WNT16 stands up as an essential gene for bone homeostasis. Here, we present new evidence of the functional role of a particular region within WNT16. Performing 4 C chromatin conformation analysis in three osteoblast-related cells (the human fetal osteoblast hFOB 1.19 cell line, Saos 2 osteosarcoma cell line and mesenchymal Stem Cells -MSC-), we identify physical interactions between the proximal part of WNT16 intron 2, shown here to be an active promoter in Saos 2 osteosarcoma cells, and several putative regulatory regions within CPED1. Analysis of previously published RNA-seq data from hFOB cells disclosed low expression of a region located downstream of this promoter. Our results suggest a novel regulatory mechanism of WNT16 in bone, mediated by physical interaction with various enhancer regions within CPED1.