Additional file 3 of Identifying and ranking causal biochemical biomarkers for breast cancer: a Mendelian randomisation study

Additional file 3: SNP Information. Table 1. Secondary trait associations of HDL cholesterol SNPs. Phenoscanner SNP associations. SNP: single nucleotide polymorphism. hg19_coordinates: the hg19 chromosome position for the input SNP. hg38_coordinates: the hg38 chromosome position for the input SNP. a1: the effect allele (aligned to the + strand). a2: the non-effect allele (aligned to the + strand). efo: the EFO ontology term for the phenotype or disease. pmid: PubMed ID. beta: association between the trait and the SNP expressed per additional copy of the effect allele (odds ratios are given on the log-scale). se: standard error of beta. p: p-value. direction: the direction of association with respect to the effect allele. n: number of individuals. n_cases: number of cases. n_controls: number of controls. n_studies: number of studies. unit: unit of analysis (IVNT stands for inverse normally rank transformed phenotype). Table 2. Secondary trait associations of alkaline phosphatase SNPs. Phenoscanner SNP associations. SNP: single nucleotide polymorphism. hg19_coordinates: the hg19 chromosome position for the input SNP. hg38_coordinates: the hg38 chromosome position for the input SNP. a1: the effect allele (aligned to the + strand). a2: the non-effect allele (aligned to the + strand). efo: the EFO ontology term for the phenotype or disease. pmid: PubMed ID. beta: association between the trait and the SNP expressed per additional copy of the effect allele (odds ratios are given on the log-scale). se: standard error of beta. p: p-value. direction: the direction of association with respect to the effect allele. n: number of individuals. n_cases: number of cases. n_controls: number of controls. n_studies: number of studies. unit: unit of analysis (IVNT stands for inverse normally rank transformed phenotype). Table 3. Secondary trait associations of testosterone SNPs. Phenoscanner SNP associations. SNP: single nucleotide polymorphism. hg19_coordinates: the hg19 chromosome position for the input SNP. hg38_coordinates: the hg38 chromosome position for the input SNP. a1: the effect allele (aligned to the + strand). a2: the non-effect allele (aligned to the + strand). efo: the EFO ontology term for the phenotype or disease. pmid: PubMed ID. beta: association between the trait and the SNP expressed per additional copy of the effect allele (odds ratios are given on the log-scale). se: standard error of beta. p: p-value. direction: the direction of association with respect to the effect allele. n: number of individuals. n_cases: number of cases. n_controls: number of controls. n_studies: number of studies. unit: unit of analysis (IVNT stands for inverse normally rank transformed phenotype). Table 4. Secondary trait associations of triglycerides SNPs. Phenoscanner SNP associations. SNP: single nucleotide polymorphism. hg19_coordinates: the hg19 chromosome position for the input SNP. hg38_coordinates: the hg38 chromosome position for the input SNP. a1: the effect allele (aligned to the + strand). a2: the non-effect allele (aligned to the + strand). efo: the EFO ontology term for the phenotype or disease. pmid: PubMed ID. beta: association between the trait and the SNP expressed per additional copy of the effect allele (odds ratios are given on the log-scale). se: standard error of beta. p: p-value. direction: the direction of association with respect to the effect allele. n: number of individuals. n_cases: number of cases. n_controls: number of controls. n_studies: number of studies. unit: unit of analysis (IVNT stands for inverse normally rank transformed phenotype). Table 5. Secondary trait associations of IGF-1 SNPs. Phenoscanner SNP associations. SNP: single nucleotide polymorphism. hg19_coordinates: the hg19 chromosome position for the input SNP. hg38_coordinates: the hg38 chromosome position for the input SNP. a1: the effect allele (aligned to the + strand). a2: the non-effect allele (aligned to the + strand). efo: the EFO ontology term for the phenotype or disease. pmid: PubMed ID. beta: association between the trait and the SNP expressed per additional copy of the effect allele (odds ratios are given on the log-scale). se: standard error of beta. p: p-value. direction: the direction of association with respect to the effect allele. n: number of individuals. n_cases: number of cases. n_controls: number of controls. n_studies: number of studies. unit: unit of analysis (IVNT stands for inverse normally rank transformed phenotype). Table 6. Secondary trait associations of apolipoprotein A SNPs. Phenoscanner SNP associations. SNP: single nucleotide polymorphism. hg19_coordinates: the hg19 chromosome position for the input SNP. hg38_coordinates: the hg38 chromosome position for the input SNP. a1: the effect allele (aligned to the + strand). a2: the non-effect allele (aligned to the + strand). efo: the EFO ontology term for the phenotype or disease. pmid: PubMed ID. beta: association between the trait and the SNP expressed per additional copy of the effect allele (odds ratios are given on the log-scale). se: standard error of beta. p: p-value. direction: the direction of association with respect to the effect allele. n: number of individuals. n_cases: number of cases. n_controls: number of controls. n_studies: number of studies. unit: unit of analysis (IVNT stands for inverse normally rank transformed phenotype). Table 7. Secondary trait associations of aspartate aminotransferase SNPs. Phenoscanner SNP associations. SNP: single nucleotide polymorphism. hg19_coordinates: the hg19 chromosome position for the input SNP. hg38_coordinates: the hg38 chromosome position for the input SNP. a1: the effect allele (aligned to the + strand). a2: the non-effect allele (aligned to the + strand). efo: the EFO ontology term for the phenotype or disease. pmid: PubMed ID. beta: association between the trait and the SNP expressed per additional copy of the effect allele (odds ratios are given on the log-scale). se: standard error of beta. p: p-value. direction: the direction of association with respect to the effect allele. n: number of individuals. n_cases: number of cases. n_controls: number of controls. n_studies: number of studies. unit: unit of analysis (IVNT stands for inverse normally rank transformed phenotype). Table 8. Genetic associations with HDL cholesterol, overall , ER-positive, and ER-negative breast cancers. Abbreviations: SNP, single nucleotide polymorphism; Alt, alternate allele (not necessarily minor allele); Ref, reference allele; SE, standard error; P, P-value; MAF, minor allele frequency (equal to ref allele when AF > 0.5, otherwise equal to alt allele - calculated using hardcall genotypes); OBC, overall breast cancer; ERpos BC, ER-positive breast cancer; ERneg BC, ER-negative breast cancer. Table 9. Genetic associations with alkaline phosphatase, overall, ER-positive, and ER-negative breast cancers. Abbreviations: SNP, single nucleotide polymorphism; Alt, alternate allele (not necessarily minor allele); Ref, reference allele; SE, standard error; P, P-value; MAF, minor allele frequency (equal to ref allele when AF > 0.5, otherwise equal to alt allele - calculated using hardcall genotypes); OBC, overall breast cancer; ERpos BC, ER positive breast cancer; ERneg BC, ER negative breast cancer. Table 10. Genetic associations with testosterone, overall , ER-positive, and ER-negative breast cancers. Abbreviations: SNP, single nucleotide polymorphism; Alt, alternate allele (not necessarily minor allele); Ref, reference allele; SE, standard error; P, P-value; MAF, minor allele frequency (equal to ref allele when AF > 0.5, otherwise equal to alt allele - calculated using hardcall genotypes); OBC, overall breast cancer; ERpos BC, ER positive breast cancer; ERneg BC, ER negative breast cancer. Table 11. Genetic associations with triglycerides, overall , ER-positive, and ER-negative breast cancers. Abbreviations: SNP, single nucleotide polymorphism; Alt, alternate allele (not necessarily minor allele); Ref, reference allele; SE, standard error; P, P-value; MAF, minor allele frequency (equal to ref allele when AF > 0.5, otherwise equal to alt allele - calculated using hardcall genotypes); OBC, overall breast cancer; ERpos BC, ER positive breast cancer; ERneg BC, ER negative breast cancer. Table 12. Genetic associations with IGF-1, overall , ER-positive, and ER-negative breast cancers. Abbreviations: SNP, single nucleotide polymorphism; Alt, alternate allele (not necessarily minor allele); Ref, reference allele; SE, standard error; P, P-value; MAF, minor allele frequency (equal to ref allele when AF > 0.5, otherwise equal to alt allele - calculated using hardcall genotypes); OBC, overall breast cancer; ERpos BC, ER positive breast cancer; ERneg BC, ER negative breast cancer. Table 13. Genetic associations with apolipoprotein A, overall , ER-positive, and ER-negative breast cancers. Abbreviations: SNP, single nucleotide polymorphism; Alt, alternate allele (not necessarily minor allele); Ref, reference allele; SE, standard error; P, P-value; MAF, minor allele frequency (equal to ref allele when AF > 0.5, otherwise equal to alt allele - calculated using hardcall genotypes); OBC, overall breast cancer; ERpos BC, ER positive breast cancer; ERneg BC, ER negative breast cancer. Table 14. Genetic associations with aspartate aminotransferase, overall , ER-positive, and ER-negative breast cancers. Abbreviations: SNP, single nucleotide polymorphism; Alt, alternate allele (not necessarily minor allele); Ref, reference allele; SE, standard error; P, P-value; MAF, minor allele frequency (equal to ref allele when AF > 0.5, otherwise equal to alt allele - calculated using hardcall genotypes); OBC, overall breast cancer; ERpos BC, ER-positive breast cancer; ERneg BC, ER-negative breast cancer.