TABLE 2.

Top single nucleotide variants in genes associated with proteinopathy.

CHR	Gene	SNV	Position	Effect/reference	Model a	F1 b		F2 b		F3 b
						$\widehat{\mathbf{\beta }}$	Q‐value c	$\widehat{\mathbf{\beta }}$	Q‐value c	$\widehat{\mathbf{\beta }}$	Q‐value c
1	GBA	rs140335079	155237596	A/T	1	0.26	0.28	−0.02	0.93	−0.68	0.015
					2	0.38	0.12	0.01	0.98	−0.69	0.017
2	BIN1	rs6733839	127135234	T/C	1	0.06	0.28	0.15	0.018	0.12	0.040
					2	0.00	0.99	0.11	0.064	0.08	0.19
7	TMEM106B	rs10950392	12223912	T/C	1	0.18	0.0017	−0.11	0.084	−0.10	0.098
					2	0.22	3.6×10−5	−0.15	0.0097	−0.10	0.14
17	GRN	rs5848 d	44352876	T/C	1	0.19	0.0018	−0.05	0.48	−0.06	0.30
					2	0.21	2.2×10−4	−0.10	0.081	−0.08	0.22
19	APOE	rs429358	44908684	C/T	1	0.36	5.1×10−8	0.64	1.1×10−23	0.22	0.0028
					2	0.14	0.037	0.50	4.5×10−16	0.06	0.38

Abbreviations: CHR, chromosome; SNV, single nucleotide variant.

^a Model 1 = adjusted for age at death, sex, and top three principal components; Model 2 = adjusted for age at death, sex, top three principal components, and other scores.

^b F1 = TDP‐43 and hippocampal sclerosis related score; F2 = Alzheimer's disease neuropathologic change related score; F3 = Lewy body pathology related score.

^c Q‐value indicates that false discovery rate (FDR) adjusted p‐value in each score and model.

^d The p‐value of Hardy‐Weinberg equilibrium test for rs5848 in AD controls was 1.2×10⁻⁶¹; however, we displayed the results because rs5848 is well‐known as TDP‐43 related single nucleotide variant.