We also found several CIN associated rare variants (see Supplementary Fig. 2), which were indexed by rs9808117 in HECW2 on chromosome 2 (MAF = 0.64%, OR = 9.10, P = 9.82 × 10−9), rs373695 in F13A1 on chromosome 6 (MAF = 0.06%, OR = 74.83, P = 1.36 × 10−8), rs7501702 ear MFAP4 on chromosome 17 (MAF = 0.33%, OR = 14.95, P = 1.76 × 10−8) and rs8024434 in NEO1 on chromosome 15 (MAF = 0.36%, OR = 19.39, P = 4.83 × 10−8)(see Supplementary Table 2). The gene discussed is MFAP4; the disease is cervical squamous intraepithelial neoplasia.