GWAS analyses were done using GEMMA (Genome-wide efficient mixed-model association) [43], separately for FinnTwin (FinnTwin12 and FinnTwin16 samples were pooled together), Young Finns Study, and FINRISK2007 cohorts. Allelic dosage data were used to account for genotype uncertainties. The genetic associations were acquired with a linear mixed model in which the rank transformed NMR was the dependent variable and the coded allele dose (represented by the posterior mean genotypes) was the independent variable. The model included age, sex, and BMI as covariates (fixed effects). In addition, population stratification and relatedness within the sample were accounted for by the covariance matrix of the random effect in the model. The covariance matrix was determined by a relatedness matrix, calculated from genome-wide genotype data and representing genetic similarity across individuals. An estimate of the genomic control inflation factor (λ) was calculated for all three cohorts with the estlambda() function of the R library GenABEL [42]. P-values below 5E-08 were considered as genome-wide significant.
