To define genomic loci of interest to the trait based on provided GWAS summary statistics, pre-calculated LD structure based on 1000G of the relevant reference population (EUR for BMI, CD and SCZ) is used. First of all, independent significant SNPs with a genome-wide significant P-value (< 5e-8) and independent from each other at r 2 < 0.6 are identified. For each independent significant SNP, all known (i.e., regardless of being available in the GWAS input) SNPs that have r 2 ≥ 0.6 with one of the independent significant SNPs are included for further annotation (candidate SNPs). These SNPs may thus include SNPs that were not available in the GWAS input, but are available in the 1000G reference panel and are in LD with an independent significant SNP. Candidate SNPs can be filtered based on a user-defined minor allele frequency (MAF, ≥0.01 by default).
