Fig. 4
Baseline and enrichment analyses of GWAS summary statistics for 31 complex traits. References of these data are provided in Supplementary Notes. a Summary of inferred effect size distributions of 31 traits. Results are from fitting the baseline model (M0) to GWAS summary statistics of 1.1 million common HapMap3 SNPs for each trait using variational inference (Methods). We summarize effect size distribution using two statistics: the estimated fraction of trait-associated SNPs (average posterior probability of a SNP being trait-associated; x-axis) and the standardized effect size of trait-associated SNPs (average posterior mean effect size of all SNPs, normalized by phenotypic standard deviation and fraction of trait-associated SNPs; y-axis). Each dot represents a trait, with horizontal and vertical point ranges indicating posterior mean and 95% credible interval. See Supplementary Notes for more details. Note that some intervals are too small to be visible due to log10 scales. See Supplementary Table 2 for numerical values of all intervals. b Pairwise sharing of 3913 pathway enrichments among 31 traits. For each pair of traits, we estimate the proportion of pathways that are enriched in both traits, among pathways enriched in at least one of the traits (Methods). Traits are clustered by hierarchical clustering as implemented in the package corrplot (Methods). Darker color and larger shape represent higher sharing. The sharing estimates are provided in Supplementary Table 3. ALS amyotrophic lateral sclerosis; DS depressive symptoms; LOAD late-onset Alzheimer’s disease; NEU neuroticism; SCZ schizophrenia; BMI body mass index; HEIGHT adult height; WHR waist-to-hip ratio; CD Crohn’s disease; IBD inflammatory bowel disease; RA rheumatoid arthritis; UC ulcerative colitis; ANM age at natural menopause; CAD coronary artery disease; FG fasting glucose; FI fasting insulin; GOUT gout; HDL high-density lipoprotein; HR heart rate; LDL low-density lipoprotein; MI myocardial infarction; T2D type 2 diabetes; TC total cholesterol; TG triglycerides; URATE serum urate; HB hemoglobin; MCH mean cell HB; MCHC MCH concentration; MCV mean cell volume; PCV packed cell volume; RBC red blood cell count
