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]

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

In reply to Re: fetching from a hash by CountZero
in thread fetching from a hash by Anonymous Monk

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