Disease and trait association information (Study) are obtained from the GWAS which links disease status (or other trait measurements) to common genetic variation. A common association significance threshold of P < 5e–8 is set for all studies. While some studies provide the complete summary statistics, others only report the lead variant (VL) at each associated locus. However, it cannot be assumed that the VL is causing the association; due to linkage disequilibrium (LD), the VL might belong to a set of SNPs that have travelled together with the true causal SNP on a haplotype block. For this reason, fine-mapping/credible set analysis and LD expansion are implemented to include all tag variants (VT) and provide a more comprehensive set of potentially causal variants linked to the trait (Figure 1C).
