Applying a Mendelian randomization (MR) framework to study causal inferences in “omics” data. In conventional MR, a genetic instrument (G) is used as a proxy for an exposure (X), to study its relationship with a disease outcome (Y). A causal relationship of X on Y exists, if G is related to Y via its effects on X. An example is the use of genetic polymorphisms related to bone mineral density (BMD) to study the causal relationship between low BMD (X) and fracture risk (Y). When applied to “omics” data, X represents an intermediate molecular trait (i.e., mRNA, DNA methylation, or protein level) mediating the relationship between genotype (G) and disease outcome (Y). Since the intermediate trait is gene-specific, finding of a causal relationship is helpful in defining which gene (or regulatory element in the case of DNA methylation) underlies the association between G and Y. Causal inference using MR relies on the exclusion of horizontal pleiotropy, confounding by linkage disequilibrium and reverse causality. (i) Causality/vertical pleiotropy: G has a causal effect on intermediate molecular trait X, which in turn has a causal effect on Y. (ii) Horizontal pleiotropy: G has a causal effect on both X and Y via independent pathways. (iii) Linkage disequilibrium: G has a causal effect on X, but its relationship with Y is a consequence of linkage disequilibrium with a separate genetic variant causal for Y. (iv) Reverse causality: G has a causal effect on Y which subsequently alters X.