||Genome-scale networks can now be reconstructed based on high-throughput data sets. Mathematical analyses of these networks are used to compute their candidate functional or phenotypic states. Analysis of functional states of networks shows that the activity of biochemical reactions can be highly correlated in physiological states, forming so-called co-sets representing functional modules of the network. Thus, detrimental sequence defects in any one of the genes encoding members of a co-set can result in similar phenotypic consequences. Here we show that causal single nucleotide polymorphisms in genes encoding mitochondrial components can be classified and correlated using co-sets.