use strict;
use warnings;

my @template = qw(
  rs12272511 rs7107801 rs11027752 rs12421837
);

my $small_matrix = <<'END';
             rs12272511 rs11027752 rs12421837
rs12272511  1.0 .844 .276
rs11027752  .267 1.0 -.980
rs12421837 -.876 .374 1.0
END

open my $fh, '<', \$small_matrix;

my %ids = map { $_ => 1 } split ' ', <$fh>;

my $fmt_id_present = join ' ', map $ids{$_} ? '%s' : '0',
  @template;
my $fmt_id_missing = join ' ', ('0') x @template;

$_ = "%s $_\n" for $fmt_id_present, $fmt_id_missing;

print "\t@template\n";

for (@template) {
    if ( $ids{$_} ) {
        printf $fmt_id_present, split ' ', <$fh>;
    }
    else {
        printf $fmt_id_missing, $_;
    }
}