TABLE 1.

Results of single‐variant meta‐analysis.

						Model 1					Model 2
Nearest gene(s)	dbSNP	Chromosome	Position	Minor/major allele	MAF	β	SE	p‐Value	Direction	I2 p‐value	β	SE	p‐Value	Direction	I2 p‐value
Common novel loci
LINC01250/TSSC1	rs78857220	2	3070309	A/G	0.018	0.69	0.14	8.70×10−7 *	+–++++–+++?+?++	0.27	0.61	0.15	4.68×10−5	+–++++–+++?+?++	0.35
SRGAP3	rs396323	3	9215296	T/C	0.101	0.32	0.06	3.74×10−7 *	++‐++++‐++++++‐++	0.55	0.29	0.07	8.87×10−6	++–++++++++++‐++	0.33
Rare novel loci
KIDINS220	rs183088158	2	8806098	T/C	0.008	1.17	0.27	1.08×10−5	???++‐+++?+???‐++	0.45	1.45	0.28	2.50×10−7 *	???++++++?+???‐++	0.67
TEX41	rs191256330	2	145902343	C/T	0.005	1.39	0.37	1.83×10−4	???+++?+‐+++???++	0.73	1.59	0.32	7.22×10−7 *	???+++++‐+++???++	0.74
UNC5C	rs969240869	4	96471106	A/G	0.001						4.50	0.91	7.69×10−7 *	??????+???+??????	0.89
IYD/PLEKHG1	rs117762284	6	150819452	A/G	0.008	2.29	0.45	4.21×10−7 *	+?++???+?++??????	0.80	1.50	0.34	1.10×10−5	+?‐+??++?++??????	0.26
SDK1	rs181767458	7	4268872	G/C	0.006	1.30	0.30	1.63×10−5	‐+?++?++?+++???++	0.11	1.61	0.33	8.74×10−7 *	‐+??+?++?+++???++	0.04
MMP16	rs138744190	8	90157165	G/A	0.004	1.71	0.41	2.51×10−5	+????+++?+?+????‐	0.28	2.10	0.42	6.05×10−7 *	+????+++?+?+????‐	0.11
MPDZ	rs141610415	9	13220518	C/T	0.002	3.50	0.68	2.40×10−7 *	????+?+???+??????	0.63	4.37	0.74	3.68×10−9 *	????+?+???+??????	0.88
ASCL1	rs556001137	12	103570373	T/G	0.003	2.21	0.45	8.12×10−7 *	??????++?++???+++	0.65	2.21	0.46	1.43×10−6	??????++?++???+++	0.48
	rs138206541	12	103716273	T/G	0.003	2.03	0.45	7.58×10−6	?‐??+?++?++????++	0.22	2.41	0.49	7.39×10−7 *	?‐??+?++?++????++	0.23
CNTNAP4	rs1010752317	16	76535070	C/A	0.003	1.87	0.42	7.31×10−6	++?++?++?+++???+?	0.99	2.26	0.46	7.71×10−7 *	++?++?++?+++???+?	0.96
TANC2	rs56285182	17	61288858	T/C	0.006	1.26	0.31	4.96×10−5	++?+++++??+‐???++	0.08	1.73	0.35	5.60×10−7 *	++?+++++??+????++	0.81
Loci previously reported in Kunkle et al. (2021)
EDEM1	rs168193	3	5302077	G/A	0.241	−0.21	0.05	2.65×10−6	+——‐+—–+‐?	0.46	−0.18	0.05	2.59×10−4	+——‐+–+–+‐?	0.43
ALCAM	rs2633682	3	104409208	A/C	0.333	−0.21	0.05	3.11×10−6	——?———+	0.39	−0.14	0.04	4.29×10−4	—————‐+	0.49
GPC6	rs9516245	13	94159800	C/T	0.039	0.46	0.10	3.30×10−6	+++++++++++++++++	0.35	0.52	0.10	5.50×10−7 *	+++++++++++++++++	0.27
VRK3	rs3745495	19	50524332	G/A	0.104	0.25	0.06	4.32×10−6	+‐+‐++++‐+++‐+‐+‐	0.16	0.30	0.06	3.18×10−6	+‐+‐++++‐+++++‐+‐	0.07
SIPA1L2	rs115684722	1	232376163	T/A	0.007	1.45	0.89	0.10	‐????+?+????????‐	0.03	0.14	0.56	0.80	‐????++?????????‐	0.76
WDR70	rs184179037	5	37483940	T/C	0.006	1.34	0.30	9.37×10−6	–+?+?+??+++?????	0.38	1.30	0.33	7.69×10−5	–+?+?+??+++?????	0.10
API5	rs569584007	11	43166842	G/T	0.005	0.75	0.41	0.07	??????+??+++?+?+‐	0.46	1.81	0.41	7.50×10−6	??????+??‐++?+?+‐	0.003
ACER3	rs115816806	11	76541840	G/A	0.006	1.66	0.62	0.007	?‐??+??+????????+	0.12	1.54	0.63	0.01	?‐??+??+????????+	0.15
PIK3C2G	rs75739461	12	18471546	A/G	0.011	0.73	0.20	3.39×10−4	‐?+++?++‐++????+‐	0.56	0.92	0.22	1.99×10−5	+?‐++?++‐++????+‐	0.46
ARRDC4/IGF1R	rs570487962	15	97992685	C/A	0.012	−1.76	0.36	1.33×10−6	???????+?????‐???	0.05	−2.35	0.42	1.65×10−8 *	???????+?????‐???	0.02
RBFOX1	rs79537509	16	8288401	T/G	0.008	1.32	0.27	1.38×10−6	‐+‐?++++?++????+?	0.49	1.43	0.30	1.34×10−6	‐+‐?++++?++????+?	0.37
Loci previously reported in Reitz et al. (2013)
ABCA7	rs115550680	19	1050420	G/A	0.061	0.33	0.08	4.67×10−5	‐++++‐++‐++++++‐?	0.11	0.45	0.09	4.30×10−7 *	‐++++‐++‐+++++++?	0.11
HMHA1	rs115553053	19	1082844	T/C	0.047	0.40	0.09	2.51×10−5	‐+++–++‐++++++++	0.26	0.50	0.10	6.97×10−7 *	++++–++‐++++++++	0.15
GRIN3B	rs115882880	19	1001777	A/C	0.098	0.29	0.07	1.18×10−5	‐++++‐+++‐++++++?	0.08	0.35	0.07	8.58×10−7 *	‐++++‐++++++++++?	0.09
NSG2/MSX2	rs145848414	5	174014114	A/G	0.035	0.45	0.11	3.74×10−5	‐+++++++++++?+++‐	0.57	0.47	0.12	7.31×10−5	‐+++++++++++?+++‐	0.42
APOE	rs157591	19	45423934	A/G	0.121	0.69	0.06	3.57×10−29 *	++++++++‐+++++++?	0.16	−0.05	0.08	0.49	‐+++‐++—–++++?	0.50

Abbreviations: dbSNP, Single Nucleotide Polymorphism Database; MAF, minor allele frequency.

^a Model 1 is adjusted for age, sex, and population stratification (PCs).

^b Model 2 is adjusted for age, sex, PCs, and APOE.

^c rs969240869 was filtered out in Model 1 due to extreme beta coefficients (|β| > 5).

^*Significant at p < 9×10⁻⁷.