All three Per3 probe sets (1421087_at, 1460662_at and 1421086_at) are associated with a significant QTL on distal chromosome 4, close to the location of the Per3 gene itself (150.38 Mb). The maximum likelihood ratio statistic is 162 at SNP marker rs6358921 (149.929 Mb). The D allele is associated with a positive-additive effect and a 1.66-fold (20.735) increase in expression per allele (Figure 1b). This cis-eQTL for Per3 was confirmed in five other brain regions (Supplementary Figure S1). This highly significant and robust cis-QTL is strong evidence that sequence variants in or near Per3 cause differences in transcript expression levels.
