One common reason that Ion AmpliSeq™ Designer filters a region would be that it is a nonunique sequence and would hybridize in other areas of the genome and thus be deleterious to your reaction. BLAST, the Basic Local Alignment Search Tool, finds regions of local similarity between sequences.
Using the UCSC Genome Browser, enter the region that has been filtered into the results of your design.
Copy the sequence, and run a BLAST search on this sequence.
Select Human, running a nucleotide query.
If the search returns multiple results for that query, Ion AmpliSeq™ Designer has filtered this to minimize off-target hybridization.
