Extended Data Fig. 8. Mapping variants associated with Late-Spike haplotype.

(a) r² between Late-Spike haplotype dosage and SNPs within 1Mb of HLA-DQB1 in Estonian cohort. Orange vertical lines indicate location of HLA-DQB1. Dots that are colored pink are intragenic SNPs in HLA-DQB1, HLA-DRB1, and HLA-DQA1. Right plot is zoomed in on HLA-DQB1 region to show top SNPs (reference genome hg19). (b) HLA-DQB1 gene expression levels (log2(FPKM+1)) at 72 hours after stimulation for individuals separated by their rs71542466 genotype. (c) Same as in (a) but in European MESA cohort (reference genome GRCh38). (d) r² comparison between Estonian and European MESA cohort, for all SNPs in the region (left) or the subset of SNPs in the regions that do not overlap HLA-DQB1, HLA-DRB1 or HLA-DQA1 start-end genomic coordinates (right). The 6 intergenic SNPs with top r² in Estonians are highlighted, with 3 of them having top r² in the European MESA cohort too. Identity line marked. These results show that our top candidate SNP rs71542466 (and the other candidate SNPs) tracks well with the Late-Spike haplotype in both the Estonian and the MESA cohort of individuals of European ancestry recruited in the United States.