To demonstrate the importance of the selection of SNPs with low background LD, we conducted PCA on the study PLCOca-NHSco using all 12,536 autosomal SNPs located on chromosome 20 without filtering out SNPs in high LD, and summarized the results in Table S5 and Figure S6. By inspecting the SNP loadings on a given PC direction, it is evident that each of the top 5 PC directions is heavily driven by regional LD patterns (Figure S6). Thus, it is not surprising to see from Table S5 that the over-dispersion is still high even after the adjustment of the top 10 PCs, in contrast to the results shown in Table 5.
