You are part way there. But really what you want is a hash of hash of arrays. Consider:

use strict;
use warnings;

my %data;

while (<DATA>) {
    chomp;
    my ($snp, $ind, @parts) = split;

    next if @parts < 2;

    $data{$ind}{$snp} = \@parts;
}

for my $ind (sort keys %data) {
    print "$ind";

    for my $snp (sort keys %{$data{$ind}}) {
        my $parts = $data{$ind}{$snp};
        
        print "\t$parts->[0]\t$parts->[1]";
    }

    print "\n";
}

__DATA__
SNP5    IND1    A5    C5    0.8
SNP2    IND1    A2    C2    0.8
SNP1    IND1    A1    C1    0.8
SNP3    IND1    A3    C3    0.8
SNP4    IND1    A4    C4    0.8
SNP5    IND2    G5    T5    0.8
SNP2    IND2    G2    T2    0.8
SNP1    IND2    G1    T1    0.8
SNP3    IND2    G3    T3    0.8
SNP4    IND2    G4    T4    0.8
[download]

Prints:

IND1    A1    C1    A2    C2    A3    C3    A4    C4    A5    C5
IND2    G1    T1    G2    T2    G3    T3    G4    T4    G5    T5
[download]