We find that TGFB1 and SMAD6 demonstrate allelic imbalance in subchondral bone (Methods, Supplementary Table 27 and Supplementary Fig. 10) and that the osteoarthritis risk allele of rs146652543 is associated with decreased expression of TGFB1. We also identify decreased protein abundance of TGFβ1 in degraded compared with intact osteoarthritis cartilage (Supplementary Table 13). This evidence concerns the gene SMAD6 and osteoarthritis.