This is not the most efficient way to process this, however intuitively its the simplest.

Initialize vectors to save output which can be combined later

snpcol=character()
gencol=character()
allelesa=character()
allelesb=character()
confcol=character()

The number of rows for final output

rowcounter=1

Foreach snp

for (i in 1:ncol(snponly)) {
    #foreach genotype
    for (j in 1:nrow(snponly)) {
      
      #only do steps if value is not NA
      if (!is.na(snponly[j,i])) {              
        alleles = unlist(strsplit(as.character(snponly[1,1]), ""))
        snpcol[rowcounter]=colnames(snponly)[i]
        gencol[rowcounter]=rownames(snponly)[j]
        allelesa[rowcounter]=alleles[1]
        allelesb[rowcounter]=alleles[2]
        confcol[rowcounter]="1"
        rowcounter=rowcounter+1
      } 
      
    }
}