Table 2.

Summary of stage 1, 2, 3 and combined meta-analysis results for SNVs at P<5×10^-8. Data includes p-values, odds ratios (OR), minor allele frequency (MAF) in cases and controls and number of subjects included in each analytical stage. For OR 95% confidence intervals see Supplementary Table 7.

SNV	rs75932628	rs143332484	rs72824905	rs616338
Chr	6	6	16	17
Position	41129252	41129207	81942028	47297297
Protein Variation	R47H	R62H	P522R	S209F
Gene	TREM2	TREM2	PLCG2	ABI3
Effect Allele	T	T	G	T
Stage 1
P	3.02E-12	3.48E-09	1.19E-05	2.16E-05
OR	2.46	1.58	0.65	1.42
MAF Cases	0.003	0.015	0.006	0.013
MAF Controls	0.001	0.010	0.011	0.010
N	30018	33786	33786	33786
Stage 2
P	4.38E-08	3.66E-07	1.35E-04	8.37E-05
OR	2.37	3.97	0.70	1.41
MAF Cases	0.004	0.014	0.006	0.010
MAF Controls	0.002	0.006	0.008	0.008
N	35831	3968	35831	35831
Stage 3
P	1.23E-06	2.45E-03	2.48E-02	1.75E-02
OR	2.58	1.55	0.69	1.58
MAF Cases	0.006	0.012	0.006	0.010
MAF Controls	0.003	0.008	0.007	0.008
N	14884	15288	15288	14876
Stage1, 2 and 3 Meta-Analysis
P	5.38E-24	1.55E-14	5.38E-10	4.56E-10
OR	2.46	1.67	0.68	1.43
MAF Cases	0.004	0.014	0.006	0.011
MAF Controls	0.002	0.009	0.009	0.008
N	80733	53042	84905	84493

Note: Concordance for alternate allele carrier genotypes between imputed versus called SNPs in Stage 3 was 75.2% for rs75932628, 91.1% for rs143332484, 95.7% for rs72824905, and 81.9% for rs616338 (Online Methods and Supplementary Table 6).