Basenji gene-specific variant scores illuminate a multiple sclerosis–associated locus. Lead variant rs74796499 is associated with multiple sclerosis (International Multiple Sclerosis Genetics Consortium 2013). Among the credible set of linked variants, Basenji predicts that rs78461372 would alter transcription of the nearby genes GPR65 and GALC. In immune cells, such as treated CD14+ cells depicted here, both genes are transcribed and the C>G introduces an ETS factor motif that enhances transcription. In contrast, in other cell types, e.g., in the insular cortex, where GPR65 is far less transcribed, Basenji predicts the same motifs play a role in repressing the gene.
