To estimate the proportion of the genetic variance that is due to cis-effects we performed quantitative linkage analysis for the subset of transcripts that have h2>0.1 and associated with a common cis-SNP at 1% FDR. IBD sharing between every pair of DZ twins was calculated by phasing all the SNPs in every cis region (~2Mb) using MERLIN 1.1.2 40 and then counting haplotypes identical in both twins (IBD=0 corresponding to both haplotypes different, IBD=1 one identical or IBD=2 both identical). IBD sharing in cis for all the probes tested for linkage were calculated.
