Table 2.1.

SNPs from the TOMM40, APOC1, APOE and PVRL2 (NECTIN2) genes that showed most significant associations in GWAS of Alzheimer’s disease in CHS, FHS, HRS and LOADFS, using logistic regression (GLIMMIX in LOADFS).

Dataset	SNP	p-Value	OR	Chr	Minor	Major	MAF case	MAF contr	Gene	Location
CHS	rs2075650	9.32E–15	2.3	19	G	A	0.22	0.12	TOMM40	Intron (LD with rs429358, rs769449 in APOE)
	rs405509	1.31E–06	1.5	19	T	G	0.53	0.43	APOE	Upstream, promoter
	rs8106922	4.54E–05	0.7	19	G	A	0.3	0.39	TOMM40	Intron
	rs6859	5.34E–05	1.4	19	A	G	0.49	0.4	PVRL2	3′-UTR
	rs769450	1.59E–04	0.7	19	A	G	0.33	0.41	APOE	Intron
FHS	rs2075650	4.02E–09	2.3	19	G	A	0.17	0.12	TOMM40	Intron (LD with rs429358, rs769449 in APOE)
	rs12721046	4.87E–09	2.2	19	A	G	0.18	0.12	APOC1	Intron (LD with rs769449 and rs429358 in APOE)
HRS	rs769449	3.00E–12	1.9	19	A	G	0.15	0.09	APOE	Intron (strong LD with rs429358 in APOE; moderate LD with rs12721046 in APOC1, rs2075650 in TOMM40)
	rs157582	3.32E–09	1.5	19	T	C	0.31	0.24	TOMM40	Intron
	rs283815	1.41E–08	1.5	19	G	A	0.31	0.25	PVRL2	3′-UTR
	rs71352238	7.54E–08	1.6	19	C	T	0.17	0.12	TOMM40	Intron
	rs2075650	1.65E–07	1.5	19	G	A	0.18	0.13	TOMM40	Intron (LD with rs429358, rs769449 in APOE)
LOADFS	rs2075650	2.86E–64	3.6	19	G	A	0.34	0.18	TOMM40	Intron (LD with rs429358 in APOE)
	rs8106922	1.14E–23	0.5	19	G	A	0.26	0.37	TOMM40	Intron
	rs157580	1.50E–23	0.5	19	G	A	0.23	0.33	TOMM40	Intron (LD with rs405509, rs769449 near APOE)
	rs405509	1.50E–20	1.7	19	T	G	0.59	0.49	APOE	Upstream, promoter
	rs6859	1.12E–18	1.7	19	A	G	0.52	0.42	PVRL2	3′-UTR
	rs439401	5.17E–17	0.6	19	T	C	0.26	0.33	APOE, APOC1	Between genes

The columns notations: dataset name, SNP name, p-value in logistic regression (GLIMMIX for LOADFS), Odds Ratio (OR) for logistic regression, chromosome (Chr), reference allele (Ref), alternative allele (Alt), minor allele frequencies (MAF) in the case and in control groups, gene’s name and location with LD information. (The ORs for LOADFS are from GLIMMIX regression.)