Supplementary tables.

Table A: Number of samples used for the GWAS for each trait. The questionnaire column indicates from which questionnaire the item was taken. Proportion of sample indicates the proportion of samples used compared to the number of people who participated in the UK biobank at baseline (501,520). Table B: Description of the phenotypes: the table reports the description and coding of the phenotypes used for the GWAS analyisis. Phenotype, name of the phenotype; Question, question asked in the tochscreen questionnaire; Answer—Converted to, coding of the phenotype; Covariates, covariates used for the analysis, standard = age+sex; Transformation, transformation applied for normalising the trait. Table C: Significant loci per trait and type. Table D. Summary statistics of top SNP per trait per locus. Locus N, genomic locus number. Chr, chromosome; Start, starting position of the locus; End ending position of the locus; rsid, per trait top SNP in the locus; a1 a0 Effect allele, Other allele; N number of samples; Beta effect of the coded allele; SE Standard error of the uncorrected effect; p p-value of the initial association; Corr.Beta, effect of a1 after the GW mediation correction procedure;Corr.SE Standard error of the corrected effect; Corr.p p-value of the corrected association; CUR corrected to raw ratio; Gene prioritised genes, if the top-SNP was between genes and the closet one was chosen, the distance from the gene was indicated; type category of the association based on the CRR values. Table E. Replication results. The table reports the replication results for the traits/SNP for which replication was availble. Locus.N locus number; rsid SNP use for replication; a0 a1, Other allele effect allele; Beta effect of the effect allele in the discovery cohort; p p-value in the discovery cohort; n number of samples used in the discovery cohort; rep_effect effect of the a1 allele in the replication cohorts; rep_p p-value in the replication cohorts; N_rep, number of samples used for replication. Table F. a: GWAS used for the Multivariate MR analysis and GW mediation analysis. Name, name of the trait; Consortium, consortium that performae the GWAS; Reference link to paper describing the GWAS; Download; source of the summary statistics. b: GWAS used for the Multivariate MR analysis and GW mediation analysis. Name, name of the trait; Consortium, consortium that performae the GWAS; Reference link to paper describing the GWAS; Download; source of the summary statistics. Table G: Full results of univariate MR. Outcome, outcome trait; Exposure, exposure trait. Method used for the MR analysis; nsnp, number of SNPs used for th IV; b effect of the exposure on the outcome; se standard error of the effect; pval, p-value; results_adjusted, Multiple test corrected pvalues. Table H: Multivariable MR results: for each food trait (otucome column) the best model used for the prior estimation is reported. Exposure column indicates the exposure used; Beta the multivariable effect of the exposure on the outcome; Se standard error of the effect; P-value p-value of the effects; Cor^2 the squared correlation between the prior and the original z-scores. Table I: Full Genetic correlation amongst food results: The table reports the full genetic correlations between the food traits using both corrected and uncorrected results. p1 trait 1; p2 trait 2; rg genetic correlation; se standard error of the genetic correlation estimate; z z-score of the genetic correlation; p p-value; the extension Raw and Corrected refer to the uncorrected and corrected results respectively. Table L: Genetic correlations between the food traits and common traits. Both uncorrected and corrected (the prefix.Corrected is used to indicate corrected results) results are reported. rg, genetic correlation, se standard error of the genetic correlation, p p.value. Table M: Interaction network results analysis performed with STRING. Table N: Comunity membership of the genes in the STRING interaction network. Table O: GO term enrichment for the 13 Detected communities. Table P. Results for tissue enrichment analysis performed on each community. Only tissues with FDR<0.05 are reported. Table Q. LD score regression intercept and heritability estimates. Table R. Proportion of genetic variance explained of each food trait by the causal health related traits. Trait, name of food trait, rg2 proportion of genetic variance explained, rg2se standard error of the proportion of explained genetic variance. Table S: Information on the outcomes used for MR. Table T. Full results of the Food Mendelian Randomization: The table reports the full resutls of the mendellian randomization of food on all the selected outcomes. Exposure: exposure trait, Outcome: outcome trait; Method: method for the main MR analysis: IVW (FE) inverse variance method fixed effect, IVW (RE) inverse variance method random effect, Wald ratio: Wald ratiomethod; nsnp, number of SNPs used for the MR; b effect size relative to the method columns; se standard error relative to the method column; pval p-value of relative to the method column; type exposure betas used (Uncorrected, Corrected); outliers number of SNPs excluded because they were foudn to be outliers at the MR radial analysis; egger.pleio p-value relative to the mr egger test for directlional pleiotropy; mr.raps.beta/me.raps.se beta and standard error relative to the MR-RAPS method; beta_egger/se_egger beta and standard error realtive to the MR-Egger analysis; beta_median/se_median beta and standard error realtive to the Median analysis; het.p Heterogeneity test p-value; qval Storeys qvalues, the qvalues have been estimated only on the CRR Uncorrected analysis; sens.het Heterogeneity test run on the estimates coming from the different methods.
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