Based on the 1000 Genomes Project LD structure, we found that rs393152 was in r2 LD > 0.8 with a number of variants within the MAPT gene on chromosome 17 (Figure 2a). Fine mapping showed that rs1981997 constituted the peak of the AD association signal within MAPT (r2 = 1.0 with rs393152 in HapMap 2; Figure 2b). Across the ADGC (risk allele = A, two tailed p-value = = 9.54 × 10−5, OR = 0.90, 95% CI = 0.85–0.95), GERAD (one tailed p-value = 0.006, OR = 0.92, 95% CI = 0.86–0.98, deCODE (one tailed p-value = 0.018, OR = 0.92, 95% CI = 0.84–0.99), Oslo (one tailed p-value = 0.047, OR = 0.85, 95% CI = 0.71–1.03) and CHARGE (one-tailed p-value = 0.0327, OR = 0.96, 95% CI = 0.84–1.08) cohorts, the leading SNP in the MAPT region, rs1981997, demonstrated a similar meta-analysis p-value to rs393152 (two-tailed meta-analysis p-value of 1.29 × 10−7, see Supplemental Figure 4) providing further evidence that our AD/PD pleiotropic variant was tagging the MAPT gene and not a false positive result. We also note
