Enrichment of TEVs within merge QTL regions and functional impact of CTCF-binding TEVs. (a) The density of TEVs within genomic intervals associated with refined ('Merge') QTLs or adjacent sequence lying within nonrefined QTLs relative to all genomic regions was tested using a genome-wide association test. SINE TEVs show a 13.9% enrichment in regions associated with refined merge QTLs over the level expected given interval size and GC composition. Both LINE and SINE TEVs show greater densities within merge QTL regions compared to surrounding non-merge QTL sequence. With the exception of ERV TEVs in merge QTL regions, all associations were statistically significant (***P < 10-3). (b) Variation in expression between genes associated with a CTCF-binding TEV. The natural log of the ratio of expression between the upstream and downstream genes (whose order was randomly assigned) was taken as a measure of the variance in expression. The presence of the CTCF binding TEV was associated with a greater degree of expression variation between flanking genes (ANOVA P < 0.001). N/s, not significant.