Mechanisms by which a SNP or other genetic variant may affect the in vivo level of activity of a protein nearby in the DNA sequence. At the DNA level, there may be an impact on the efficiency of transcription through effects on regulatory (a) and transcription factor (b) binding. At the RNA level, message stability and efficiency of translation may be altered by binding of protein protective factors (c) and microRNAs (d); or by a change in message structure propensities (e); or a change in sequence due to altered splicing either through direct impact on a splice junction (f) or on an auxiliary splicing signal (g). At the protein level, there may be an effect on the efficiency of folding (h) or protein half-life through destabilization of the tertiary structure (i). These variants may also cause aggregation, with toxic consequences. There may also be an effect on protein function (j), including ligand binding, catalysis, allosteric regulation, post-translational modification, and transport.