr10:43474600-43475000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:43474600-43475400	Enhancers	Brain Germinal Matrix	brain
8	chr10:43474800-43475000	Enhancers	K562	blood
9	chr10:43474800-43475200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr10:43474800-43475200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:43474800-43475200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:43474800-43475400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr10:43474800-43475400	Weak transcription	Gastric	stomach
14	chr10:43474800-43476000	Enhancers	Pancreas	Pancrea
15	chr10:43475000-43475200	Enhancers	Stomach Mucosa	stomach
16	chr10:43475000-43477200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:43475200-43475600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr10:43475200-43475600	Enhancers	Dnd41	blood
19	chr10:43475400-43475600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr10:43475400-43475600	Bivalent Enhancer	Fetal Stomach	stomach
21	chr10:43475400-43476600	Weak transcription	Stomach Mucosa	stomach
22	chr10:43475400-43477600	Enhancers	Gastric	stomach
23	chr10:43475600-43477800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr10:43476000-43476200	Weak transcription	Pancreas	Pancrea
25	chr10:43476000-43476200	Active TSS	Spleen	Spleen
26	chr10:43476000-43479000	Enhancers	Fetal Intestine Small	intestine
27	chr10:43476200-43477200	Enhancers	Pancreas	Pancrea
28	chr10:43476200-43482600	Weak transcription	Spleen	Spleen
29	chr10:43476400-43479800	Enhancers	Fetal Intestine Large	intestine
30	chr10:43476600-43477800	Enhancers	Stomach Mucosa	stomach
31	chr10:43476800-43477400	Enhancers	Left Ventricle	heart
32	chr10:43477200-43477600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:43477200-43477600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr10:43477200-43477600	Enhancers	Esophagus	oesophagus
35	chr10:43477200-43478000	Enhancers	Duodenum Mucosa	Duodenum
36	chr10:43477600-43478800	Weak transcription	Gastric	stomach
37	chr10:43477600-43479000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:43477600-43482600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr10:43478000-43478600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr10:43478400-43479400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr10:43478600-43478800	Enhancers	Duodenum Mucosa	Duodenum
42	chr10:43478800-43479000	Enhancers	Gastric	stomach
43	chr10:43479000-43479200	Enhancers	Fetal Muscle Leg	muscle
44	chr10:43479000-43479400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:43479000-43479600	Weak transcription	Gastric	stomach
46	chr10:43479400-43482800	Weak transcription	Fetal Muscle Leg	muscle
47	chr10:43479600-43479800	Enhancers	Gastric	stomach
48	chr10:43480800-43481000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr10:43481000-43481200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr10:43481200-43482800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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