Skip to main content

Table 2 Top CpG sites differentially methylated in knee/hip OA compared to OA-free cartilagea

From: Genome-wide DNA methylation study of hip and knee cartilage reveals embryonic organ and skeletal system morphogenesis as major pathways involved in osteoarthritis

CpG Δβ P-value Gene symbol UCSC location group UCSC island group Enhancer
cg22669656 −0.22 0.0004 PGS1 Body   Yes
cg11905061 0.21 0.0004 AGAP1 Body S_Shore  
cg27390206 −0.21 0.0002 BLMH Body   Yes
cg09140531 −0.21 0.0004     Yes
cg14223856 −0.21 0.0005     Yes
cg13688786 −0.20 0.0003 MYO18A Body   Yes
cg22022821 −0.20 0.0002     
cg10340048 −0.20 0.0002     Yes
cg02464866 −0.20 0.0004    N_Shore Yes
cg05033952 −0.20 0.0001    N_Shore  
cg19629120 −0.19 0.0005 EFCAB6 3'UTR   
cg04973183 −0.19 0.0004     Yes
cg00150785 −0.19 0.0004    N_Shore Yes
cg12027254 −0.19 0.00004 TNRC6C Body   Yes
cg14068309 −0.19 0.0002 EIF2B1 3'UTR   
cg13556934 −0.18 0.0003    N_Shelf Yes
cg14022778 −0.18 0.0004 FHAD1 Body   
cg02017450 0.18 0.0004     Yes
cg23074762 −0.18 0.0002 CHSY1 Body   Yes
cg04228742 −0.18 0.0002     
cg22203890 −0.18 0.0005     
cg17611936 0.18 0.0003 PRKAG2 Body   
cg07107113 −0.17 0.0004 FBLIM1 5'UTR S_Shore  
cg12582728 −0.17 0.0004     Yes
cg07404223 −0.17 0.0002     Yes
cg25002179 −0.16 0.0005 STARD13 5'UTR;Body;TSS1500   Yes
cg17025149 −0.16 0.0001     Yes
cg26043955 −0.16 0.0004     Yes
cg26919145 −0.16 0.0002 LDLRAD3 Body   Yes
cg09425279 −0.16 0.0003    N_Shelf  
cg06712559 0.16 0.0004 AGRN Body Island Yes
cg02099390 −0.16 0.0002 OSBPL10 Body   Yes
cg11805414 −0.16 0.0005     Yes
cg04038680 −0.16 0.0002 SHISA9 Body   Yes
cg25341923 −0.15 0.0001 KRTAP4-7 TSS1500   
cg14728071 −0.15 0.00004 MLLT10 3'UTR   
cg03667871 −0.15 0.0004 NEK7 TSS1500 N_Shore  
cg13258453 −0.15 0.0002     Yes
cg23010507 −0.15 0.0001    S_Shelf Yes
cg12158488 −0.15 0.0002     Yes
  1. aΔβ: difference in methylation value between sample groups (OA cartilage - intact); UCSC: University of California, Santa Cruz; 5’-UTR: 5’-untranslated region; N: North; S: South; TSS 200: within 200 bp of transcription start site
\