1. A computer-implemented method of identifying elements associated with a trait, the method comprising selecting a set of discovery samples, wherein the set of discovery samples consist of samples from a single individual, samples from a single pedigree, samples from a subset of a single cohort, or samples from a single cohort; identifying, by the computer, variant genetic elements in the discovery samples; filtering, by the computer, the variant genetic elements to select candidate variant genetic elements, wherein the variant genetic elements are filtered by selecting variant genetic elements that are present in a threshold number of sequence reads, are present in a threshold percentage of sequence reads, are represented by a threshold read quality score at variant base(s), are present in sequence reads from in a threshold number of strands, are aligned at a threshold level to a reference sequence, are aligned at a threshold level to a second reference sequence, are variants that do not have biasing features bases within a threshold number of nucleotides of the variant or a combination; prioritizing, by the computer, the candidate variant genetic elements to select relevant variant genetic elements; and identifying, by the computer, an association of a relevant element with a relevant component phenotype of the trait, wherein the relevant element is selected from the relevant variant genetic elements and wherein the relevant element is an element having a threshold value of importance of the element to homeostatis relevant to the trait, intensity of the perturbation of the element, duration of the effect of the element, or a combination, wherein the relevant component phenotype is a component phenotype having a threshold value of severity, age of onset, specificity to the trait, or a combination, and wherein the association of the relevant element with the relevant component phenotype identifies the relevant element as an element associated with the trait.