one would do a foreach (<INPUT>){}

No one wouldn't. One might do while (<$inFile>) {...} however. Perl for loops like to work with lists of things and will generally create a list (except in a few special cases) which in the code you suggested would slurp the entire file into memory - something that should generally be avoided.

That aside, I find your sample code very 'busy' with repeated code and needless (and poorly named) variables. Contrast it with the following:

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 %temp
+Hash2;
    print "\n";
}
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In a teaching context it is desirable to present the cleanest code you can and to demonstrate best practises. Worthwhile exercises for the reader generally entail extending the code in various ways - not in trying to compensate for the sample's deficiencies.