Data on rs1229984 are not available in many GWAS, because it was not included in many genotyping arrays, is not well imputed, its MAF in Europeans falls below the usual cutoff (0.05), and it may fail QC due to differences in MAF among subgroups that lead to apparent violation of Hardy-Weinberg equilibrium (e.g. (Clarke et al., 2017)). In the PGC-SUD meta-analysis, there are data on rs1229984 in only 40% of the subjects (Walters et al., 2018). Thus, in some studies the strongest association of AD is with other SNPs that are in LD with rs1229984.
