Table 1.
SNP-by-AD status interaction meta-analysis for ε2-associated group-specific SNPs in the pooled samples of AD and NAD groups.
| SNPs | SNP-by-AD Status Interaction Effect | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rep/Meta | CHR | Locus | Gene | SNP | POS | EA | EAF | N | BETA | SE | P-value | Effects |
| AD-Meta | 1p13.3 | 1 | VAV3 | rs77841908 | 107713714 | T | 0.012 | 5568 | 3.268 | 0.751 | 1.39E-05 | +??++ |
| AD-Meta | 4p12 | 2 | GNPDA2 | rs7667144 | 44988902 | T | 0.240 | 10493 | −0.585 | 0.124 | 2.22E-06 | −−−−− |
| AD-Meta | 4p12 | 2 | GNPDA2 | rs34071858 | 44989232 | G | 0.240 | 10489 | −0.587 | 0.124 | 2.12E-06 | −−−−− |
| AD-Meta | 4p12 | 2 | GNPDA2 | rs7436238 | 44995666 | A | 0.239 | 10477 | −0.585 | 0.124 | 2.35E-06 | −−−−− |
| AD-Meta | 8q24.3 | 3 | MROH5 | rs77186917 | 141434800 | C | 0.047 | 7334 | 1.317 | 0.265 | 6.87E-07 | −+?−+ |
| AD-Rep | 9p24.1 | 4 | RIC1 | rs74364314 | 5640617 | G | 0.016 | 3025 | 2.685 | 0.701 | 1.28E-04 | +???+ |
| AD-Meta | 9p23 | 5 | MPDZ | rs7848179 | 13030037 | A | 0.028 | 10493 | 1.417 | 0.323 | 1.16E-05 | +++−+ |
| AD-Meta | 9p23 | 5 | MPDZ | rs113433603 | 13036364 | T | 0.026 | 10493 | 1.623 | 0.337 | 1.53E-06 | +++−+ |
| NAD-Meta | 10p13 | 6 | FRMD4A | rs3101357 | 14077721 | T | 0.382 | 10492 | 0.459 | 0.111 | 3.82E-05 | −++++ |
| AD-Meta | 11q22.3 | 7 | DDX10 | rs2884183 | 109127412 | T | 0.212 | 10474 | 0.736 | 0.131 | 1.76E-08 | +++++ |
| AD-Meta | 16q24.1 | 8 | IRF8 | rs16882 | 85901967 | C | 0.180 | 10489 | 0.615 | 0.136 | 6.20E-06 | +++++ |
| AD-Meta | 16q24.1 | 8 | IRF8 | rs305082 | 85903372 | C | 0.183 | 10463 | 0.616 | 0.135 | 5.27E-06 | +++++ |
| AD-Meta | 16q24.1 | 8 | IRF8 | rs8052521 | 85925123 | T | 0.248 | 10473 | 0.550 | 0.122 | 7.26E-06 | +++++ |
| AD-Meta | 16q24.1 | 8 | IRF8 | rs880364 | 85925559 | G | 0.249 | 10472 | 0.543 | 0.122 | 9.39E-06 | +++++ |
| AD-Meta | 16q24.1 | 8 | IRF8 | rs880365 | 85925756 | T | 0.246 | 10471 | 0.508 | 0.123 | 3.77E-05 | +++++ |
| AD-Meta | 16q24.1 | 8 | IRF8 | rs880366 | 85925832 | C | 0.248 | 10472 | 0.551 | 0.123 | 6.96E-06 | +++++ |
| AD-Meta | 17q25.1 | 9 | SDK2 | rs9895288 | 73623974 | A | 0.075 | 10490 | 0.902 | 0.198 | 5.16E-06 | +++−+ |
| AD-Meta | 17q25.1 | 9 | SDK2 | rs75122991 | 73639797 | G | 0.067 | 10490 | 0.974 | 0.209 | 3.13E-06 | +++−+ |
| AD-Meta | 17q25.1 | 9 | SDK2 | rs28527783 | 73640957 | T | 0.068 | 10491 | 0.983 | 0.209 | 2.52E-06 | +++−+ |
| AD-Meta | 17q25.1 | 9 | SDK2 | rs76380229 | 73643396 | T | 0.067 | 10489 | 0.989 | 0.209 | 2.23E-06 | +++−+ |
| AD-Meta/NAD-Meta | 19q13.31 | 10 | CEACAM22P | rs144439590 | 44537330 | T | 0.026 | 5568 | 1.896 | 0.470 | 5.56E-05 | +??−+ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | CEACAM16 | rs11881756 | 44717621 | C | 0.107 | 4791 | 0.964 | 0.193 | 5.75E-07 | ++??+ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | BCL3 | rs1531517 | 44738916 | A | 0.072 | 7332 | 1.529 | 0.221 | 4.54E-12 | ++?−+ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | BCL3 | rs4803750 | 44744370 | G | 0.067 | 7326 | 1.535 | 0.224 | 7.56E-12 | ++?−+ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | BCL3 | rs10401176 | 44750234 | T | 0.117 | 4791 | 0.872 | 0.183 | 1.84E-06 | ++??+ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | BCL3 | rs62117205 | 44752009 | C | 0.066 | 7334 | 1.589 | 0.225 | 1.74E-12 | ++?−+ |
| AD-Meta/NAD-Meta | 19q13.32 | 10 | NECTIN2 | rs7254892 | 44886339 | A | 0.031 | 2296 | 2.952 | 0.469 | 3.18E-10 | ????+ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | APOE | rs75627662 | 44910319 | T | 0.082 | 7334 | 2.211 | 0.079 | 2.07E-171 | ++?++ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | APOE | rs72654473 | 44911142 | A | 0.091 | 7332 | 2.074 | 0.101 | 8.90E-94 | +−?++ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | APOC1 | rs445925 | 44912383 | A | 0.092 | 7333 | 2.164 | 0.102 | 1.58E-99 | +−?++ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | APOC1 | rs483082 | 44912921 | T | 0.104 | 7334 | 1.894 | 0.111 | 9.78E-65 | +−?++ |
| AD-Rep/NAD-Rep | 19q13.32 | 10 | APOC1P1 | rs141622900 | 44923535 | A | 0.046 | 3025 | 4.825 | 0.320 | 2.89E-51 | +???+ |
| AD-Meta | 20q13.2 | 11 | ZFP64 | rs6021874 | 52342233 | C | 0.085 | 10486 | 0.865 | 0.184 | 2.66E-06 | −++++ |
| AD-Meta | 20q13.2 | 11 | ZFP64 | rs6021877 | 52345128 | T | 0.085 | 10492 | 0.839 | 0.184 | 4.98E-06 | −++++ |
| AD-Meta | 20q13.2 | 11 | ZFP64 | rs2426435 | 52357570 | A | 0.082 | 10481 | 0.847 | 0.186 | 5.55E-06 | −++++ |
Abbreviations: AD = Alzheimer’s disease-affected group; NAD = Alzheimer’s disease-unaffected group; SNP = single-nucleotide polymorphism; Rep/Meta = SNP identified at the stage one of our two-stage genetic analysis by the discovery-replication strategy (i.e., nonADGC and ADGC as discovery and replication sets or vice versa) or in the meta-analysis of five datasets under consideration (i.e., combined nonADGC and ADGC); CHR = chromosomal region (i.e., cytogenetic band); POS = SNP position based on Human Genome version 38 (hg38); EA = effect allele; EAF = effect allele frequency; N = Number of subjects; BETA and SE = effect size and its standard error; Effects = directions of effects in the ADSP, LOADFS, FHS, CHS, ADGC datasets, respectively.