The disease-associated variant is located in a genomic region that interacts with the immunoglobulin superfamily containing leucine-rich repeat 2 gene ISLR2 on chromatin conformation capture analysis in macrophages (Supplementary Fig. 12A) and CD8 T cells (Supplementary Fig. 12B); moreover, a variant in complete LD (rs80140040) with the meningitis susceptibility SNP shows evidence of an eQTL with ISLR2 in a number of tissues, including brain (p = 0.02). Here, ISLR2 is linked to infectious meningitis.