Additional file 11 of DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures

Additional file 11: Table S7. Genetically influenced CpG site-metabolic measure associations. Results for the cis-SNP analysis are presented. “Coef_discovery” and “P_discovery”: coefficient and p value for the discovery analysis for the given CpG site-trait pair. “Count_conf_SNPs”: number of SNPs which, when added singly to the metabolic measure-CpG site regression model, cause the pair to lose its statistical significance, as defined by the discovery threshold (p = 4.73e−10). “Coef_adj” and “p_adj”: coefficient and p value of the CpG in the model with the addition of the SNP causing the greatest effect (largest change in p value). “top_SNP”: name of the SNP causing the largest effect. “Loses_significance” indicates whether the addition of any SNP to the CpG-metabolic measure regression model causes the association to lose significance (i.e., “Count_conf_SNPs” > 0). “Probable_SNP_confounding” indicates the addition of at least one single SNP to the model renders the association insignificant and drastically alters the results, indicated likely SNP confounding by 1 or more SNPs. NAs within the table indicate the absence of a SNP fulfilling the requirements of our conditional analyses for the CpG-metabolic measure pair (i.e., the absence of a SNP being associated with both the CpG site and the metabolic measure). CHR: chromosome, pos: position, UCSC_RefGene_Name_CpG: annotated gene name of the CpG site, all as given by the Illumina manifest file. N: number of observations in the model incorporating the SNP. 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). *Drastic increase (factor > 100) of p value after addition of the SNP to the regression model.