The present invention discloses disease-linked SNPs, microRNAs, and microRNA-targeted mRNAs relevant to the pathogenesis of several major human disorders including, but not limited to, multiple types of cancers, type 2 diabetes, type 1 diabetes, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, bipolar disorder. Also provided are methods for the identification of disease phenotype-defining sets of SNPs, microRNAs, and mRNAs that are defined here as a “consensus disease phenocode” as well as methods of using the information provided by these consensus disease phenocodes for various diagnostic, prognostic, and/or therapeutic applications.