PCR amplification and sequencing of your region of interest might be an option, depending on what you are exactly looking for and how large the region you are interested in is.

Yes, PCR amplification using SNP genotyping could be done to know the sequence variants..

We frequently use single stranded conformational polymorphism (SSCP) for screening for variants. It can be 100% accurate for PCR products under 300 bp.

Dear Bamidele,

Various method can be applied for SNP genotyping including Allele specific PCR, RFLP, DNA sequencing, Melting curve analysis (using probes or dyes), pyrosequencing, Taqman allelic discrimination assay, reverse hybridization, and others. You should select among them based on your budget, applicability of the method for that SNP, sample numbers, availability of the technology and allele burden of the SNP.

Best

Designing Primers, PCR amplification and sequencing of your region of interest might be a good option.

I am grateful for all the articulate contributions from everyone of you. I think I have alternative option in hand now.

Thanks

Try ligase chain reaction.