Table 2.
List of novel candidate variants significantly associated within APOE ε4 carriers (Combined P value < 0.000001).
| Chromosome | SNP | Positiona | Assigned genesb | Functional refGene | Minor/major allele | Cohort | MAF in cases | MAF in controls | P valuec | OR (CI, 95%) | East Asian frequencyd | European frequency (non-Finnish)d |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10 | rs1890078 | 108978236 | SORCS1,LINC01435 | intergenic | C/T | Discovery | 0.065 | 0.14 | 1.29.E−04 | 0.43 (0.28-0.67) | 0.090 | 0.072 |
| Replication | 0.071 | 0.15 | 1.39.E−03 | 0.43 (0.24–0.75) | ||||||||
| Combined | 0.067 | 0.14 | 6.64.E−07 | 0.43 (0.30–0.61) | ||||||||
| 15 | rs12594991 | 93516427 | CHD2 | intronic | A/G | Discovery | 0.23 | 0.13 | 2.26.E−04 | 2.04 (1.42–2.94) | 0.15 | 0.52 |
| Replication | 0.24 | 0.11 | 1.40.E−04 | 2.56 (1.53–4.26) | ||||||||
| Combined | 0.24 | 0.12 | 2.03.E−07 | 2.21 (1.64–2.97) |
AD Alzheimer’s disease, MAF minor allele frequency, OR odds ratio, CI confidence interval, SNP single nucleotide polymorphism, NA not available.
aPhysical position based on human reference genome build hg19 (GRCh37).
bThe nearest gene to each SNP is underlined.
cP values were calculated using Cochran-Armitage trend test.
dPopulation frequency based on gnomAD database (http://gnomad.broadinstitute.org/).