To determine whether any of the cisSNPs significant at q<0.05 influenced risk of AD, we obtained meta-analyses results from the ADGC [28]. The cohorts that are assessed by ADGC, as well as the methodological details of the meta-analyses are described in detail in a recent publication [28]. Briefly, the meta-analyses of the ADGC dataset results reported here (Supplementary Tables 17 and 18 in Dataset S1) are generated from the combined analyses of stage 1 and stage 2 cohorts (Text S1), with detailed descriptions provided elsewhere [28]. Stage 1 cohorts are comprised of 8,309 LOAD cases and 7,366 cognitively normal elder controls. Stage 2 has 3,531 LOAD vs. 3,565 control subjects. Each cohort was tested for AD risk association using a logistic regression approach, assuming an additive model and adjusting for age, sex, APOE ε4 dosage and principal components from EIGENSTRAT [59]. The meta-analyses results were generated using the inverse variance method implemented in the software package METAL [61].
