Forest plot of component effects of complete GWAS predictive model based on training set of SNPs.
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posted on 2015-10-16, 03:17 authored by Damien C. Croteau-Chonka, Angela J. Rogers, Towfique Raj, Michael J. McGeachie, Weiliang Qiu, John P. Ziniti, Benjamin J. Stubbs, Liming Liang, Fernando D. Martinez, Robert C. Strunk, Robert F. Lemanske Jr, Andrew H. Liu, Barbara E. Stranger, Vincent J. Carey, Benjamin A. RabyOdds ratios (black squares) from the complete multivariate model (“chromstate+eqtl [M3]”) for features predicting the membership of a SNP in the NHGRI GWAS Catalog are shown here with standard errors (gray lines). Smaller models are shown for comparison in S2 Fig. Four classes of SNP annotation are represented in the model, each with multiple levels: distance from gene, MAF, chromatin state in GM12878 LCLs (12), and evidence of eQTL association based on meta-analysis FDR. The base levels for each annotation are “0 kb (within gene)” [Distance from Gene], “>10%” [MAF], “Heterochromatin (13)” [ChromHMM], and “>50%” [FDR].
