In line with other work, we define the effective number of SNPs, S, as the number of haplotype blocks (i.e., independent chromosome segments) [40], where variation in each block is tagged by precisely one genotyped SNP. By genotyped SNPs we also mean imputed SNPs. Hence, in our framework, there are S SNPs contributing to the polygenic score. Due to linkage disequilibrium (LD) this number is likely to be substantially lower than the total number of SNPs in the genome [41], and is inferred to lie between as little as 60,000 [15] and as much as 5 million [41].
