How do you create a loop to check values in one dataset are between two values in another dataset then count the number of minor alleles?

In R, I want to create a loop that:

If a given position on the second file (positions) is between the start and end positions (V4 and V5) on the first file, it will go through the line on the second file (X6114.... etc) and find the less frequently occurring letter (minor allele) and add it a count to V9 (the gene name).

Files

Is there a way of doing this with only 1 loop?