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Table 5 Alterations in TAD structure after TNF stimulation and genes in stimulation-specific TADs

From: Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability

Locus Chr TAD_diff Type of difference Enriched_in Expressed in FLS Differential expressed in FLS (p adj < 0.05)
9 chr1 Differential Strength Change Basal RC3H1; RABGAP1L; PRDX6; KLHL20; GAS5-AS1; GAS5; ZBTB37 GAS5; PRDX6; ZBTB37; RABGAP1L; RC3H1
10 chr2 Differential Complex Basal LBH; LCLAT1; YPEL5 LBH; LCLAT1
13 chr2 Differential Merge Stim NPAS2 NPAS2
19 chr3 Differential Strength Change Basal CMC1; SLC4A7; AZI2 CMC1
20 chr3 Differential Split Basal SLMAP; FLNB; FLNB-AS1; PXK; PDHB PXK; FLNB
21 chr3 Differential Strength Change Basal PCCB; PPP2R3A; MSL2; STAG1 PCCB
22 chr4 Differential Strength Change Basal WDR1; ZNF518B  
27 chr6 Differential Strength Change Basal SRPK1; MAPK14; PI16; LHFPL5; BRPF3; KCTD20; STK38; SRSF3; PANDAR; CDKN1A; C6orf89; MTCH1 SRPK1; C6orf89; STK38; MTCH1; KCTD20; BRPF3; CDKN1A; SRSF3
28 chr6 Differential Strength Change Stim RSPH9; VEGFA; CDC5L; TMEM63B; HSP90AB1; SLC35B2 TMEM63B; CDC5L
29 chr6 Differential Strength Change Stim IFNGR1; WAKMAR2; TNFAIP3 TNFAIP3; IFNGR1
30 chr6 Differential Strength Change Stim IFNGR1; WAKMAR2; TNFAIP3 TNFAIP3; IFNGR1
32 chr6 Differential Strength Change Basal RPS6KA2; AFDN  
33 chr7 Differential Strength Change Stim CREB5; TAX1BP1; JAZF1 JAZF1; TAX1BP1
47 chr11 Differential Strength Change Basal TRIM44; FJX1; COMMD9 COMMD9
48 chr11 Differential Strength Change Basal FADS2; SLC15A3; TKFC; INCENP; AHNAK; INTS5; CCDC86; PRPF19; TMEM109; TMEM132A; VPS37C; DDB1; CYB561A3; TMEM138; CPSF7; MYRF; FEN1; FADS1; FADS3; RAB3IL1; BEST1; FTH1; EEF1G; TUT1; MTA2; EML3; ROM1; GANAB; LBHD1; CSKMT; UQCC3; UBXN1; LRRN4CL; HNRNPUL2-BSCL2; HNRNPUL2; TMEM179B; TMEM223; NXF1; STX5; RNU2-2P; SLC3A2 TMEM132A; FTH1; SLC15A3; FADS1; AHNAK; VPS37C; INCENP; RAB3IL1; LRRN4CL; EEF1G; TMEM138; ROM1; TUT1; DDB1; FADS2; CCDC86; MTA2; TMEM109
49 chr11 Differential Strength Change Basal ACAT1; ATM; CUL5; NPAT; POGLUT3 ATM; ACAT1; NPAT; CUL5
57 chr14 Differential Strength Change Basal ZFYVE26; ZFP36L1  
65 chr18 Differential Split Basal SPIRE1; SEH1L; CEP192; AFG3L2; CEP76 CEP76; CEP192; SPIRE1; SEH1L
72 chr22 Differential Strength Change Basal MAPK1; UBE2L3; PPIL2; YPEL1; PPM1F MAPK1; UBE2L3
73 chr22 Differential Strength Change Basal JOSD1; GTPBP1; SUN2; CBX6; APOBEC3C; CBX7; RPL3; MIEF1; ATF4; RPS19BP1 GTPBP1; RPL3; SUN2; ATF4; CBX6