Nucleotide variants in microRNA regions have been associated with disease, nevertheless still few studies have addressed the allele-dependent effect of these changes. We studied microRNA genetic variation in human populations and found that while low frequency variants accumulate indistinctly in microRNA regions, the mature and seed regions tent to be depleted of high frequency variants, probably as a result of purifying selection. Comparison of pairwise population fixation indexes among regions showed that the seed had higher population fixation indexes than the other regions suggesting the existence of local adaptation in the seed region. We further performed functional studies of three microRNA variants associated with cancer (rs2910164:C > G in MIR146A, rs11614913:C > T in MIR196A2 and rs3746444:A > G in both, MIR499A and MIR499B). We found differences in the expression between alleles and in the regulation of several genes involved in cancer, such as TP53, KIT, CDH1, CLH and TERT, which may result in changes in regulatory networks related to tumorigenesis. Furthermore, luciferase-based assays showed that MIR499A could be regulating the cadherin CDH1 and the cell adhesion molecule CLH1 in an allele-dependent fashion. A better understanding of the effect of microRNA variants associated with disease could be key in our way to a more personalized medicine. This article is protected by copyright. All rights reserved.