So, you want to overlap known microRNA loci with loci you got from a GWAS study?

Exactly

One very simple possibility is using BEDtools (https://code.google.com/p/bedtools/). In this package, there is a tool called intersectBED. You need both your lists in BED format and then you can call it like this: 'intersectBED -a GWA.bed -b microRNA.bed -wa -wb -s'. It will return you all overlapping loci.