Variant report

Variant	rs2404604
Chromosome Location	chr15:76991105-76991106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1011083	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011084	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152247	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10851888	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10851889	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072600	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072602	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072607	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072610	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072611	0.84[AMR][1000 genomes]
rs11072612	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072613	0.88[AMR][1000 genomes]
rs11072614	0.84[AMR][1000 genomes]
rs11072616	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072618	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072619	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072620	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072625	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072626	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072628	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072631	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11629727	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630185	0.87[AMR][1000 genomes]
rs11630402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631082	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11631394	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632670	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632765	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633309	0.88[AMR][1000 genomes]
rs11633869	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11634266	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11635162	0.88[AMR][1000 genomes]
rs11635273	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636612	0.82[AMR][1000 genomes]
rs11637096	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11637494	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11852395	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11852777	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11854850	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11855296	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855762	0.88[EUR][1000 genomes]
rs12437981	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12439141	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440511	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440691	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591622	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592686	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898416	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12898810	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12904149	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904417	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905181	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12910081	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910820	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12913024	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12914196	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12915184	0.88[AMR][1000 genomes]
rs1443115	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1484990	0.81[ASN][1000 genomes]
rs1603860	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1809875	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2120109	0.91[AFR][1000 genomes]
rs2164102	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2404734	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454451	0.81[EUR][1000 genomes]
rs28823285	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28895952	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34103231	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34215663	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34998733	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35374222	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35710279	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36114653	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3910756	0.84[AMR][1000 genomes]
rs4312276	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886816	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886819	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886823	0.81[AMR][1000 genomes]
rs4886837	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55746932	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56339024	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57682236	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60702982	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62026889	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62026898	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165053	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178250	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7181506	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8025991	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8029283	0.83[EUR][1000 genomes]
rs920712	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9635380	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs965818	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv904404	chr15:76869929-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
11	nsv904405	chr15:76869929-77047915	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
12	nsv904406	chr15:76869929-77085283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv904407	chr15:76869929-77121196	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
14	nsv904408	chr15:76884127-77085283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1046858	chr15:76892097-77020971	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv542440	chr15:76892097-77020971	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1043066	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv542441	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv904409	chr15:76893186-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv904410	chr15:76893186-77047915	ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv904411	chr15:76893186-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv904412	chr15:76910031-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv904413	chr15:76923917-76995150	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv457206	chr15:76971456-77121196	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv570110	chr15:76971456-77121196	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2404604	SCAPER	cis	Esophagus Mucosa	GTEx
rs2404604	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs2404604	SCAPER	cis	Whole Blood	GTEx
rs2404604	SCAPER	cis	Esophagus Muscularis	GTEx
rs2404604	SCAPER	cis	Muscle Skeletal	GTEx
rs2404604	SCAPER	cis	Artery Tibial	GTEx
rs2404604	SCAPER	cis	Adipose Subcutaneous	GTEx
rs2404604	SCAPER	cis	Thyroid	GTEx
rs2404604	SCAPER	cis	lung	GTEx
rs2404604	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2404604	SCAPER	cis	Nerve Tibial	GTEx
rs2404604	ISL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76882200-76991400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:76902600-76992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:76936600-76991800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:76940200-76991800	Weak transcription	Left Ventricle	heart
5	chr15:76941400-76991600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:76942400-76991800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:76947400-76991600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr15:76947400-76991600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:76954200-76992000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:76957600-76991600	Weak transcription	Liver	Liver
11	chr15:76957800-76991200	Weak transcription	Primary T cells from cord blood	blood
12	chr15:76961200-76992000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:76972400-76991400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:76972600-76991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:76972600-76991800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:76973200-76991600	Weak transcription	Primary B cells from cord blood	blood
17	chr15:76973200-76991800	Weak transcription	Aorta	Aorta
18	chr15:76975000-76991800	Weak transcription	Thymus	Thymus
19	chr15:76975200-76991800	Weak transcription	Fetal Stomach	stomach
20	chr15:76976800-76991200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:76980200-76991800	Weak transcription	Fetal Intestine Small	intestine
22	chr15:76981800-76991800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:76982400-76991200	Weak transcription	Adipose Nuclei	Adipose
24	chr15:76982400-76991600	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:76984200-77008200	Weak transcription	Fetal Lung	lung
26	chr15:76984400-76991600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:76986200-76991800	Weak transcription	Pancreas	Pancrea
28	chr15:76986400-76992000	Weak transcription	HepG2	liver
29	chr15:76986400-77002200	Weak transcription	Psoas Muscle	Psoas
30	chr15:76987400-76991800	Weak transcription	Right Ventricle	heart
31	chr15:76988400-76991800	Weak transcription	Dnd41	blood
32	chr15:76989200-76991400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:76989200-76991800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:76989400-76991800	Weak transcription	Fetal Brain Female	brain
35	chr15:76989400-76991800	Weak transcription	GM12878-XiMat	blood
36	chr15:76989400-76992000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:76989600-76991200	Weak transcription	Fetal Thymus	thymus
38	chr15:76989600-76991400	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:76989600-76991600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:76989600-76991800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:76989600-77055800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:76989800-76991600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:76989800-76991600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:76989800-76991600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:76989800-76991600	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:76989800-76991600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:76989800-76991600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:76990000-76991600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:76990000-76991600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:76990000-76991600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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