Cis-eQTL associated with the same expression trait were in high LD (Figure 3). Significant eSNPs within 50-kb windows were grouped into clusters based on the inferred r2 values between them. The median size of these clusters was 2; however, in some instances this number was as high as 33. Sixty-five percent of all cis-eQTL clusters contained 2 or more eSNPs (Figure 4). The total number of significant clusters was 4196 (Supplementary Table 2) and all of the associated expression traits were present in the single SNP–based results, although the reverse statement was not true. Notably, the concordance of significant expression traits between 1-mb and 50-kb window analyses increased to 92.7% after correction for high LD.
