Fig. 1: Overview of synovium eQTLs.

a Overview of the study design. eQTL, expression quantitative trait loci; PRE, potential regulatory element; eQTac, expression quantitative trait accessible chromatin. b Distribution of all lead SNPs and significant (FDR < 0.05) lead eSNPs relative to the target genes body. The position of upstream SNPs was relative to target gene TSS, the position of downstream SNPs was relative to target gene TES, and the position of SNPs located on the target gene was (distance to TSS) / (target gene length). Pie plot showed functional annotation for all lead eSNPs by ANNOVAR. c The lead SNPs effect sizes in different distances to target gene TSS. Distances to TSS were split into ten intervals according to the quantiles, larger quantile number indicates larger distance values. N = 4765 significant lead eQTLs. d The target gene expression coefficient of variations (CVs) in different lead SNP effect sizes. Lead SNP effect sizes were split into ten intervals according to the quantiles, larger quantile number indicates larger effect size values. Gene expression values were used as covariates for CVs. N = 4765 significant lead eQTLs. The boxplots in (c) and (d) represent 25th, 50th, and 75th percentiles, and whiskers extend to 1.5 times the interquartile range. Orange rhombuses represent the mean of each box. The fitting line to the median values is shown in blue. e The three-dimensional bar graph showed the target gene expression CVs in different lead SNPs effect sizes and different distances to target gene TSS, larger quantile number indicates larger distance/effect size values. The widths of the bar represent the count of genes in this interval. Gene expression values were used as covariates for CVs. f The tolerance to loss-of-function mutations of eGene and non-eGene in different expression levels. The tolerance was denoted by 1-pLI, in which pLI represent the probability of being loss-of-function (LoF) intolerant. The red line and blue line represent the median of each box. Panel a was partly generated using Servier Medical Art, provided by Servier, licensed under a Creative Commons Attribution 3.0 Unported License.