Overall, we identify three new susceptibility loci: 1p36.32 near AJAP1, encoding adherens junction associated protein 1 (rs241215, Pcombined=2.95 × 10−9); 2q36.1 between PAX3 and EPHA4, encoding paired box 3 and EPH receptor A4, respectively (rs13398147, Pcombined=7.59 × 10−13); and 18q21.33 near BCL-2, encoding B-cell CLL/lymphoma 2 (rs4940576, Pcombined=2.22 × 10−12). Here, PAX3 is linked to B-cell chronic lymphocytic leukemia.