Additional file 2 of DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures

Additional file 2: Table S2. Epigenome-wide association study (EWAS) of metabolic measures. Presented are CpG site-metabolic measurement pairs statistically significantly associated in the KORA F4 discovery study. Results for the discovery analysis in KORA (“KORA”), the sensitivity analysis in KORA (“_KORA_Sens”), LOLIPOP (“_LOLIPOP”), NFBC1966 (“_NFBC”), and Young Finns (“_YFS”) studies, as well as the results for the meta-analysis (“_MA”) of these three replication studies, are presented. The scaled coefficients of the sensitivity analysis in KORA (“Coef_KORA_scaled”, i.e., both the log-transformed metabolite measure and methylation beta value were z-transformed prior to analysis) are also presented. The coefficients and p values for the discovery KORA analysis were calculated based on the results of 10 MICE imputed datasets and combined using the commands pool.scalar and micombine.chisquare, from the R packages mice and micetools, respectively. Discovery (KORA F4) significance based on p value < 4.73e−10; meta-analysis significance based on p value < 1.80e−4 (based on 274 pairs tested for replication). Gene, CHR, and Pos: gene, chromosome, and position annotation for the CpG site taken from the Illumina 450 K annotation file; Coef: coefficient of the CpG site from the regression analysis; SE: standard error of the coefficient; P: p value for the regression coefficient; N: number of observations; P_Bonf: Bonferroni-corrected p value for the given analysis; Explained_variance_KORA: percentage of explained variance of the log-transformed metabolic measure by the CpG; Stat_Sig_MA: statistically significant in the meta-analysis of the three replication studies. Unless otherwise specified, all coefficients are change in natural log-transformed metabolite measurement unit (as given in Additional file 1: Table S1) per unit increase in methylation (beta value on 0–1 scale).