The availability of dense panels of common single nucleotide polymorphisms and of sequence variants has facilitated the study of statistical features of the genetic architecture of complex traits and diseases via whole-genome regressions (WGR). At the onset, traits were analyzed trait by trait but recently WGR have been extended for analysis of several traits jointly. The expectation is that such an approach would offer insight into mechanisms that cause trait associations, such as pleiotropy. We demonstrate that correlation parameters inferred using markers can give a distorted picture of the genetic correlation between traits. In the absence of knowledge of linkage disequilibrium relationships between quantitative or disease trait loci and markers, speculating about genetic correlation and its causes (such as pleiotropy) using genomic data is conjectural.