Given that the CC and FS phenotypic approaches provide conceptually different but otherwise complementary information, we estimated the overlap in their association signals. These phenotypes were highly correlated in the different cohorts (0.88–0.94). Overall rank-based correlations between the CC and FS association effects were 0.61. The degree of correlation increased with decreasing p-value threshold, ranging from 0.275 to 0.899 (Supplementary Table S3). The most significant SNPs all have the same direction of effect (top 1,000 SNPs in CC and top 1,500 SNPs in FS); indeed, among the approximately 30% of total SNPs with opposite sign, none had even suggestively significant association (P<1×10−5). However, among ~1.4M independent SNPS (pruned at r2=0.4), significantly more with P<10−5 were identified for the FS phenotype than for the CC phenotype: 42 verses 18 (test p-value=0.0034).
