The identification of genetic variants affecting gene expression, namely 
expression quantitative trait loci (eQTLs), has contributed to the understanding 
of mechanisms underlying human traits and diseases. The majority of these 
variants map in non-coding regulatory regions of the genome and their 
identification remains challenging. Here, we use natural genetic variation and 
CAGE transcriptomes from 154 EBV-transformed lymphoblastoid cell lines, derived 
from unrelated individuals, to map 5376 and 110 regulatory variants associated 
with promoter usage (puQTLs) and enhancer activity (eaQTLs), respectively. We 
characterize five categories of genes associated with puQTLs, distinguishing 
single from multi-promoter genes. Among multi-promoter genes, we find puQTL 
effects either specific to a single promoter or to multiple promoters with 
variable effect orientations. Regulatory variants associated with opposite 
effects on different mRNA isoforms suggest compensatory mechanisms occurring 
between alternative promoters. Our analyses identify differential promoter usage 
and modulation of enhancer activity as molecular mechanisms underlying eQTLs 
related to regulatory elements.