We set out to develop an improved understanding of the impact and interpretability of rare noncoding variants. Our approach involved combining high-quality genomes and transcriptomes within a single large family to identify cis-eQTLs and compare these to cis-eQTLs discovered in a large population sample. Through the use of RNA-seq data, we were also able to conduct comparable analyses for alternative splicing and ASE. Our analyses focused on the enrichment of rare and potentially regulatory variants in large-effect eQTLs and sQTLs in the family, and we sought to identify the properties of genes that exhibit such effects. Furthermore, we investigated the degree to which family transcriptome data enable the detection of noncoding annotation relevant to interpreting rare noncoding variants genome-wide.