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

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

SNP1 Chr_1 Position_1a SNP2 Chr_2 Position_2a 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
  1. 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;
  2. aSNP positions were in build 37, assembly hg19