Table 1.
Lead significant genetic variants by genomic region, credible sets of non-HLA signals, and potential mapped genes proposed by gene prioritisation
| Base pair (hg38) | rs identification | Nearest gene | Effect allele | p value | OR (95% CI) | Number of SNPs in LD block | Number of SNPs in credible set (ΣPP >0·95) | Credible set of SNPs | Candidate genes | |
|---|---|---|---|---|---|---|---|---|---|---|
| 6p21.32 | 32652425 | rs41269974 | HLA-DQA1* | A | 1·60 × 10−87 | 2·03 (1·90–2·17) | .. | .. | .. | .. |
| 6q26 | 160722158 | rs4252114 | PLG | C | 1·38 × 10−13 | 1·25 (1·18–1·32) | 347 | 3 | rs4252114, rs1897108, rs1321197 | PLG |
| 8p21.1 | 27755870 | rs11782624 | CCDC25 | T | 1·28 × 10−8 | 1·18 (1·12–1·25) | 81 | 1 | rs9644049 | CCDC25, CLU, ELP3, ESCO2, LEPROTL1, PBK, SCARA3, SCARA5, TMEM66 |
| 15q26.1 | 88906856 | rs8029053 | MFGE8 | T | 4·96 × 10−8 | 1·19 (1·12–1·26) | 20 | 1 | rs11073821 | ACAN, HAPLN3, MFGE8 |
| 17q11.2 | 28367840 | rs704 | VTN | A | 2·75 × 10−9 | 0·84 (0·79–0·89) | 55 | 13 | rs704, rs3093680, rs1007398, rs4795435, rs1128162, rs1128161, rs2227736, rs2227735, rs10853128, rs2239908, rs6505077, rs8081240, rs8079943 | FOXN1, IFT20, LGALS9, NUFIP2, POLDIP2, SARM1, SEBOX, SLC13A2, SLC46A1, TMEM199, TMEM97, TNFAIP1, VTN |
Independent genetic variants that reached genome-wide significance in the meta-analysis are shown. OR=odds ratio. SNP=single nucleotide polymorphism. LD=linkage disequilibrium. ΣPP=sum of posterior probability.
*
Fine mapping of the HLA region was extended (see table 2).