use warnings;
use strict;

my $counter = 0;
my %hash;
while (<DATA>) {
    my @splits = split;
    my $snp = $splits[0];
    $counter++ if not exists $hash{$snp};
    print "$counter $snp\n";
    $hash{$snp}++;
}

__DATA__
foo	abc
foo	cde
bar	xyz

##</code><code>##

1 foo
1 foo
2 bar