Assuming you want to include the contents of the file named in your file" field, the script could be as follows:

use Modern::Perl;

my %data = (
    'LB2241-RCC' => {
        'rs6557634' => {
            'plex' => 'W30467',
            'gt'   => 'T',
            'file' => 'file1.csv'
        },
        'rs1032807' => {
            'plex' => 'W30569',
            'gt'   => 'G',
            'file' => 'file1.csv'
        },
    }
);

foreach my $sample ( keys %data ) {
    foreach my $snpid ( keys %{ $data{$sample} } ) {
        my $plex = $data{$sample}->{$snpid}{'plex'};
        my $gt   = $data{$sample}->{$snpid}{'gt'};
        my $file = $data{$sample}->{$snpid}{'file'};
        open my $FH, '<', "./$file" or die $!;
        my $content = join ', ', <$FH>;
        say "$plex, $sample, $gt, $content";
    }
}
[download]

Output:

W30569, LB2241-RCC, G, T,T,C,CA,GT,T,GA,C,A,G,CT,T,T,CA,AG,TC,G,GA,C,T
+C,CT,AG,AG,C,GT,GA,G,GA,T
W30467, LB2241-RCC, T, T,T,C,CA,GT,T,GA,C,A,G,CT,T,T,CA,AG,TC,G,GA,C,T
+C,CT,AG,AG,C,GT,GA,G,GA,T
[download]