Most biological traits are regulated by both genetic and environmental factors. Individual loci contributing to the phenotypic diversity in a population are generally identified by their contributions to the trait mean.Genome-wide association (GWA) analyses can also detect loci based on variance differences between genotypes and several hypotheses have been proposed regarding the possible genetic mechanisms leading to such signals. Little is, however, known about what causes them and whether this genetic varianceheterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a varianceheterogeneity GWA (vGWA) signal for leaf molybdenum concentrations in Arabidopsis thaliana. Here, finemapping of this association to a ~78 kb Linkage Disequilibrium (LD)-block reveals that it emerges from the independent effects of three genetic polymorphisms on the high-variance associated version of this LDblock. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation ("missing heritability"). Two of the three polymorphisms on the high-variance LD-block are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ~25 kb downstream of this gene. A fourth independent association was also detected ~600 kb upstream of the LD-block. Testing of T-DNA knockout alleles for genes in the associated regions suggest AT2G25660 (unknown function) and AT2G26975 (Copper Transporter 6; COPT6) as the strongest candidates for the associations outside MOT1. Our results show that multi-allelic genetic architectures within a single LD-block can lead to a variance-heterogeneity between genotypes in natural populations. Further they provide novel insights into the genetic regulation of ion homeostasis in A. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations.