my $ctr;
while($line2=<geneREAD>)
{
	$ctr=0;
	chomp($line2);
	if($line2=~ m/^Gene:\s*(.*)/)
	{
		$geneName= $1;
		#print "$geneName\n";
		if(grep(/^$geneName$/, @geneArr))
		{
			while(substr($line2, 0 , 3) ne "---")
			{
				#print "$line2\n";
				$line2=<geneREAD>;
				chomp($line2);
				if($line2=~ m/(\d*)\s*([A-Z]*)\s*(\d*)-(\d*)/)
				{
					$epitope= $1;
					$epiSeq= $2;
					$locBeg=$3;
					$locEnd=$4;
					
					foreach $snpID(@ {$snpHash{$geneName}})
					{
						#print "$snpID $HoProPos{$snpID}\n";
						if($locBeg <= $HoProPos{$snpID} && $HoProPos{$snpID} <= $locEnd)
						{
							if($ctr== 0)
							{print OUT "Gene: $geneName\n";}
							print OUT "SNP $snpID found in epitope $epitope at protein position $HoProPos{$snpID}\n";
							$ctr=1;
						}
					}
					#print "$1 $2 $3 $4\n"
				}
			}
		}
	}
}