LD calculation is the first step to characterize risk loci of GWAS by computing population specific LD structure, so called clumping which identifies independent significant SNPs and defines the genomic risk loci. PLINK26 is the most widely used software for this task which takes GWAS summary statistics (requiring a reference panel) or genotype data as input. In FUMA, this task is automated by using pairwise LD (r 2) of SNPs in the reference panel (1000 genomes project phase 327) pre-computed by PLINK, resulting in a list of independent significant SNPs, lead SNPs and genomic risk loci based on the GWAS input file. FUMA also adds SNPs to the identified risk loci that do not have a P-value (i.e., they were not available in the GWAS input file), but that are LD proxies of the identified lead SNPs, as these SNPs might be causally relevant. Alternatively, users can pre-compute lead SNPs or risk loci and upload these to FUMA.
