Table 2. Genetic colocalization with quantitative trait locus data.

Colocalization was evaluated for genes in each AD associated locus using a 2Mb window centered on the lead variant. Evidence for colocalization was considered at colocalization posterior probability (PP4)>0.7 (bolded). The table presents PP4 results and is restricted to genes and datasets/tissues where at least one colocalization reached PP4>0.7. As such, the table is partitioned into 4 common variant loci that showed colocalization support. Bolded entries with an asterisk (*) indicate the lead variant was also a significant QTL in the respective data/tissue. Missing entries indicate that no QTL data were available. The total number of times a gene was prioritized (PP4>0.7) is summarized to help identify the most likely causal gene per locus (blue bolded genes and numbers). Overlapping datasets were considered as those where subjects partially or fully overlapped (non-overlapping datasets are separated by dashed lines).

Dataset	Tissue	QTL	SLC9A7								ZNF280C				ADGRG4					MTM1
			ENSG00000286306	KRBOX4	CHST7	SLC9A7	RP2	JADE3	UBA1	ELK1	ELF4	AIFM1	ZNF280C	RBMX2	FHL1	MAP7D3	BRS3	HTATSF1	AL683813.2	MTMR1
Wingo et al. 2023 (AD Knowledge Portal)	Brain - Dorsolateral prefrontal cortex	pQTL				0.56	0.89*		0.05			0.02			0.12	0.05		0.03		0.01
Wingo et al. 2023 (AD Knowledge Portal)	Brain - Dorsolateral prefrontal cortex	eQTL		0.77*	0.95*	0.56	0.04	0.70*	0.04	0.00		0.16	0.45	0.00	0.78*	0.93*		0.05		0.05
CommonMind (eQTL Catalogue)	Brain - Dorsolateral prefrontal cortex	eQTL	0.88	0.04	0.92*	0.86*	0.07	0.07	0.93*	0.04	0.05	0.12	0.09	0.29	0.13	0.92*	0.04	0.03		0.16
GTEx	Brain - (9 brain areas)	eQTL		0.74	0.86*	0.64	0.13	0.51	0.12	0.33	0.11	0.56	0.77*	0.07	0.10	0.77*	0.04	0.04	0.07	0.88
GTEx	Whole blood	eQTL		0.23	0.20	0.39	0.03	0.06	0.07	0.03	0.02	0.19	0.05	0.02	0.02	0.92*		0.01	0.02	0.01
GTEx	Other (20 tissues not brain or blood)	eQTL		0.92	0.71	0.98*	0.14	0.76	0.10	0.16	0.78*	0.78*	0.92*	0.77	0.13	0.89*	0.73	0.87*	0.77	0.79
Fairfax et al. 2014 (eQTL Catalogue)	Monocytes (4 conditions)	eQTL		0.10	0.27	0.93*	0.50	0.10	0.13	0.86	0.01	0.73	0.19	0.04	0.85	0.13	0.04	0.07		0.18
CEDAR (eQTL Catalogue)	Monocytes	eQTL		0.05	0.15	0.93*	0.05	0.43	0.12	0.08	0.06	0.78*	0.04	0.05	0.29	0.08	0.04	0.06		0.11
No. times prioritized across datasets & tissues			1	4	10	12	1	2	1	1	1	6	17	1	2	10	1	2	1	2
No. times prioritized in non-overlapping datasets			1	2	3	4	1	2	1	1	1	3	1	1	2	3	1	1	1	1

Abbreviations: QTL, quantitative trait locus; eQTL, expression quantitative trait locus; pQTL, protein quantitative trait locus; No., number.