UCK2(A) and GINM1(B) have the lowest permutation pvalues among the 46 leading genes in Table 1. Each image consists of a top and bottom image. The top image shows all genes located at the risk locus according to the genomic position (hg19). Based on the joint modeling, genes are labeled as leading in dark blue (joint-conditionally independent), conditional on leading genes(s) in light blue, or correlated with leading genes in green (predicted expressionR2> 0.9); marginally associated genes (pTWAS≥ 0.01 or ppermutation≥ 0.05) and genes not tested (e.g., due to lack of a significant prediction model) are indicated with empty boxes with dark and light outlines, respectively. The bottom image shows results from the SNP-level GWAS-conditional analysis. Each point illustrates the association between a single SNP at the locus and TGCT status: gray points indicate the marginal association of a SNP with TGCT status (GWAS association) and green points indicate the association of the same SNP with TGCTs after conditioning of predicted expression of the leading gene at each locus (here,UCK2andGINM1). The horizontal dashed line indicates the genome-wide significance threshold (p= 5 x 10−8).
