Table 2.

Associations between SNPs and Aβ positivity in the two datasets

SNP	EA	Analysis 1							Analysis 2
		Discovery data		Replication data			Meta-analysis		Discovery data		Replication data			Meta-analysis
		OR	p	OR	p	p†	OR	p	OR	p	OR	p	p†	OR	p
rs73375428	G	0.519	2.71 × 10−7	0.550	0.040	0.0163	0.526	3.35 × 10−8	0.535	1.23 × 10−5	0.481	0.022	0.0101	0.516	8.00 × 10−7
rs2903923	G	0.529	5.15 × 10−7	0.539	0.032	0.0136	0.536	4.97 × 10−8	0.546	2.19 × 10−5	0.478	0.020	0.0058	0.510	1.32 × 10−6
rs3828947	C	0.529	5.15 × 10−7	0.547	0.036	0.0155	0.536	5.59 × 10−8	0.546	2.19 × 10−5	0.480	0.020	0.0056	0.515	1.39 × 10−6
rs11983537	T	0.558	7.58 × 10−7	0.539	0.026	0.0127	0.563	5.92 × 10−8	0.570	1.99 × 10−5	0.492	0.020	0.0091	0.517	1.22 × 10−6
rs112599253	T	0.561	1.56 × 10−7	0.723	0.214				0.586	6.69 × 10−5	0.698	0.210
rs79761449	T	0.564	2.50 × 10−7	0.723	0.214				0.579	5.22 × 10−5	0.698	0.210
rs6971106	T	0.564	2.50 × 10−7	0.723	0.214				0.579	5.22 × 10−5	0.698	0.210
rs6978259	C	0.522	4.62 × 10−7	0.566	0.060				0.521	7.90 × 10−6	0.515	0.040
rs6958464	T	0.526	6.28 × 10−7	0.555	0.056				0.524	9.63 × 10−6	0.484	0.028

Analysis 1 is a logistic regression analysis, expressed as Aβ positivity = β₀ + β₁ age + β₂ sex + β₃ PC₁ + β₄ PC₂ + β₅ PC₃ + β₆ SNP

Analysis 2 is a logistic regression analysis, expressed as Aβ positivity = β₀ + β₁ age + β₂ sex + β₃ PC₁ + β₄ PC₂ + β₅ PC₃ + β₆ APOE ɛ4+ β₇ SNP

^†P values were calculated using permutation tests

Abbreviations: BP base pair, C cytosine, CHR chromosome, EA effective allele, OR odds ratio, G guanine, SNP single nucleotide polymorphism, T thymine