Variant report

Variant	rs6657290
Chromosome Location	chr1:78085954-78085955
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1038983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10873953	0.84[ASN][1000 genomes]
rs10873955	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11162365	0.88[EUR][1000 genomes]
rs11162366	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11162368	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162369	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11162370	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11162372	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162374	0.91[ASN][1000 genomes]
rs11162378	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11162380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11162383	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11162386	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11162387	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11578805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1166584	0.80[AMR][1000 genomes]
rs1166586	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12026939	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12132838	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12135104	0.87[ASN][1000 genomes]
rs12142441	0.80[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs12142671	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12717767	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12717768	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1389789	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389790	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539739	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1565852	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs166770	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2031342	0.80[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs203229	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs2088058	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2147318	0.94[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2296227	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs278832	0.80[ASN][1000 genomes]
rs278833	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278834	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278836	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278837	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278840	0.87[ASN][1000 genomes]
rs278841	0.85[ASN][1000 genomes]
rs278842	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs278843	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278844	0.83[ASN][1000 genomes]
rs278847	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278848	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278850	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278851	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278854	0.94[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278855	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278857	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278858	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278860	0.83[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278863	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278864	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs366467	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs371076	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3767037	0.80[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs3767038	0.80[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs4949661	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4949816	0.94[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4949817	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949818	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949822	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56688304	0.86[EUR][1000 genomes]
rs574973	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6603955	0.81[EUR][1000 genomes]
rs6603956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6603958	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6603960	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6661656	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670660	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6672200	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6674638	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687501	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6687596	0.86[EUR][1000 genomes]
rs6691317	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6693100	0.81[EUR][1000 genomes]
rs6698151	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6699205	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6699311	0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs717333	0.80[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7521042	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7524866	0.93[CEU][hapmap]
rs7535781	0.80[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7543037	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs7543125	0.84[EUR][1000 genomes]
rs7545175	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7546365	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7552291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7556227	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7556523	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8179272	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs872342	0.80[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9662527	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9988619	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6657290	AK5	cis	parietal	SCAN
rs6657290	PIGK	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78047800-78086200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:78047800-78090000	Weak transcription	NH-A	brain
3	chr1:78048000-78097400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:78063600-78097600	Weak transcription	Fetal Brain Male	brain
5	chr1:78070600-78098000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:78071000-78098000	Weak transcription	Colonic Mucosa	Colon
7	chr1:78071200-78098000	Weak transcription	Small Intestine	intestine
8	chr1:78071400-78097800	Weak transcription	Aorta	Aorta
9	chr1:78071800-78097800	Weak transcription	Ovary	ovary
10	chr1:78071800-78097800	Weak transcription	Pancreas	Pancrea
11	chr1:78072000-78094600	Weak transcription	Left Ventricle	heart
12	chr1:78072000-78097600	Weak transcription	Gastric	stomach
13	chr1:78072200-78086400	Weak transcription	HMEC	breast
14	chr1:78072200-78090600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:78072200-78098000	Weak transcription	Spleen	Spleen
16	chr1:78072400-78087200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:78072400-78097800	Weak transcription	Lung	lung
18	chr1:78072600-78086200	Weak transcription	Fetal Thymus	thymus
19	chr1:78072600-78097800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:78072800-78086400	Weak transcription	Fetal Kidney	kidney
21	chr1:78073000-78090000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:78073200-78097400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:78073600-78086800	Weak transcription	Fetal Stomach	stomach
24	chr1:78074400-78086200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:78074600-78092000	Weak transcription	Fetal Heart	heart
26	chr1:78075000-78096000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:78075000-78097800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:78075200-78098000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:78075400-78086800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:78075400-78087000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:78075400-78090800	Weak transcription	Hela-S3	cervix
32	chr1:78075400-78097800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:78075600-78090400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:78075600-78095800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:78075600-78097600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:78076000-78090400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:78076400-78086000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:78076400-78089000	Weak transcription	HepG2	liver
39	chr1:78076400-78113000	Weak transcription	Psoas Muscle	Psoas
40	chr1:78076600-78086200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:78077400-78087000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:78077400-78090200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:78077400-78090400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:78077400-78096400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:78077600-78090400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:78077600-78095600	Weak transcription	Adipose Nuclei	Adipose
47	chr1:78077800-78086200	Weak transcription	Fetal Lung	lung
48	chr1:78078400-78086200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:78078800-78088600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:78079200-78086800	Weak transcription	Placenta	Placenta

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