Hi All,
A neat and quick solution for this task was suggested by my colleague and I want to share it with you all.

1. Load SNPs into a hash
2. Loop through the target region which is of the format:
   chr start end
3. Foreach target region, set a counter, as long as the counter is less than end, check if each position in the target region is in the SNP hash, if so, print the SNP hash value.

Since the SNPs is in a hash, the lookup is really quick !