To determine the potential impact of non-coding SNPs on Per3 transcription, we predicted impact scores for these SNPs based on overlap with conserved functional elements. There are 159 SNPs and 18 indels (Supplementary Table S3) within 5 kb upstream or downstream of the transcription start site of Per3. Although the majority of these sequence variants have low-impact scores, two SNPs—rs32260283 and rs32042445—and an indel at 150.418813 Mb are all within 1 kb of the Per3 transcription start site and are located in conserved regulatory elements (Open Regulatory Annotation Database ID: OREG0048389 and OREG0033366). We searched the TRANSFAC database for DNA motifs in the upstream region of Per3 that may be disrupted by these variants.37 We found that an indel (-/T) disrupts a putative stress response core element (STRE: CCCCT/AGGGG) in BXD strains that inherit the B allele. This site is a potential candidate for the cis-QTL underlying the expression difference and the massive cis-eQTL associated with Per3.
