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. Author manuscript; available in PMC: 2014 Oct 1.
Published in final edited form as: Hum Genet. 2013 Jun 12;132(10):1165–1176. doi: 10.1007/s00439-013-1319-y

Table 3. Most significant SNP Combinations detected by GMDR program and best constituent genotype combination for gene 9 gene interactions in primary population.

Best SNP combinations Best constituent genotype combinations
Combination Test accuracy CVC P value* Combination % in AD cases (N = 500) % in controls (N = 280) OR (95 % CI) P value#
SLC6A4: HTTLPR, rs1042173
HTR3B: rs1176744, rs3782025		 0.8503 10 <1 × 10−6 5HTTLPR-LL/LS rs1042173-TT/TG rs1176744-AC rs3782025-AG 13.02 2.96 2.712 (1.578, 4.661) 0.0003
SLC6A4: HTTLPR
HTR3A: rs10160548
HTR3B: rs1176744, rs3782025		 0.7402 10 <1 × 10−6 5HTTLPR-LL/LS rs10160548-GT/TT rs1176744-AC rs3782025-AG 13.61 3.11 2.802 (1.648, 4.765) 0.0001
SLC6A4: HTTLPR, rs1042173
HTR3A: rs10160548
HTR3B: rs1176744, rs3782025		 0.5836 9 0.0042 5HTTLPR-LL/LS rs1042173-TT/TG rs10160548-GT/TT rs1176744-AC rs3782025-AG 11.83 2.37 3.095 (1.715, 5.583) 0.0002
*

Empirical P value from 106 permutation tests;

#

Chi square P values for comparisons between those carrying the genotype combination vs. non-carriers in AD cases and controls