In that case, the following should be close to what you’re looking for:

use strict;
use warnings;

open(my $f1, '<', $ARGV[0])
    or die "Could not open '$ARGV[0]' for reading, stopped";

open(my $f2, '<', $ARGV[1])
    or die "Could not open '$ARGV[1]' for reading, stopped";

my @arr1 = <$f1>;
my @arr2 = <$f2>;

close $f1
    or die "Could not close '$ARGV[0]', stopped";

close $f2
    or die "Could not close '$ARGV[1]', stopped";

my %hash;

for my $element (@arr2)
{
    push @{ $hash{$1} }, $2
        if $element =~ m{ ^ \s* (rs\d+) \s+ \** (\w{2}) }x;
}

my $i = 0;

for my $element (@arr1)
{
    if (my ($rsid, $base1, $description) =
        $element =~ m{ ^ \s* (rs\d+) \s+ \** (\w{2}) \** \s+ (.*) $ }x
+)
    {
        if (exists $hash{$1})
        {
            for my $base2 (@{ $hash{$1} })
            {
                print "$rsid $base1 $base2 $description\n";
                ++$i;
            }
        }
    }
}

print "Found $i matches\n";
[download]

Output:

23:14 >perl 1852_SoPW.pl file1 file2
rs492602 CC GG Vitamin B12 deficiency    FUT2    Higher levels of vita
+min B12
rs492602 CC CC Vitamin B12 deficiency    FUT2    Higher levels of vita
+min B12
rs492602 CT GG Vitamin B12 deficiency    FUT2    Normal levels of vita
+min B12
rs492602 CT CC Vitamin B12 deficiency    FUT2    Normal levels of vita
+min B12
rs492602 TT GG Vitamin B12 deficiency    FUT2    Normal levels of vita
+min B12
rs492602 TT CC Vitamin B12 deficiency    FUT2    Normal levels of vita
+min B12
Found 6 matches

23:14 >
[download]

Hope that helps,