Table 2.

Summary of association from meta-analysis in people with European ancestry.

Gene	Variant	MAFa	AD-ORb	Meta-analysis
				NP-OR	P-value	Q-valuec
Braak NFT stage
BIN1	rs6733839	0.38	1.17	1.30	2.6 × 10−8	1.5 × 10−6
CR1	rs679515	0.17	1.13	1.24	3.8 × 10−4	0.011
MME	rs16824536	0.032	0.92	0.70	9.8 × 10−4	0.016
COX7C	rs62374257	0.21	1.07	1.20	0.0011	0.016
SPI1	rs10437655	0.38	1.06	1.13	0.0064	0.071
EED/PICALM	rs3851179	0.37	0.90	0.88	0.0089	0.075
INPP5D	rs10933431	0.23	0.93	0.86	0.0094	0.075
Neocortical neuritic plaques
BIN1	rs6733839	0.38	1.17	1.21	3.9 × 10−5	0.0022
EED/PICALM	rs3851179	0.37	0.90	0.85	0.0010	0.021
MME	rs16824536	0.032	0.92	0.70	0.0011	0.021
APH1B	rs117618017	0.14	1.11	1.23	0.0020	0.026
RBCK1	rs1358782	0.27	0.95	0.85	0.0023	0.026
FERMT2	rs17125924	0.080	1.10	1.25	0.0047	0.044
PTK2B	rs73223431	0.35	1.07	1.13	0.0088	0.071
TDP-43 in any brain regions
TMEM106B	rs13237518	0.40	0.96	0.78	1.0 × 10−4	0.0059
SORL1	rs74685827	0.015	1.19	1.85	0.0042	0.092
GRN	rs5848	0.30	1.07	1.22	0.0049	0.092
TPCN1	rs6489896	0.094	1.08	1.42	0.0071	0.10
Lewy bodies in any brain regions
BIN1	rs6733839	0.38	1.17	1.16	0.0012	0.068
USP6NL	rs7912495	0.45	1.06	1.14	0.0043	0.12
Hippocampal sclerosis
TMEM106B	rs13237518	0.40	0.96	0.64	9.3 × 10−7	5.2 × 10−5
GRN	rs5848	0.30	1.07	1.53	2.1 × 10−6	5.8 × 10−5
WNT3	rs199515	0.22	0.94	0.69	0.0014	0.025
TNIP1	rs871269	0.34	0.96	0.75	0.0018	0.025
ACE	rs4277405	0.37	0.94	1.12	0.0082	0.089
SCIMP	rs7225151	0.14	1.08	1.36	0.0095	0.089

Abbreviations: AD = Alzheimer’s disease; MAF = minor allele frequency; NFT = neurofibrillary tangle; NP = neuropathology; OR = odds ratio; TDP-43 = TAR DNA binding protein 43 kDa.

^aMAFs are calculated from 1000 genome phase 3 in Europeans (EUR) population.

^bAD-OR represents clinical AD related odds ratios reported in “New insights into the genetic etiology of Alzheimer’s disease and related dementias” (Bellenguez et al., 2022).

^cQ-value indicates the false discovery rate (FDR) adjusted p-value with the Benjamini-Hochberg procedure.