By combining the ENCODE ChIA-PET data and CRISPR-Cas9 technology, we were able to show that the strong intergenic enhancer covering the rs11055880 position endogenously regulates the expression of ATF7IP. We also validated the direct link between the risk-associated G allele at rs12142375 and increased PDE4B expression by eQTL analysis in clinical samples of B-cell lymphoblastic leukemia. Here, ATF7IP is linked to precursor B-cell acute lymphoblastic leukemia.