Table 1.
List of known loci significantly associated with AD in the customized genotyping AD chip application set (n = 1437).
| Total group (n = 1437) | APOE ε4 carriers (n = 287) | APOE ε4 non-carriers (n = 1150) | IGAP studya | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus | SNPb | Positionc | Nearby genes to each SNPd | Minor/major allele | MAF in cases | MAF in controls | P valuee | OR (CI, 95%) | MAF in cases | MAF in controls | P valuee | OR (CI, 95%) | MAF in cases | MAF in controls | P valuee | OR (CI, 95%) | Non-effect/effect alleles | Beta (SE)f | P valuee |
| 1q32.2 | rs12743911 | 207816480 | CR1,CR1L | T/C | 0.45 | 0.41 | 3.38.E−02 | 1.18 (1.02–1.38) | 0.44 | 0.44 | 9.78.E–01 | 1.00 (0.70–1.41) | 0.45 | 0.4 | 3.18.E−02 | 1.22 (1.02–1.46) | C/T | 0.06 (0.02) | 3.24.E−04 |
| 2q14.3 | rs13025765 | 127886233 | BIN1,CYP27C1 | T/C | 0.36 | 0.31 | 2.75.E−03 | 1.27 (1.08–1.49) | 0.37 | 0.34 | 5.08.E–01 | 1.13 (0.79−1.63) | 0.36 | 0.3 | 1.04.E−02 | 1.27 (1.05–1.53) | C/T | 0.13 (0.02) | 7.87.E−13 |
| 6p12.3 | rs12202615 | 47618171 | CD2AP,ADGRF2 | C/T | 0.14 | 0.094 | 3.54.E−04 | 1.50 (1.18–1.91) | NA | NA | NA | NA | 0.14 | 0.09 | 6.45.E−04 | 1.56 (1.19–2.05) | T/C | 0.08 (0.02) | 4.68.E−06 |
| 7p14.1 | rs10261983 | 37885121 | GPR141,NME8 | C/T | 0.45 | 0.50 | 1.16.E−02 | 0.82 (0.71–0.96) | 0.43 | 0.51 | 7.69.E–02 | 0.73 (0.51–1.03) | 0.46 | 0.50 | 1.21.E−01 | 0.87 (0.73–1.04) | C/T | −0.07 (0.02) | 1.28.E−05 |
| 7q22.1 | rs2405442 | 99971313 | PILRA | C/T | 0.44 | 0.40 | 2.80.E−02 | 1.18 (1.02–1.38) | 0.44 | 0.42 | 7.47.E−01 | 1.06 (0.75−1.50) | 0.44 | 0.39 | 4.12.E−02 | 1.20 (1.00–1.44) | C/T | −0.07 (0.02) | 4.23.E−05 |
| 7q35 | rs11771145 | 143110762 | EPHA1-AS1 | G/A | 0.51 | 0.46 | 4.75.E−03 | 1.24 (1.06–1.44) | 0.51 | 0.42 | 4.73.E−02 | 1.43 (1.00−2.02) | 0.51 | 0.46 | 2.90.E−02 | 1.21 (1.01–1.45) | G/A | −0.1 (0.02) | 8.76.E−10 |
| 8p21.1 | rs4732729 | 27461492 | CLU | C/A | 0.22 | 0.26 | 1.32.E−02 | 0.80 (0.67–0.96) | 0.22 | 0.28 | 1.45.E−01 | 0.75 (0.50–1.11) | 0.22 | 0.26 | 3.79.E−02 | 0.80 (0.65–0.99) | C/A | 0.11 (0.02) | 1.26.E−09 |
| 11q14.2 | rs3851179 | 85868640 | PICALM,EED | T/C | 0.34 | 0.4 | 2.25.E−03 | 0.78 (0.67–0.92) | 0.35 | 0.41 | 1.66.E−01 | 0.77 (0.54−1.11) | 0.34 | 0.4 | 6.35.E−03 | 0.78 (0.64–0.93) | C/T | −0.13 (0.02) | 2.84.E−15 |
| 11q24.1 | rs4936632 | 121335728 | SORL1 | A/G | 0.44 | 0.48 | 1.26.E−02 | 0.83 (0.71–0.96) | 0.43 | 0.5 | 1.18.E−01 | 0.77 (0.54−1.09) | 0.44 | 0.48 | 5.32.E−02 | 0.84 (0.70–1.01) | G/A | −0.02 (0.02) | 1.49.E−01 |
| 14q32.12 | rs7154691 | 92934699 | SLC24A4 | A/G | 0.51 | 0.47 | 3.31.E−02 | 1.18 (1.01–1.37) | 0.47 | 0.53 | 1.68.E−01 | 0.78 (0.55−1.11) | 0.50 | 0.47 | 1.75.E−01 | 1.13 (0.95–1.35) | G/A | 0.08 (0.02) | 1.34.E−05 |
| 19p13.3 | rs4147911 | 1047687 | ABCA7 | G/C | 0.37 | 0.33 | 1.77.E−02 | 1.22 (1.04–1.43) | 0.35 | 0.34 | 9.47.E−01 | 1.01 (0.70–1.46) | 0.39 | 0.33 | 6.03.E−03 | 1.30 (1.08–1.57) | C/G | 0.19 (0.03) | 1.25.E−08 |
| 19q13.32 | rs429358 | 45411941 | APOE | C/T | 0.22 | 0.056 | 2.59.E−33 | 4.81 (3.76–6.16) | 0.36 | 0.48 | 1.80.E−06 | 0.61 (0.43–0.87) | NA | NA | NA | NA | T/C | 1.35 (0.03) | 6.70.E−536 |
AD Alzheimer’s disease, MAF minor allele frequency, OR odds ratio, CI confidence interval, SNP single nucleotide polymorphism, NA not available.
aNon-effect/effect alleles, Beta and P values in the International Genomics of Alzheimer’s Project (IGAP).
bThe most significant SNPs associated with AD in the total sample set within each locus.
cPhysical position based on human reference genome build hg19 (GRCh37).
dThe nearest gene to each SNP is underlined.
eP values were calculated using Cochran-Armitage trend test.
fOverall estimated effect size and standard error for the effect allele.