Mapping cis-acting expression quantitative trait loci (cis-eQTL) has become a popular approach for characterizing proximal genetic regulatory variants. In this paper, we describe and characterize log allelic fold change (aFC), the magnitude of expression change associated with a given genetic variant, as a biologically interpretable unit for quantifying the effect size of cis-eQTLs and a mathematically convenient approach for systematic modeling of cis-regulation. This measure is mathematically independent from expression level and allele frequency, additive, applicable to multiallelic variants, and generalizable to multiple independent variants. We provide efficient tools and guidelines for estimating aFC from both eQTL and allelic expression data sets and apply it to Genotype Tissue Expression (GTEx) data. We show that aFC estimates independently derived from eQTL and allelic expression data are highly consistent, and identify technical and biological correlates of eQTL effect size. We generalize aFC to analyze genes with two eQTLs in GTEx and show that in nearly all cases the two eQTLs act independently in regulating gene expression. In summary, aFC is a solid measure of cis-regulatory effect size that allows quantitative interpretation of cellular regulatory events from population data, and it is a valuable approach for investigating novel aspects of eQTL data sets.

绘制顺式作用表达数量性状位点（ cis -eQTL）已成为表征近端遗传调控变异的流行方法。在本文中，我们描述和表征了对数等位基因折叠变化（aFC），即与给定遗传变异相关的表达变化的幅度，作为量化顺式-eQTL效应大小的生物学可解释单位以及系统建模的数学上方便的方法顺式调节。该测量在数学上独立于表达水平和等位基因频率，可累加，适用于多等位基因变体，并且可推广到多个独立变体。我们提供有效的工具和指南，用于根据 eQTL 和等位基因表达数据集估算 aFC，并将其应用于基因型组织表达 (GTEx) 数据。我们表明，从 eQTL 和等位基因表达数据独立得出的 aFC 估计值高度一致，并确定了 eQTL 效应大小的技术和生物学相关性。我们将 aFC 推广到 GTEx 中分析具有两个 eQTL 的基因，并表明几乎在所有情况下这两个 eQTL 都独立地调节基因表达。总之，aFC 是顺式调节效应大小的可靠衡量标准，允许从群体数据中定量解释细胞调节事件，并且它是研究 eQTL 数据集新方面的有价值的方法。