11.7 Splicing QTLs

In addition to variants that impact gene expression, there are splicing quantitative trait loci (sQTLs) that alter how a gene is spliced. Some sQTL mechanisms include:

  • Create or destroying a splicing donor/acceptor site
  • Changing the binding site for a protein that regulates splicing
  • Altering a splicing factor protein itself
Fig. 7. sQTLs may alter splice donor/acceptor sites, or binding sites for transcription factors that regulate splicing.
Fig. 7. sQTLs may alter splice donor/acceptor sites, or binding sites for transcription factors that regulate splicing.
sQTLs in GTEx

The GTEx Portal also provides a list of sQTLs for each gene. Note that the violin plots for these QTLs refer to a specific intron of DNMT3A whose inclusion rate is affected by each SNP.

Fig. 8. The A allele at the chr2_25530386_G_A_b38 SNP reduces excision of the chr2:25246776:25247051:clu_42604 intron of DNMT3A.
Fig. 8. The A allele at the chr2_25530386_G_A_b38 SNP reduces excision of the chr2:25246776:25247051:clu_42604 intron of DNMT3A.
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