PTPN6 and chronic kidney disease: These CpGs were cg12065228 in PQLC2, intergenic cg19942083 near PTPN6/PHB2, cg12116137 in PRPF8, cg09022230 in TNRC18, and cg27660627 in ANKRD11. For each of these five CpGs, hypermethylation was associated with higher eGFR and lower percentage of renal fibrosis, consistent with fibrosis as a pathological correlate of CKD and marker of impaired kidney function (Supplementary Figs. 7–10).