Abstract: Current models for the genetics of common diseases suggest that diseases are the result of the sum of variants which on their own produce a small effect on the disease phenotype. Because of this small effect, common disease variants are very difficult to find, even with the application of the powerful new methods for the study of gene variants?disease association. An alternative approach based on the functional changes due to the variants is described here. The focus is set on regulatory variants because they fit best the current models. Regulatory variants filtered by the application of bioinformatic methods are analysed in order to select those best suited for subsequent association studies. No single method can characterize the functional consequences of a variant. We compare current available and future developments of the major methods and discuss their possible application in the study of the genetics of common disease.

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