Extended Data Fig. 3. Evaluation of genetic associations of replicated mQTLs from CKD patients in a healthy population sample.

(a) Each point represents the index SNP of one of 90 associations that could be matched between the Metabolon platforms of the GCKD and SHIP-Trend studies (see Supplementary Table 5). Dot size is proportional to the −log₁₀(P value) in GCKD and error bars represent 1.96× standard errors in each study. The red line corresponds to a linear regression based on the effect estimates of the most significant index SNP in each of the 35 unique genetic regions into which the 90 associations map. (b) 81 mQTLs with −log₁₀ (P value) >12 are plotted. In subsequent panels, the color codes correspond to the detection mode of the mass spectrometer (c), metabolite super pathway (d), differences in relative standard deviation based on measurements of duplicate samples as a measure of precision (e), and the percent of imputed values in GCKD (f). For strata with at least 10 matched mQTLs, additional regression lines were added with color-coding corresponding to the respective legends.