Meh. Remove the two pushes. Should just be:

while (<LIST1>) {
    ($V1, $V2) = split /\t/;
    $all_V1{$V1}++;
    $all_V2{$V2}++;
}
[download]

... the pushes were left overs from an earlier response I typed up but didn't submit, which used arrays.

I'll correct the code in my original answer too.