Table 3.
Prioritised causal genes for the pleiotropic loci based on functional annotation by FUMA
| Region | Gene | Lead SNP | Nominated genes by proximity | Nominated genes by eQTL | Nominated genes by sQTL | Nominated genes by CI | Nominated genes by eQTL+CI | Nominated genes by eQTL+promoter |
| 1p31.3 | IL23R/IL12RB2 | rs11209039 | IL12RB2 | IL23R, MIER1, SLC35D1 | C1orf141 | |||
| 1q32.1 | IL10 | rs3024490 | IL10 | IL10, IL19, IL24, FAIM3 | IL19, FCMR, PIGR, FCAMR, C1orf116, YOD1, PFKB2, CR1, CR2, MAPKAPK2 | IL19 | YOD1, PFKB2, CR1, CR2, MAPKAPK2 | |
| 2q13 | BCL2L11 | rs72836352 | ACOXL, BCL2L11 | BCL11A, BCL2L11, C3AR1, CPVL, CSFR1, FAM46A, LARGE, MS4A14, MS4A7, MTSS1, PEA15, TNFRSF8 | ACOXL | BCL2L11 | ||
| 2q33.2 | CTLA4 | rs62184865 | CTLA4 | CTLA4 | ||||
| 3p21.31 | CCR3 | rs2087726 | CCR1, CCR3 | ABCB1, AGAP1, AUTS2, CAMTA1, CCR1, CCR2, CCR3, CCR5, CCR9, CCRL2, CFH, COLQ, CXCR6, CYP2E1, CYTH3, DPP4, ELOVL4, FYCO1, GZMK, IL7R, KDSR, KLRB1, LTK, LZTFL1, NCALD, RORA, RORC, SACM1L, SLAMF1, SMAD3, SYTL2, TDGF1, XCR1 | LZTFL1, FYCO1, CCR3 | CCR1, CCR2, CCR5, CCR9, CCRL2, CXCR6, FYCO1, LZTFL1, SACM1L, XCR1 | CCR1, CCR2, CCR5, CCR9, CCRL2, CXCR6, FYCO1, LZTFL1, SACM1L, XCR1 | |
| 4p16.2 | CPLX1 | rs4690319 | CPLX1 | CPLX1, CRIPAK, DGKQ, GAK, IDUA, MFSD7, MYL5, PCGF3, TMEM175, UVSSA | ||||
| 5q22.1 | TSLP | rs1837253 | TSLP | |||||
| 5q31.1 | P4HA2 | rs128738 | C5orf56, CSF2, IL3, P4HA2 | ACSL6, C5orf56, CDC42SE2, FNIP1, HINT1, LYRM7, P4HA2, RAD50, RAPGEF6, SLC224A, SLC22A5 | P4HA2, CDC42SE2, HINT | C5orf56, PDLIM4, RAD50, RAPGEF6, SLC22A5 | C5orf56, RAD50, RAPGEF6, SLC22A5 | |
| 5q31.1 | IRF1 | rs6894249 | C5orf56, IRF1, P4HA2 | ACSL6, AFF4, ALDH1A1, APBA2, C1QA, C1QB, C5orf56, CACNA2D3, CTSL, CYP2S1, CYP4F22, DDX58, EPB41L3, FAM26E, IL15, IL5, IRF1, KCNMA1, LAP3, LGALS3BP, MYOF, P4HA2, PDE7B, RAD50, SLC22A4, SLC22A5, STAT1, TCN2, TRANK1, TSPAN2, VAMP5, WARS | P4HA2, RAD50, IRF1, SLC22A4 | AFF4, C5orf56, CCNI2, GDF9, HSPA4, IL13, IL4, IL5, IRF1, KIF3A, LEAP2, PDL1M4, RAD50, SEPT8, SHROOM1, SLC22A5, SOWAHA, UQCRO, ZCCHC10 | AFF4, C5orf56, IL5, IRF1, RAD50, SLC22A5 | IL5, IRF1 |
| 5q33.3 | IL12B | rs7725339 | IL12B | NSMCE1, RNF145 | RNF145, UBLCP1 | RNF145 | ||
| 5q33.3 | IL12B | rs60689680 | RNF145 | ADRA1B, C5orf54, RNF145, TTC1, UBLCP1 | RNF145 | |||
| 6q26 | PLG | rs4252120 | PLG | AGPAT4, MAP3K4, PLG | ||||
| 6q23.3 | IFNGR1 | rs4896243 | IFNGR1, IL22RA2 | IFNGR1 | IFNGR1, TNFAIP3, IL20RA | IFNGR1 | IFNGR1 | |
| 8p21.2 | PTK2B | rs73223431 | PTK2B | CHRNA2, CTNNA1, EPHX2, PTK2B, TRIM35 | PTK2B | CLU, PTK2B, TRIM35 | PTK2B, TRIM35 | PTK2B, TRIM35 |
| 10q21.2 | ZNF365/ADO | rs10995248 | ZNF365 | ADO, EGR2, RTKN2 | ADO, ARID5B, EGR2, JMJD1C, NRBF2 | ADO, EGR2 | ||
| 21q22.2 | chr21q22 | rs2242944 | ETS2, HMGN1, LCA5L, WRB | ETS2 | ETS2 |
Genes nominated by eQTL + promoter and also with CI are highlighted in bold
CI, chromatin interaction; eQTL, expression quantitative trait loci; sQTL, splicing quantitative trait loci.