We next sought to identify eQTL hotspots (SNPs influencing numerous transcripts). We grouped the 304 distant eQTL SNPs into 203 regional clusters (Supplementary Figure 10). 160 clusters included only one SNP and the other 43 clusters spanned 2 kb to 2 Mb (median size 89 kb). Eleven clusters associated with ≥6 genes were considered potential hotspots, showing agreement with analogous results from NESDA. For each of the 304 SNPs, we estimated the proportion of associated transcripts, using NESDA data to avoid selection bias. These values were < 0.008 for a wide range of NTR eQTL strengths (Figure 5c), many times lower than reported for three tissues in the MuTHER study.8 We conclude that eQTL hotspots and significant distant eQTLs influence relatively few genes in peripheral blood.
