CHEK2 and breast cancer: Also these GWAS index SNPs remained statistically significant after adjusting for eQTL/sQTL of nearby genes including CHEK2 (Table S3 in Additional file 1). Together, the discovery of CHEK2 in our ER + TWAS, alongside the lack of overlap and correlation between SNPs used in expression prediction models and GWAS index variants, suggest that common variants which modulate CHEK2 expression likely play a role in breast cancer risk, and these common variants are etiologically distinct from those identified in previous GWAS studies.