Table 1.

Genes reaching statistical significance (FDR ≤ 0.05) for association with LOAD conditional on association with MDD.

SNP	Chr.	Positiona	Nearest gene	minor allele	MAF	Conditional FDR Q(LOAD|MDD)	LOAD Beta	LOAD Beta SE	LOAD P-value	MDD OR	MDD OR SE	MDD P-value
rs35677603	11	47,268,310	ACP2	T	0.31	1.58E−03	−0.078	0.016	4.05E−07	0.985	0.009	8.59E−02
rs3017432	21	28,147,728	ADAMTS1	T	0.59	2.98E−03	−0.074	0.015	1.05E−06	0.982	0.008	2.84E−02
rs11823949	11	47,723,512	AGBL2	A	0.35	1.98E−05	−0.097	0.017	4.40E−09	0.974	0.009	3.45E−03
rs35589443	2	127,847,736	BIN1	A	0.03	1.43E−03	−0.265	0.052	3.65E−07	1.047	0.027	9.53E−02
rs12419692	11	47,624,714	C1QTNF4	A	0.35	2.81E−05	−0.087	0.015	7.21E−09	0.977	0.008	5.11E−03
rs1317149	11	47,486,885	CELF1	T	0.36	2.17E−05	−0.089	0.015	3.45E−09	0.980	0.008	1.43E−02
rs11576522	1	207,789,269	CR1	A	0.63	2.85E−04	0.079	0.015	6.56E−08	1.017	0.009	5.87E−02
rs11039138	11	47,249,223	DDB2	A	0.37	9.00E−03	0.070	0.015	2.45E−06	1.015	0.008	7.91E−02
rs76184771	19	18,567,189	ELL	A	0.13	2.03E−02	−0.091	0.021	1.29E−05	1.030	0.011	9.58E−03
rs75010292	2	55,172,536	EML6	A	0.11	2.63E−02	−0.098	0.023	1.72E−05	0.967	0.013	7.70E−03
rs17125924	14	53,391,680	FERMT2	A	0.08	2.58E−03	−0.122	0.025	6.62E−07	1.026	0.014	5.79E−02
rs4742958	9	108,411,944	FKTN	T	0.14	4.44E−02	−0.128	0.030	1.56E−05	0.967	0.016	3.21E−02
rs7130758	11	47,749,960	FNBP4	T	0.36	3.27E−05	−0.088	0.015	1.01E−08	0.978	0.009	8.73E−03
rs11021857	11	11,472,193	GALNT18	A	0.07	4.92E−02	0.122	0.030	3.68E−05	1.049	0.017	4.60E−03
rs9270208	6	32,556,402	HLA-DRB1	T	0.68	4.29E−02	−0.077	0.018	1.49E−05	1.016	0.009	8.02E−02
rs2385088	19	18,545,540	ISYNA1	A	0.34	3.80E−02	−0.066	0.015	1.26E−05	1.016	0.008	6.29E−02
rs3859570	19	18,510,925	LRRC25	T	0.41	1.26E−02	−0.069	0.016	7.84E−06	1.023	0.009	9.53E−03
rs67871383	11	47,335,838	MADD	T	0.32	3.53E−04	0.082	0.015	8.28E−08	1.017	0.009	4.22E−02
rs2047007	1	40,427,975	MFSD2A	T	0.23	4.07E−02	0.071	0.017	2.83E−05	1.027	0.009	3.42E−03
rs1125357b	11	59,885,493	MS4A2	A	0.42	8.87E−09	0.107	0.015	3.09E−13	0.984	0.009	7.20E−02
rs1026254b	11	60,030,457	MS4A4A	T	0.60	2.84E−10	−0.116	0.015	2.42E−15	1.014	0.008	8.87E−02
rs1582763b	11	60,021,948	MS4A4E	A	0.36	1.40E−10	−0.123	0.015	1.19E−16	1.016	0.009	9.38E−02
rs624663b	11	59,945,065	MS4A6A	T	0.56	1.33E−08	0.104	0.014	6.34E−13	0.984	0.008	4.91E−02
rs10838738	11	47,663,049	MTCH2	A	0.35	2.56E−05	0.087	0.015	5.99E−09	1.025	0.008	2.82E−03
rs61781278	1	40,376,741	MYCL	A	0.19	4.30E−02	0.076	0.018	1.76E−05	1.022	0.010	2.47E−02
rs11605348	11	47,606,483	NDUFS3	A	0.35	3.47E−06	−0.097	0.016	4.25E−10	0.978	0.009	8.36E−03
rs7105282	11	47,805,614	NUP160	A	0.36	4.54E−05	−0.091	0.016	1.63E−08	0.974	0.009	3.15E−03
rs541458b	11	85,788,351	PICALM	T	0.68	1.01E−08	0.112	0.015	3.69E−13	0.984	0.010	8.07E−02
rs60075622	11	47,449,101	PSMC3	T	0.33	7.86E−06	0.092	0.015	1.30E−09	1.023	0.008	6.24E−03
rs755951	8	27,226,790	PTK2B	A	0.39	1.72E−04	−0.082	0.015	3.79E−08	1.015	0.008	6.82E−02
rs7106956	11	47,458,765	RAPSN	T	0.33	8.34E−06	0.092	0.015	1.28E−09	1.023	0.008	6.10E−03
rs755554	11	47,432,034	SLC39A13	C	0.67	4.90E−06	0.095	0.015	6.29E−10	1.024	0.009	4.71E−03
rs3781832	11	121,436,270	SORL1	T	0.10	2.89E−02	−0.098	0.022	1.09E−05	0.972	0.013	2.53E−02
rs67472071	11	47,391,745	SPI1	A	0.33	1.05E−06	−0.098	0.015	1.14E−10	0.980	0.008	1.96E−02
rs7258465	19	18,533,642	SSBP4	T	0.34	3.58E−02	−0.066	0.015	1.17E−05	1.017	0.008	4.36E−02
rs7011101	8	71,501,474	TRAM1	A	0.10	1.91E−02	−0.105	0.023	5.67E−06	1.022	0.013	9.91E−02
rs4929858	11	49,070,655	TRIM64C	A	0.63	2.80E−02	0.065	0.015	1.85E−05	1.036	0.008	1.85E−05
rs61781270	1	40,349,428	TRIT1	A	0.20	2.32E−02	0.077	0.017	7.11E−06	1.017	0.009	7.17E−02
rs66555393	8	71,628,753	XKR9	A	0.10	3.02E−02	0.106	0.024	9.54E−06	0.977	0.014	9.31E−02
rs17376517	3	44,765,221	ZNF502	T	0.05	4.63E−02	−0.141	0.033	1.65E−05	0.969	0.018	7.22E−02

SNP single-nucleotide polymorphism, MAF minor allele frequency, LOAD late-onset Alzheimer’s disease, MDD major depressive disorder, FDR false discovery rate.

^aBuild 37, assembly hg19.

^bSNP that were highly significant (FDR Q ≤ 5 × 10⁻⁸) in the Q(LOAD|MDD) analysis excluding the APOE and were used for the eQTL analysis (Fig 4b).