biostudies-literatureJiang FNational Natural Science Foundation of China (National Science Foundation of China)1409https://www.ebi.ac.uk/biostudies/studies/S-EPMC10869817biostudies-literatureUnknown15(1)The synovium is an important component of any synovial joint and is the major target tissue of inflammatory arthritis. However, the multi-omics landscape of synovium required for functional inference is absent from large-scale resources. Here we integrate genomics with transcriptomics and chromatin accessibility features of human synovium in up to 245 arthritic patients, to characterize the landscape of genetic regulation on gene expression and the regulatory mechanisms mediating arthritic diseases predisposition. We identify 4765 independent primary and 616 secondary cis-expression quantitative trait loci (cis-eQTLs) in the synovium and find that the eQTLs with multiple independent signals have stronger effects and heritability than single independent eQTLs. Integration of genome-wide assNature communicationsA landscape of gene expression regulation for synovium in arthritis.PMC10869817821708963217061632370653Zhu DLJiang FGuo YYang NWang CGao HWZhang DJWu HYang ZDong SSHu SYTian WYang TLChen XFWang NNSong HMHe CYfalseA landscape of gene expression regulation for synovium in arthritis.The synovium is an important component of any synovial joint and is the major target tissue of inflammatory arthritis. However, the multi-omics landscape of synovium required for functional inference is absent from large-scale resources. Here we integrate genomics with transcriptomics and chromatin accessibility features of human synovium in up to 245 arthritic patients, to characterize the landscape of genetic regulation on gene expression and the regulatory mechanisms mediating arthritic diseases predisposition. We identify 4765 independent primary and 616 secondary cis-expression quantitative trait loci (cis-eQTLs) in the synovium and find that the eQTLs with multiple independent signals have stronger effects and heritability than single independent eQTLs. Integration of genome-wide ass2024-01-01T00:00:00Z2024 Feb2026-07-15T02:16:43.386Z2025-04-05T09:07:50.05ZS-EPMC108698173836085010.1038/s41467-024-45652-x