while (<$snpIn>) {
    next unless /^(\w+)\s+(\d+\.\d+)/;
    $snpLookup{$1} = $2;
}

##</code><code>##

while (<$mapIn>) {
    next unless /^(\w+)\s+(\w+)/ and exists $snpLookup{$1};
    print "$1    $2\n";
}