foreach $line (@data) {
    if ( $line =~ /$one/  && $line =~ /$two/ ) {
        if ( $line =~ /(.*?)\s+(.*?)\s+(.*?)\s+(.*)+/ ) {
            $chr  = $1;
            $pos1 = $2;
            $pos2 = $3;
        }
     ...
    }
}

##</code><code>##

if (index($line,$one) != -1 && index($line,$two) != -1) {
...
}