Table 2.

Nagelkerke's R2 at differenct p value thresholds

	PRS (All SNPs)			PRS.noAPOE (except APOE region)
pT	Nagelkerke's R2	p value	#SNPs	Nagelkerke's R2	p value	#SNPs
p < 5 × 10–8	0.148	5.92 × 10–8	81	0.081	4.57 × 10–5	44
p < 1 × 10–6	0.143	9.91 × 10–8	107	0.067	2.07 × 10–4	70
p < 1 × 10–5	0.167	1.40 × 10–8	173	0.085	3.18 × 10–5	131
p < 1 × 10–4	0.091	1.53 × 10–5	410	0.029	0.013	364
p < 1 × 10–3	0.034	6.85 × 10–3	1,696	0.014	0.077	1,642
p < 1 × 10–2	0.004	0.324	10,101	0.007	0.213	10,041
p < 0.05	0.000	0.929	33,065	0.000	0.979	32,999
p < 0.5	0.005	0.288	121,721	0.004	0.332	121,647
p < 1.0	0.006	0.262	158,289	0.005	0.303	158,208

The highest accuracy was highlighted in bold

P value was calculated by Wald test