So you want something like:

use strict;
use warnings;

my $first_line = <DATA>;
chomp $first_line;
my $snp_id_count;

#my $num_of_strains = 48;
print "snp_id\tstrain_id\trs_value\n";
my $skip_strain = '=';
while (<DATA>) {
    chomp;
    my @fields = split /\t/;
    my $rs     = $fields[2];
    my @ids    = @fields[4 .. $#fields];
    my $strainId;
    
    $snp_id_count++;
    
    for my $id (@ids) {
        ++$strainId;
        next if $id eq '=';
        print "$snp_id_count\t$strainId\t$rs\n";
    }
}


__DATA__
#chr  loc    rs    observ 129S1 129S4 129X1 A/J
1    3.013441    rs31192577    A/T    T    T    T    =
1    3.036178    rs32166183    A/C    C    C    C    A
1    3.036265    rs30543887    A/G    G    G    A    A
1    3.039187    rs6365082    G/T    =    =    T    T
[download]

Prints:

snp_id    strain_id    rs_value
1    1    rs31192577
1    2    rs31192577
1    3    rs31192577
2    1    rs32166183
2    2    rs32166183
2    3    rs32166183
2    4    rs32166183
3    1    rs30543887
3    2    rs30543887
3    3    rs30543887
3    4    rs30543887
4    3    rs6365082
4    4    rs6365082
[download]

If you add further columns for more strain Ids it will 'Just Work'™.