Table 1.
Genome-wide association study of neuropathology-based AD traits
| Locus | CHR:POS | Top SNP ID | AD traits | A1 | P | Effect | Nearest Gene Position (distance) | MAF |
|---|---|---|---|---|---|---|---|---|
| 2q14.3 | chr2:127,133,851 | rs4663105 | ncAD | C | 7.94 × 10–9 | − 5.77 | BIN1b/intergenic (26,495) | 0.4 |
| chr19:44,893,408 | rs59007384 | ncAD | T | 3.9 × 10−31 | 15.52 | APOE regiona/intronic | 0.30 | |
| 19q13.32 | chr19:44,888,997 | rs6857 | Braak stage | T | 2.7 × 10−70 | 17.73 | APOE regiona/intronic | 0.25 |
| chr19:44,892,887 | rs11556505 | NP score | T | 5.2 × 10−52 | 15.18 | APOE regiona/intronic | 0.22 |
The total sample for the ncAD case–control GWAS was 5384 cases and 1576 controls on 6,394,125 SNPs. The total sample for Braak stage and NP score GWASs was 6960 individuals on 6,542,713 and 6,475,755 SNPs respectively. CHR chromosome; SNP, single-nucleotide polymorphism; A1, effect allele; MAF: minor allele frequency; Effect: Z score effect of A1 allele; Significant genome-wide association P < 5 × 10−8 a: Genes have been identified as genome-wide significant in both previous clinical AD GWAS and neuropathological AD GWAS. b: Genes have been identified as genome-wide significant in previous clinical AD GWAS
ncAD: neuropathology-confirmed AD