The strongest signal in the primary European ancestry meta-analysis, rs7868992, was also the top locus in the secondary meta-analysis, which incorporated an additional 496 non-European cases and controls from the CVCR and ANT Latin American population isolates (Figure S9). In this combined analysis, rs7868992 initially achieved a p-value of 2.94 ×10−8, surpassing the threshold for genome-wide significance. However, following imputation, this signal decreased to p=3.61 ×10−7, most likely due to the incorporation of imputed data from the 148 European-ancestry cases genotyped on the Illumina 370K, which does not directly interrogate rs7868992. Nonetheless, rs7868992 performed robustly on the other Illumina platforms used in this study based on review of the normalized intensity plots (Figure S9d) and the 100% concordance rate in all cross-platform comparisons of this SNP in HapMap duplicates from the Illumina database (Supplementary Materials). Therefore, rs7868992 remains a promising candidate, but cannot be considered a TS susceptibility variant unless it is replicated in an independent sample.
