Table 1

Overview of the results of the different loop algorithms used in this study to identify chromatin loops

Loop algorithmLoopsCTCF FwdCTCF RevEP loopsAPAESNP
SIP32 5200.760.7546054247355610
FanC23 8440.960.967713702412 08410
Mustache35 8060.770.774587449238366
HiCExplorer22 3080.790.804590412633757
  • Results of the loop algorithms used in this study. Loops is the total number of loops identified. CTCF Fwd and CTCF Rev is the ratio of loop anchors with CTCF binding motifs as derived from the JASPAR 2022 database.28 EP loops is the number of enhancer-promoter loops with active enhancers and promoters as identified by overlap with public ATAC-seq11 and ChIP-seq12 peaks (H3K4me1, H3K4me3, H3K27ac). SNP is the number of active enhancers with a SNP from the osteoarthritis-related variants from the 95% credible sets, with a posterior probability of causality >3% from Boer et al3 residing within the active enhancer region.

  • AE, active enhancers; AP, active promoters; SNP, single-nucleotide polymorphism.