We therefore performed quantitative linkage analysis in the cis-regions of those transcripts with h2>0.1 and associated with a common cis-SNP using a global regression approach that analyze the data of all expression traits (Nadipose=2537, NLCL=3157, Nskin=1493) in a single linear regression. We phased all SNPs in each cis-region (~2Mb) and counted the haplotypes shared identity-by-descent (IBD) for all DZ twin pairs. We then estimated the average heritability at each cis region using the global regression approach which is based on the Haseman-Elston algorithm but including all selected transcripts into account. We noted that on average 30% (adipose), 35% (LCL) and 36% (skin) of the total genetic variance is explained by variants in cis which is in fact on average 40% more than if only common cis-SNPs identified from our cis-eQTL analysis are included (Table 2). This added genetic component is likely due to low frequency / rare cis-variants and should be considered as a lower bound as our sample size limited us to conduct the analyses on a subset of the heritable transcripts.
