Functional annotation of four types of disease associated variants. (A), (B), (C) and (D) are the annotation results for Complex disease variants, Mendelian disease variants, Cancer predisposing germline mutations and Recurrent cancer somatic mutations using Ensembl Variants Effect Predictor respectively. Majority of complex disease variants are noncoding variants. Mendelian disease variants and recurrent cancer somatic mutations share similar pattern of functional effects. Compared with complex disease variants, more other three types of disease variants locate within coding region. (E) The histogram for the distribution of consequences of the four types of disease variants. The consequences by Mendelian disease variants, cancer predisposing germline variants and recurrent cancer somatic mutations are more serious than that of complex disease variants.