We also repeated our analyses using a random set of 12,111 SNPs matched with GWS SNPs on MAF and LD. Loci for these 12,111 random SNPs were defined similarly as for GWS loci. To match random SNPs with GWS SNPs on MAF and LD, we first created 28 MAF-LD classes of HM3 SNPs (7 MAF classes × 4 LD score classes). MAF classes were defined as <1%; between 1% and 5%; between 5% and 10%; between 10% and 20%; between 20% and 30%; between 30% and 40%; and between 40% and 50%. LD score classes were defined using quartiles of the HM3 LD score distribution. We next matched GWS SNPs in each of the 28 MAF-LD classes, with the same number of SNPs randomly sampled from that MAF-LD class.
