my %dispatch:
sub create_function {
    my $id = shift;
    open my $fh, ">", "file_nr_$id" or die "... $!";
    return sub { my $line = shift; print $fh $line; }
}

$dispatch{$_} = create_functions($_) for @list_of_chromosomes;

# ...
# later when reading the file, assuming you have obtained a $line and an id $id from the input:
$dispatch{id}->($line);