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TopSNP. Pvalue: smallest single-SNP GWAS p-value in the segment. GCTA: a tool for Genome-wide Complex Trait Analysis. For a case-control study, under the assumption of threshold model, cases are sampled from the individuals with disease liabilities ( y ) exceeding the threshold of normal distribution truncating the proportion of K (disease prevalence) and controls are sampled from the remaining individuals. Specify the number of cases and the number of controls, e.