Genome-wide epistasis analysis for Alzheimer’s disease and implications for genetic risk prediction

Table 3 Significant genetic interactions with a false discovery rate (FDR) < 0.1

SNP1	Chr_1	Position_1^a	SNP2	Chr_2	Position_2^a	P	FDR	Gene_1	Gene_2
Genetic interaction identified by BOOST
rs354709	2	143886953	rs2164808	2	25377176	1.47E−10	0.058	ARHGAP15	EFR3B; RP11-509E16.1
Genetic interactions identified by logistic regression
rs6952399	7	45210711	rs6974494	7	83743961	1.88E−10	0.048	RAMP3	SEMA3A
rs17856580	16	27246617	rs1048159	17	54912339	2.43E−10	0.048	NSMCE1	DGKE; C17orf67
Genetic interactions identified by joint effect
rs6952399	7	45210711	rs6974494	7	83743961	5.08E−10	0.076	RAMP3	SEMA3A
rs217362	7	44618599	rs8004063	14	23732479	7.61E−10	0.076	DDX56; TMED4	C14orf164; RNU6-1046P
rs4574537	5	137419728	rs2301600	19	35786868	7.70E−10	0.076	WNT8A	MAG
rs2075302	2	163076146	rs374479	5	80998915	8.03E−10	0.076	FAP	SSBP2
rs8580	7	44620836	rs8004063	14	23732479	9.70E−10	0.076	TMED4	C14orf164; RNU6-1046P

Chr_1, chromosome of SNP1; Gene_1, genes within 5 kb of SNP1; Chr_2, chromosome of SNP2; Gene_2, genes within 5 kb of SNP2;
^aSNP positions were in build 37, assembly hg19

ISSN: 1758-9193