To add to wsfp's excellent answer, this is an almost classic case where a hash will make the code simpler and (probably) quicker:

#!/usr/local/bin/perl

use strict;
use warnings;

my %hash;
@hash{qw(one three)} = undef;

while(my $var1 = <DATA>){ 
    chomp $var1;
    if (exists $hash{$var1}) {
        print "line is $.\n";  
    }
}

__DATA__
one
two
three
four
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