Fig. 7

Chromatin loops connect SNPs to the genes causing phenotypic changes and spatially distinct chromatin connectivity networks defined by flowering-time control genes. a Pie chart for the proportion of trait-associated significant SNPs involved in active-, repressive- and inactive-mark associated chromatin loops and not involved in chromatin interactions. b, c Mapping browser screenshot showing the H3K4me1-associated chromatin interactions, ChIP-seq, ATAC-seq, and RNA-seq profiles, and SNPs at MED12 and FRIGIDA loci (b) and H3K27me3-associated chromatin interactions, ChIP-seq, ATAC-seq, and RNA-seq profiles, and SNPs at FT locus (c). Light green boxes indicate the SNP-associated anchor peaks and flowering-time control gene loci. d Flowering-time control gene-associated chromatin connectivity network during floral induction. The connectivity was built through one hop of all interactions mediated from 190 genes. Large circles represent the key flowering-time control genes. Small circles with gene symbol represent the node genes implicated in flowering-time control. Small circles without gene symbol represent the connecting genes. Colors represent their 3D network specificities. e Co-expression analysis of genes in floral transition-associated subnetworks. The PCC of subnetworks were calculated. Random, randomly selected gene pairs with the same physical distance. Total, all representative chromatin mark-associated anchor gene pairs. **p < 0.01, *p < 0.05 from Wilcoxon test. NS, no significant difference