In this study, 3D structural genomic analysis from Hi-C and Capture Hi-C, expression profiling of PCOS patients and PCOS-like models, ChIP-Seq analysis of androgen receptor (AR) in STON1 and FSHR, and single-cell sequencing of ovary tissue were used to synthesize the 3D interactions, adipocyte metabolism association with STON1, and CD4 immune association with FSHR at the rs13405728 locus in PCOS. Here, FSHR is linked to polycystic ovary syndrome.