The large sample size in our study and the high density of imputed SNP markers allow us to identify lung cancer subtype-specific epistasis including RGL1:RAD51B in NSCLC (OR = 0.40, p = 9.71x10-11), SYNE1:RNF43 in ADE cohort (OR = 0.73, p = 1.01x10-12), and FHIT:TSPAN8 in SQC cohort (OR = 0.60, p = 7.62x10-11). Here, RNF43 is linked to lung cancer.