We next identified SNPs associated with changes in the relative abundances of specific cell types. We refer to such relationships with the term fQTLs. In total, we identified 1672 distinct SNPs constituting 4199 fQTLs (fig. S34). The excitatory neurons Ex4 and Ex5 were associated with the most fQTLs (1060 and 896, respectively). The biological mechanism governing an fQTL may involve other QTL types, such as eQTLs. An illustrative example is the FZD9 gene (Fig. 4D): We found that the expression levels of this gene were associated with a neighboring noncoding SNP via an eQTL, and this same SNP was associated with the proportion of Ex3 cells via an fQTL. Perhaps connected to this, deletion variants upstream of FZD9 had previously been associated with cell fraction changes related to Williams syndrome (40).
