TWAS identified ATXN2 (AS: Z-score: 4.805, P = 1.55×10−6; AIS: Z-score: 5.137, P = 2.79×10−7) and CDK6 (AS: Z-score: − 4.638, P = 3.52 × 10−6; AIS: Z-score: − 4.463, P = 8.08 × 10−6) whose cis-regulated brain mRNA expression was both associated with AS and AIS, and the expression of NBEAL1 (Z-score: 4.646, P = 3.38 × 10−6) was also associated with AIS (Additional file 1: Table S6 and S7). This evidence concerns the gene CDK6 and androgen insensitivity syndrome.