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Table 5 Top two-way models identified by ES-MDR in OncoArray-TRICL data

From: A new efficient method to detect genetic interactions for lung cancer GWAS

Gene(s) 1 SNP 1 (GRCh37/hg19) Gene Region 1 Alleles (Major/Minor) MAFa (1000 Genomes) Gene(s) 2 SNP 2 (GRCh37/hg19) Gene Region 2 Alleles (Major/Minor) MAF (1000 Genomes) ES-MDR Test Score OncoArray-genotyped (HRa) Log-rank test statistic Permutation P value
BRCA1 rs749410065 delTa –/T NAa CBR1, LOC100133286 rs151043730 missense, ncRNAa G/A 0.001 13.77 1.24 65.74 < 0.0001
BRCA1 rs749410065 delTa –/T NAa NAPG rs3865365 near 5′ end of genes G/A 0.06 13.43 1.23 61.74 < 0.0001
C6orf10 rs16870005 Intron C/T 0.01 BRCA1 rs749410065 delTa –/T NAa 13.42 1.25 67.66 < 0.0001
C1orf21, LOC107985236 rs7535067 Intron, 3′ UTRa C/A,T 0.19 BRCA1 rs749410065 delTa –/T NAa 13.39 1.24 61.92 < 0.0001
PSMB9, LOC100294145 rs57092860 Intergenic T/C,G 0.01 BRCA1 rs749410065 delTa –/T NAa 13.37 1.25 67.82 < 0.0001
CTNND2 rs7732411 Intron T/C 0.08 BRCA1 rs749410065 delTa –/T NAa 13.32 1.25 67.53 < 0.0001
TRAM2-AS1, LOC730101 rs182398206 Intergenic A/G 0.01 BRCA1 rs749410065 delTa –/T NAa 13.30 1.25 70.95 < 0.0001
MIR4417, MIR4689 rs6698924 Intergenic A/C 0.02 BRCA1 rs749410065 delTa –/T NAa 13.29 1.25 68.74 < 0.0001
BRCA1 rs749410065 delTa –/T NAa TFAP2C, BMP7 rs186132350 Intergenic T/A 0.01 13.29 1.25 69.79 < 0.0001
HRAT92, PRKAR1B rs142263110 Intergenic G/A 0.002 BRCA1 rs749410065 delTa –/T NAa 13.28 1.25 69.36 < 0.0001
  1. aUTR, untranslated region; delTa, NC_000017.10:g.41196821delT; ncRNA, noncoding transcript variant; HR, hazard ratio; NA, not available