Table 2.

Results with p<1×10⁻⁴ in all models tested

Chr	SNP	A1 *	A2 †	Freq ‡	Gene	eQTLs §	Beta¶	PGEE	PGEEλ #	PLME	Direction**
1	rs61776523	A	G	0.86	Y_RNA	-	−0.51	5.99E-05	5.97E-05	6.28E-05	+----x----++
2	rs62146087	A	G	0.62	CD8B	CD8B, PLGLB1	0.40	1.96E-05	2.47E-05	7.49E-05	+++++++-+x-+
2	rs10930401	T	C	0.88	intergenic	METTL5	−0.49	7.00E-05	6.85E-05	7.81E-05	-------+--x-
2	rs11683533	G	A	0.63	intergenic	-	−0.45	2.09E-06	6.50E-06	9.10E-05	---------+--
3	rs1447793	G	A	0.95	ROBO2	-	0.89	5.73E-05	1.19E-05	2.22E-05	+x+++++x-+xx
3	rs79279449	T	C	0.84	LSAMP	-	−0.48	2.54E-05	8.21E-05	1.77E-05	-+--+------x
3	rs28853947	C	T	0.70	RP11–384F7.1	-	−0.45	2.29E-06	5.93E-07	8.59E-05	--------+++x
3	rs4857800	T	A	0.65	intergenic	-	−0.40	7.90E-06	1.03E-06	8.39E-05	-----+----++
4	rs12501599	G	C	0.78	CLNK	ZNF518B	0.46	1.34E-05	7.35E-05	2.42E-05	++++-+++++++
4	rs2168075	A	G	0.45	CCSER1	CCSER1	−0.37	4.62E-05	8.89E-05	9.38E-05	--------+-+-
4	rs1304013	C	T	0.73	intergenic	-	0.50	4.73E-07	8.82E-06	2.48E-05	-++++++x-+++
6	rs9393409	A	G	0.36	intergenic	-	−0.39	2.70E-05	1.81E-05	9.17E-05	-----x++---+
6	rs9380681	T	C	0.70	intergenic	-	0.46	1.40E-06	1.80E-06	3.09E-05	++++-++x-+-+
6	rs45604140	C	G	0.90	PTK7	DNPH1, KLHDC3	−0.54	6.07E-05	1.98E-05	7.15E-06	-+----+---++
6	rs4897203	T	C	0.09	TRDN	-	0.74	1.34E-06	2.14E-06	9.56E-07	+++++++-+-++
7	rs7806833	T	G	0.22	SCIN	-	−0.46	4.99E-05	5.64E-05	4.44E-05	----------+-
7	rs39437	G	C	0.16	OSBPL3-CYCS	-	0.51	4.68E-06	2.15E-06	9.70E-05	++++++++-++-
7	rs17150563	T	C	0.72	intergenic	HIBADH, TAX1BP1	0.40	6.08E-05	2.13E-05	3.61E-05	++-++++x-+-+
7	rs7792776	G	A	0.87	intergenic	-	−0.55	1.08E-05	1.68E-05	2.07E-05	----------+-
7	rs6959165	A	G	0.45	HECW1	-	0.36	2.96E-05	1.82E-05	1.64E-05	+++++++x--++
7	rs60465337	C	T	0.97	CNTNAP2	-	1.03	8.59E-07	4.06E-07	2.86E-05	++++++++++x-
8	rs16877878	A	G	0.96	RP11–566H8.3	-	1.18	1.13E-05	9.35E-05	1.33E-05	x+++++x++++x
10	rs182768834	G	A	0.95	intergenic	-	−0.87	1.60E-06	9.96E-06	6.31E-05	----------x-
11	rs61897000	G	A	0.66	CHRDL2	XRRA1	−0.36	7.25E-05	1.69E-05	6.44E-05	--+-----+-++
12	rs7301894	A	G	0.44	ANO2	-	−0.34	8.59E-05	6.21E-05	7.54E-05	-------x+--+
12	rs10785192	T	A	0.07	RP11–585P4.5	RP11–585P4.5, GLIPR1L2	−0.69	2.23E-05	5.99E-05	1.69E-06	--+--------x
12	rs660322	G	A	0.24	TMEM132D	-	0.53	1.07E-05	9.44E-06	1.14E-05	x+-+++++-xx+
15	rs2899492	C	T	0.16	FAM214A	ARPP19	0.62	5.94E-07	9.70E-07	1.37E-05	++-++++x+xx+
15	rs8041705	T	C	0.56	HMGB1P8	-	−0.41	1.76E-05	2.66E-05	2.22E-05	-----x---x+-
15	rs12324317	T	C	0.61	RLBP1	RLBP1, POLG	−0.40	1.80E-05	2.11E-05	1.91E-05	----+-+x+-+-
15	rs9788714	G	A	0.62	RLBP1-FANCI	POLG	−0.42	2.50E-06	1.70E-06	1.70E-06	-----++-+-+x
15	rs2238301	A	G	0.61	FANCI	POLG	−0.46	3.30E-07	1.59E-07	3.15E-07	------+-+-+x
15	rs3176205	T	C	0.61	POLG	POLG	−0.46	2.75E-07	1.49E-07	1.11E-07	-----++-+-+x
16	rs4949142	A	G	0.85	intergenic	-	−0.60	5.83E-07	4.02E-07	7.82E-06	-------x--x+
16	rs12448088	G	C	0.40	PLCG2	-	−0.41	2.91E-05	2.36E-05	1.10E-05	+---x----x-+
17	rs2071194	C	A	0.36	EVPL	TEN1	0.41	1.44E-05	3.84E-05	6.67E-05	+++++++x-+++

^*effect allele,

^†other allele,

^‡frequency of effect allele,

^§Expression Quantitative Trait Locus: genes differentially expressed by SNP genotype according to GTEx database,

^¶beta from GEE model including all cohorts,

^#p-value from GEE model excluding cohorts with λ>1.2,

^**effect direction in individual cohorts from the GEE model including all cohorts. The order of the symbols is Pfizer, 3C, ADNI, Flurizan, NACC, ROS/MAP1, Semagacestat, ADNeuroMed, ACT, WashU, WHICAP, ROS/MAP2.