Table 1. X chromosome-wide association study of Alzheimer’s disease: Associated lead variants.
The Direction column indicates the association effect direction across meta-analyzed cohorts following the order of ADGC, ADSP, UKB, FinnGen, MVP-1 (using health registry status), and MVP-2 (using proxy status). A question mark indicates the variant was not available in the respective cohort. Variants are annotated using dbSNP153. Association signals passing genome-wide significance are bolded.
| Lead variant | Nearest protein coding gene | Consequence | BP | EA | OA | No. Subjects | EAF | OR [95%-CI] ‡ | P | Direction |
|---|---|---|---|---|---|---|---|---|---|---|
| rs150798997 | NLGN4X | intergenic | 5,733,126 | A | T | 1,145,553 | 0.32% | 0.644 [0.537, 0.772] | 2.08E-06 | − ? − − − − |
| rs12852495 | MID1 | intronic | 10,458,864 | T | C | 1,151,353 | 0.26% | 1.538 [1.276, 1.855] | 6.60E-06 | + + + + + + |
| rs2142791 | SLC9A7 | intronic | 46,691,127 | C | A | 1,152,185 | 46.12% | 1.054 [1.035, 1.075] | 3.78E-08 | + + + + + + |
| rs209215 | ZNF280C | intronic | 130,251,839 | T | C | 1,145,797 | 39.90% | 1.048 [1.028, 1.069] | 2.70E-06 | + ? + + + + |
| rs5975709 † | MAP7D3 | intronic | 136,256,153 | C | T | 1,145,797 | 43.25% | 0.953 [0.935, 0.972] | 1.02E-06 | − ? − − − − |
| rs5930938 † | ADGRG4 | intronic | 136,380,525 | T | C | 733,616 | 32.62% | 0.943 [0.921, 0.965] | 7.55E-07 | − ? − ? − − |
| rs146964414 | MTM1 | intronic | 150,608,170 | T | C | 1,152,184 | 8.23% | 1.096 [1.060, 1.133] | 8.10E-08 | + − + + + + |
The odds ratios are reported with regard to a single active allele. In women, due to random XCI, the relative risk conferred would be half that reported here.
Rs5975709 was the lead variant in its respective locus, but it had no association results in ADSP and FinnGen. The second most significant variant in this locus, rs5930938, did have association results in FinnGen and was therefore additionally listed to provide additional insight.
Abbreviations: OR, odds ratio; CI, confidence interval; EA, effect allele; OA, other allele; EAF, effect allele frequency; BP, base pair; No., number.