The significant association of HLA-DQA1 lead SNP (rs9272050) was replicated in invasive cervical cancer (p=7·90 × 10−8), CIN3 (p=0·0005), and cervical dysplasia (p=5·33 × 10−10) phenotypes. Here, HLA-DQA1 is linked to cervical intraepithelial neoplasia.