. 2023 Oct 4;15:79. doi: 10.1186/s13073-023-01233-z

Table 2.

Independent genome-wide significant loci. Independent SNPs, which had genome-wide significant associations with a Biomarker PC in either main effect, sex-stratified or sex interaction models. See also Supplementary Tables for fine-mapping and replication analyses of the PC5 signal near GRIN2D

SNP	Chr:Pos	Location	Locus	EA	EAF	R²_imp	Main effect			Male Stratified			Female Stratified			Sex Interaction
SNP	Chr:Pos	Location	Locus	EA	EAF	R²_imp	β	SE	p	β	SE	p	β	SE	p	β	SE	p
Tau pathology/Degeneration (PC1)
rs140169162	17:30886881	Intron	MYO1D	G	0.98	0.69	0.64	0.19	8.6E−04	−0.02	0.26	9.4E−01	1.61	0.30	4.9E−08	0.84	0.23	3.0E−04
Aβ Pathology (PC2)
rs1638675	10:119178376	Intergenic	-	A	0.57	0.89	−0.08	0.05	7.1E−02	−0.33	0.07	1.0E−06	0.18	0.06	4.2E−03	0.50	0.09	3.5E−08
rs12972156	19:45387459	Intron	APOE	C	0.74	0.98	0.43	0.05	9.5E−20	0.46	0.07	6.9E−11	0.39	0.07	2.3E−09	−0.04	0.09	6.5E−01
rs157582	19:45396219	Intron	APOE	C	0.65	1.00	0.37	0.04	9.5E−18	0.40	0.06	2.6E−10	0.33	0.06	3.5E−08	−0.05	0.09	5.6E−01
rs10119	19:45406673	3′-UTR	APOE	G	0.60	0.95	0.34	0.04	6.4E−15	0.43	0.06	4.9E−11	0.29	0.06	2.6E−06	−0.12	0.09	1.5E−01
rs429358	19:45411941	Exon	APOE	T	0.70	0.99	0.50	0.04	1.3E−29	0.55	0.06	1.2E−17	0.44	0.06	4.3E−12	−0.09	0.09	3.0E−01
rs75627662	19:45413576	Intergenic	APOE	C	0.71	0.98	0.35	0.05	1.2E−13	0.38	0.07	4.4E−08	0.31	0.07	2.7E−06	−0.05	0.09	6.2E−01
rs157595	19:45425460	Intergenic	APOE	A	0.33	0.96	0.28	0.05	1.6E−09	0.28	0.07	7.1E−05	0.24	0.06	2.3E−04	0.00	0.09	9.8E−01
rs111789331	19:45427125	Intergenic	APOE	T	0.73	0.95	0.45	0.05	8.3E−21	0.46	0.07	1.7E−10	0.45	0.07	1.6E−11	0.02	0.09	8.0E−01
Injury/Inflammation (PC3)
rs114211800	5:158973225	Intron	LOC105377684	G	0.98	0.91	−0.74	0.17	7.2E−06	−1.23	0.22	1.7E−08	−0.11	0.26	6.9E−01	1.07	0.34	1.5E−03
rs2302634	7:12270770	Intron	TMEM106B	T	0.58	1.00	0.26	0.04	1.3E−09	0.34	0.06	3.2E−08	0.18	0.06	2.9E−03	−0.16	0.09	6.2E−02
rs56194026	15:74831534	Intergenic	ARID3B	C	0.92	0.90	−0.03	0.08	7.2E−01	−0.50	0.12	1.6E−05	0.41	0.12	5.3E−04	0.90	0.16	4.7E−08
Non-AD Inflammation (PC4)
rs7551263	1:203150756	Intron	CHI3L1	T	0.84	0.99	−0.33	0.06	6.0E−09	−0.30	0.08	8.7E−05	-0.40	0.09	3.1E−06	0.07	0.12	5.5E−01
rs10399931	1:203156080	Intergenic	CHI3L1	T	0.24	0.98	−0.39	0.05	5.7E−17	−0.36	0.07	2.7E−07	−0.45	0.07	1.0E−11	−0.12	0.09	1.9E−01
rs12670437	7:76390507	Intergenic	-	G	0.98	0.87	−0.49	0.15	9.9E−04	−1.20	0.22	2.4E−08	0.20	0.21	3.3E−01	1.24	0.32	1.2E−04
rs145791381	9:24796757	Intergenic	-	T	0.98	0.93	−1.01	0.18	2.7E−08	−1.27	0.21	2.7E−09	−0.41	0.36	2.6E−01	NA	NA	NA
rs16974493	13:110307768	Intergenic	-	T	0.97	0.98	0.59	0.14	1.5E−05	0.18	0.22	4.2E−01	0.97	0.17	2.2E−08	0.77	0.27	5.2E−03
rs150326618	14:52641990	Intergenic	-	G	0.98	0.80	0.57	0.17	9.8E−04	0.09	0.24	7.2E−01	1.39	0.25	2.6E−08	1.13	0.35	1.3E−03
Non-AD Synaptic Functioning (PC5)
rs275844	19:48884949	Intergenic	GRIN2D	G	0.88	0.93	−0.30	0.07	9.6E−06	−0.39	0.10	4.0E−05	−0.20	0.10	4.2E−02	0.22	0.14	1.1E−01
rs8111684	19:48947326	3′-UTR	GRIN2D	G	0.26	1.00	0.19	0.05	9.8E−05	0.24	0.07	8.4E−04	0.12	0.07	7.9E−02	0.11	0.10	2.9E−01
rs3107911	19:48964305	Intron	GRIN2D	C	0.15	0.96	0.31	0.06	5.0E−07	0.38	0.09	8.7E−06	0.21	0.09	2.0E−02	0.17	0.13	1.7E−01

SNP RS ID, Chr:Pos Chromosome:Position Build 37, EA effect allele, SE standard error, R²_imp Imputation Quality, β effect of one copy of the effect allele on biomarker PCs in SD. In case of sex interaction, the effect specific to females, SE standard error, p p-value, NA rs145791381 interaction models failed to converge due to too high multicollinearity