Fig. 2
Conditional analysis to prioritize XFS associated genes: a) Manhattan plot for PrediXcan analysis of European ancestry individuals in tissues with predicted gene expression for a) LOXL1 and b) conditioned on LOXL1 predicted gene expressions c) Manhattan plot for PrediXcan analysis of European ancestry individuals in tissues with predicted gene expression for STOML1 and d) conditioned on STOML1 predicted gene expressions e) correlation in gene expression in for genes in chr15q22–25 in lung tissue for i) reference GTEx data f) predicted gene expression in BioVU cohort. In each case on the X axis is plot of variant/gene associations along the chromosomes, while Y axis represent the significance levels for the associations. The legend for PrediXcan analysis on the GTEx tissues, a color for each tissue, is on the right. For both plots the blue dotted line is the “suggestive” genome-wide significant threshold (p < 1e-4), while the red line is the genome-wide significant threshold. On the lower plot, the gene labels are for genes reported/mapped to genome-wide significant signals in GWAS result, while in the upper plot is for genes that are associated at genome-wide significant threshold. For genes associated with XFS at genome-wide threshold in more than one tissues, only the tissue with lowest p-value is labeled. g linkage disequilibrium between variants in prediction models for LOXL1 and other chr15q22–25 genes associated with XFS in lung tissue based on pairwise r2 and D′ parameters. Relative genome location for variants in each gene models are roughly demarcated by diagonal lines next to gene symbols. Proximate location for the variant shared between LOXL1 and STOML1, rs12102019 is labelled