Fig. 5: Functional and genomic characterization of Jomon-related marker SNPs.

a Stratified LD score regression analysis is conducted with major 10 cell type groups. False discovery rate (FDR) is calculated using the Benjamini-Hochberg method. A dotted vertical line represents the FDR of 0.1. b Violin plots compare the lengths of regions in strong LD with each of 132 Jomon-related SNPs (r² > 0.8) to those of 132 frequency-matched non-Jomon-related SNPs. Dots represent the mean lengths, with bars showing the standard deviations. A p-value (3.1 × 10⁻³²) is calculated by the Wilcoxon rank sum test, reflecting a two-sided test. c A locus plot highlights a Jomon-related SNP, which is shown as a purple diamond in the upper plot, that is linked with the longest haplotype among all 132 variants. A dashed line defines a statistical significance as a p-value of 5.0 × 10⁻⁸. Lower plots represent the protein-coding genes, based on GENCODE, that are present in the highlighted region. The P-value is computed by inverse variance weighted meta-analysis using METAL. All statistical tests are two-sided and unadjusted for multiple comparisons. GI Gastrointestinal, CNS Central nerve system, LD Linkage disequilibrium, SNP Single nucleotide polymorphism.