Table 1.
Promoter capture Hi‐C target genes for the 23 SSc‐associated regions in CD4+ T cells and CD14+ monocytes*
| Chr | Base position (start–end)† | GWAS locus‡ | Promoter capture Hi‐C target genes§ | CD4+ versus CD14+ | ||
|---|---|---|---|---|---|---|
| CD4+ T cells | CD14+ monocytes | Differential interactions | Differential expression | |||
| 1 | 67326053–67448804 | rs3790566 (IL12RB2) | – | – | – | – |
| 1 | 167445635–167465040 | rs2056626 (CD247) | CD247, CREG1 | – | CD247, CREG1 | CD247, CREG1 |
| 1 | 173337507–173391947 | rs1857066 (TNFSF4‐LOC100506023‐PRDX6) | – | – | – | – |
| 2 | 190642047–190698201 | rs16832798 (NAB1) | MFSD6, NEMP2 | MFSD6, NEMP2, HIBCH;INPP1 | MFSD6, NEMP2, HIBCH;INPP1 | MFSD6, NEMP2, HIBCH, INPP1 |
| 2 | 191035723–191108308 | rs3821236 (STAT4) | STAT4, NABP1 | – | STAT4, NABP1 | STAT4, NABP1 |
| 3 | 58084620–58482701 | rs4076852 (FLNB‐DNASE1L3‐PXK) | RPP14, KCTD6 | RPP14, KCTD6 | RPP14, KCTD6 | KCTD6 |
|
3 |
119384733–119546340 |
rs9884090 (POGLUT1‐TIMMDC1‐CD80‐ARHGAP31) | TMEM39A;POGLUT1 | – | TMEM39A;POGLUT1 | TMEM39A, POGLUT1 |
| 3 | 160002484–160030580 | rs589446 (IL12A) | – | SMC4;IFT80 | SMC4;IFT80 | SMC4, IFT80 |
| 4 | 960523–990021 | rs11724804 (DGKQ) | GAK;TMEM175, FGFRL1 | GAK;TMEM175, FGFRL1 | FGFRL1 | GAK, TMEM175, FGFRL1 |
| 4 | 102477892–102615256 | rs230534 (NFKB1) | SLC39A8, NFKB1, UBE2D3;CISD2, SLC9B1, BDH2 | SLC39A8, UBE2D3;CISD2, BDH2 | SLC39A8, NFKB1, UBE2D3;CISD2, SLC9B1, BDH2 |
SLC39A8, UBE2D3, CISD2, BDH2 |
| 5 | 151064651–151080486 | rs3792783 (TNIP1) | – | – | – | – |
| 6 | 106181815–106339294 | rs633724 (ATG5) | – | – | – | – |
| 7 | 128933913–129095960 | rs36073657 (IRF5‐TNPO3) | – | – | – | – |
| 8 | 11474517–11544554 | rs2736340 (FAM167A‐BLK) | – | – | – | – |
| 8 | 60638547–60664239 | rs685985 (RAB2A‐CHD7) | ASPH, SDCBP, CHD7 | – | ASPH, SDCBP | ASPH, SDCBP, CHD7 |
| 11 | 554659–619789 | rs6598008 (CDHR5‐IRF7) | – | – | – | – |
| 11 | 2311894–2363262 | rs2651804 (TSPAN32,CD81‐AS1) | TSSC4 | – | TSSC4 | TSSC4 |
| 11 | 118704617–118875175 | rs11217020 (DDX6) | CXCR5, UPK2, DDX6, IFT46;ARCN1 | CXCR5 | CXCR5, UPK2, DDX6 | CXCR5, DDX6, ARCN1 |
| 15 | 74739180–75148328 | rs1378942 (CSK) | CSK, CLK3, ULK3,SCAMP2, MPI, FAM219B, COX5A | CSK, CLK3, ULK3, SCAMP2, MPI, FAM219B, COX5A, C15orf39 | CSK, ULK3, SCAMP2, MPI, FAM219B, COX5A, C15orf39 | CSK, CLK3, ULK3, SCAMP2, MPI, FAM219B, COX5A, C15orf39 |
| 16 | 85932852–85979945 | rs11117420 (IRF8) | – | IRF8 | IRF8 | IRF8 |
| 17 | 39747478–39933464 | rs883770 (IKZF3‐GSDMB) | IKZF3, ERBB2, PSMD3 | ERBB2 | IKZF3, ERBB2, PSMD3 | IKZF3, ERBB2, PSMD3 |
| 17 | 75193533–75279345 | rs1005714 (NUP85‐GRB2) | – | – | – | – |
| 19 | 18068862–18093031 | rs2305743 (IL12RB1) | PIK3R2, RAB3A | RAB3A | PIK3R2, RAB3A | – |
*
Genes classically associated with systemic sclerosis (SSc) through proximity to genome‐wide association study (GWAS) loci are set in bold. Chr = chromosome.
†
Base position in GRCh38 (hg 38) assembly.
‡
Locus as defined by López‐Isac et al (ref. 9).
§
Genes corresponding with promoter interacting regions overlapping enhancer regions and SSc‐associated GWAS single‐nucleotide polymorphisms.