Supplementary Figure 8: Proportion of SNPs creating a cis regulatory effect. | Nature Genetics

Supplementary Figure 8: Proportion of SNPs creating a cis regulatory effect.

From: Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

Supplementary Figure 8

Estimation of the proportion of SNPs creating cis regulatory effects. As shown at the top of this figure, WSB/EiJ is of M. m. domesticus origin and CAST/EiJ is of M. m. castaneous origin for 91% of the genome. For such regions, we found 5,045 genes with a cis eQTL between WSB/EiJ and CAST/EiJ out of a total of 10,011 possible genes (50%), defined as having at least one strain-informative expressed SNP. These 10,011 genes are known to possess a total of 6,167,501 SNPs between WSB/EiJ and CAST/EiJ, considering the entire gene body with 10 kb upstream and downstream. Because each cis eQTL must result from at least one regulatory variant, we can estimate the minimum proportion of SNPs creating a cis regulatory effect as 0.082% of all new variants (5,045 cis eQTLs/6,167,501 SNPs). The same logic follows for every other cross and genomic regions with different phylogenies. Overall, the mean percentage of SNPs creating a cis eQTL is 0.10% (±0.02%, 95% confidence interval).

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