According to the findings of genotype‐phenotype association analysis in this study, we propose that a combined panel for the detection of α/β‐globin gene clusters and key modifier genes including BCL11A, MYB‐HBS1L, KLF1, HBG1/HBG2, and DNMT1 is capable for precise diagnosis of thalassemia while the average cost would be ≈50 US dollars per sample, which makes this method to have promising application prospects in the population screening of thalassemia. Here, DNMT1 is linked to thalassemia.