foreach (@list1){
    @temp=split(/\s+/, $_);
}

##</code><code>##

# create lookup table

while (<FH2>) {   
    chomp;
    $CVDgenes{$_} = 1;
}

# go through the other file and check if its entries 
# are found in the lookup table:

while (<FH1>){
    chomp;
    my ($gene, $gid) = split(/\s+/, $_);
    if (exists $CVDgenes{$gene}) {
        print "The GID for gene $gene is $gid\n";
    }
}