Overall when taking all transcripts into account, we found that common cis-SNPs (MAF >5%) explain on average only 9% (adipose), 12% (LCL), and 10% (skin) of the total genetic variance at each locus (Fig.2). Less than a third (27% (adipose), 33% (LCL) and 21% (skin)) of the transcripts are in fact associated with a cis-variant at 1% FDR so when focusing on these transcripts only and taking independent cis-effects into account, the cis-component accounts for a greater proportion of the genetic variance, namely on average 25% (adipose), 31% (LCL) and 32% (skin). Notably, the effect of common cis-variants increases as heritability increases. If we filter to transcripts that are highly heritable in all tissues (h2>0.6 across all tissues, N=24), ~95% of these transcripts are associated with a cis variant and at 18 of the 24, a single cis-SNP explains over 50% of the genetic variance (Supplementary Table 5).
