Fig. 4
Gene mapping and annotation analysis of rs11130424. A The regional plot for rs11130424. –log10 P-values are shown along the left y-axis, and the right y-axis corresponds to recombination rate, plotted as a blue line. The x-axis indicates chromosomal position. The variants are colored according to their correlation (r2) with the lead variant (see legend). B Linkage disequilibrium (LD) analysis spanning the physical position from 54.554 to 54.604 Mb of chromosome 3. The color key indicates the level of LD (r2) between variants in 1000 Genomes Project East Asian populations. C The association between different genotypes at rs11130424 and methylation levels at the significant CpG probe cg04394267. The level of methylation at the CpG probe is shown as the β-value. The box plots show the distribution of the methylation levels in each genotype category with error bars representing the 25% and 75% quantiles. D 3D chromatin interaction and eQTL analysis of rs11130424. Circos plot showing genes on chromosome 3 interacted with rs11130424 by 3D chromatin interaction. The most outer layer showed the –log10(P values) of chromosome 3 in the GWAS analysis. Only SNPs with P < 0.05 are displayed. Links colored orange are chromatin interactions