The OP wanted the same number in front of each occurence of the same ID, not a slowly increasing number counting different IDs so far. This can be achieved with a hash storing unique numbers rather than repetition counts.

use warnings;
use strict;

my $counter = 0;
my %hash;
while (<DATA>) {
    my @splits = split;
    my $snp = $splits[0];
    $hash{$snp} ||= ++$counter;
    print "$hash{$snp} $snp\n";
}

__DATA__
foo     abc
foo     cde
bar     xyz
foo     hij
[download]

This should output:

1 foo
1 foo
2 bar
1 foo
[download]

... rather than:

1 foo
1 foo
2 bar
2 foo
[download]