DOI: 10.6084/m9.figshare.12586331
title: Additional file 1 of Genetic colocalization atlas points to common regulatory sites and genes for hematopoietic traits and hematopoietic contributions to disease phenotypes

description: Additional file 1: Table S1. Genome wide association study summary statistics used in our analysis. The trait(s) queried are shown, along with study Pubmed identification number (PMID). UK Biobank studies can be found using the link provided. Total European sample sizes, including cases and controls where appropriate, are shown for each study. PMIDs for data downloaded from the NHGRI-EBI GWAS Catalog can be found at the bottom of this table. Table S2. Traits and SNPs identified by colocalization analysis [5] of 34 hematopoietic traits. All identified sites are shown in this table. Candidate SNPs are indicated as chr:pos. The posterior probability of colocalization, regional (genomic) probability of colocalization, and posterior probability explained at each locus are indicated. Table S3. Traits and SNPs identified by colocalization analysis [5] of 17 hematopoietic traits with genetic correlation (rg) 0.9). Table S5. ‘RBC trait only’ sites at which only the indicated red blood cell traits colocalized, excluding platelet or white blood cell traits. Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Rbc, red blood cell count. Hct, hematocrit. Mcv, mean red cell corpuscular volume. Rdw, red cell distribution width. Table S6. Gene ontology pathway analysis of genes regulated by eQTLs linked to ‘RBC trait only’ sites. Shown are pathways with p 0.9). Plt, platelet count. Pct, platelet-crit. Mpv, mean platelet volume. Pdw, platelet distribution width. Table S8. Gene ontology pathway analysis of genes regulated by eQTLs linked to ‘platelet trait only’ sites. Shown are pathways with p 0.9). Table S12. Colocalization sites for neutrophil count (neut) and Asthma. Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S13. Colocalization sites for eosinophil percentage of white blood cells (eo%) and Asthma. Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S14. Colocalization sites for monocyte count (mono) and Asthma. Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S15. Colocalization sites for mean platelet volume (mpv) and coronary artery disease (cad). Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S16. Colocalization sites for reticulocyte count (ret) and coronary artery disease (cad). Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S17. Colocalization sites for lymphocyte count (lymph) and coronary artery disease (cad). Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S18. Colocalization sites for eosinophil percentage of white blood cells (eo%) and Eczema. Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S19. Mendelian randomization analysis results for the indicated exposure and outcome traits. Outcomes reflect increased risk of eczema (odds ratio) or depressive symptoms (in standard deviation units) per 1 standard deviation increase in exposure by inverse variance weighted, weighted median, and MR-Egger methods. Factors used to calculate genetic variance explained (R2 [29]) and instrument strength (F-statistics [28]) are shown to the right of the primary results. Instruments with F-statistics &gt; 10 were considered devoid of weak instrument bias [28]. Table S20. Instrumental variable data for MR experiments estimating effects of eosinophil percentage of white blood cells (eo%) on Eczema. The rsID (hg19), chromosome, position, effect allele, other (non-effect) allele, effect sizes and standard errors are shown for each SNP. Table S21. Colocalization sites for red blood cell count (rbc), basophil cell count (baso) and depressive symptoms (DepSx). Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S22. Instrumental variable data for MR experiments estimating effects of red blood cell count (rbc) on depressive symptoms (DepSx). The rsID (hg19), chromosome, position, effect allele, other (non-effect) allele, effect sizes and standard errors are shown for each SNP. Table S23. Instrumental variable data for MR experiments estimating effects of basophil cell count (baso) on depressive symptoms (DepSx). The rsID (hg19), chromosome, position, effect allele, other (non-effect) allele, effect sizes and standard errors are shown for each SNP. Table S24. Colocalization sites for breast cancer and schizophrenia. Gene symbols for the nearest gene, all eQTLs, all eQTLs in whole blood, and all sQTLs (sQTLseekeR and Altrans methods) are shown in the indicated columns related to the indicated SNP (rsID) and any SNPs in high linkage disequilibrium (r2 &gt; 0.9). Table S25. Analysis of a coding variant (rs2476601) that causes a missense mutation in PTPN22 shows significant colocalization with white blood cell (wbc) count and Crohn’s disease. The effect sizes and direction (+/−) are shown. Table S26. Colocalization analysis for a coding variant (rs1800562) in HFE, mutations in which cause hereditary hemochromatosis. Effects on total cholesterol (TC), low density lipoprotein (LDL), and red blood cell traits (high light scatter reticulocyte count, hlr; high light scatter reticulocyte percentage, hlr_p; mean corpuscular hemoglobin concentration, mchc; red cell distribution width, rdw; reticulocyte count, ret; reticulocyte percentage, ret_p), with significant colocalization signal at this locus, are shown. Table S27. Colocalization analysis for a coding variant (rs17600346) in Tumor necrosis factor (TNF)-related apoptosis inducing ligand (TRAIL, also known as TNF10), based on targeted analysis of the 50 kb region surrounding this site. Effects on colocalized white blood cell (granulocyte percentage of myeloid white blood cells, gran_p_myeloid_wbc; monocyte percentage, mono_p) and platelet traits (platelet-crit, pct; platelet count, plt) are shown.