Table 2:

COLOC and SMR analysis of the 13 significant genes in the discovery AD PWAS. Eleven genes had evidence consistent with a causal role by either COLOC or SMR.

			COLOC		SMR
	Gene	Chr	H4	Causal variant	SMR.p	HEIDI.p	Causal variant
1	CTSH	15	0.962	yes	3.1×10−5	0.464	yes
2	DOC2A	16	0.907	yes	1.0×10−3	0.742	yes
3	ICA1L	2	0.672	yes	4.1×10−4	0.977	yes
4	LACTB	15	0.754	yes	3.8×10−4	0.070	yes
5	PLEKHA1*	10	0.581	yes	3.0×10−3	0.455	yes
6	SNX32	11	0.975	yes	2.7×10−5	0.588	yes
7	STX4*	16	0.918	yes	5.0×10−3	0.808	yes
8	ACE	17	0.976	yes	4.0×10−3	0.039	no
9	RTFDC1	20	0.643	yes	4.6×10−5	0.034	no
10	CARHSP1	16	0.188	no	1.2×10−2	0.397	yes
11	STX6	1	0.072	no	1.0×10−2	0.748	yes
12	EPHX2	8	0	no	7.1×10−7	0.008	no
13	PVR*	19	0.022	no	1.4×10−5	n/a	n/a

For the 13 FDR-significant genes in the discovery AD PWAS, the result of COLOC H₄, which is the Bayesian posterior probability that a genetic variant is shared by both traits (i.e., gene and AD), and P values for SMR and SMR HEIDI tests are given.

^(*)Asterisk denotes genes not found in the confirmatory PWAS. n/a (not applicable) indicates undetermined result since the number of pQTL SNPs were too small for HEIDI to test. Genes were sorted by whether they are consistent with being a causal variant.