Of the 19 replicated eGFR- and/or CKD-associated CpGs, five (in or near PTPN6/PHB2, ANKRD11, TNRC18, PQLC2, and PRPF8) also showed a significant association between DNA methylation from human kidney cortex samples and the degree of fibrosis in the corresponding kidney biopsies. Here, PTPN6 is linked to chronic kidney disease.