my %dataHash;

foreach (@lines) {
    my ($key1, $key2, $val1, $val2, $rest) = split(/\s+/, $_, 5);
    my $combinedValue = "$val1,$val2";
    $key1 =~ /SNP(\d+)/;

    $dataHash{$key2}{$1} = $combinedValue;
}

foreach my $key (sort keys %dataHash) {
    my %tempHash2 = %{$dataHash{$key}};

    print $key;
    printf(" %2s %2s", split(',', $tempHash2{$_})) for sort keys %tempHash2;
    print "\n";
}