We next sought to gain insights into whether loci harbor multiple independent variants. While FUMA25 annotations reported independent lead SNPs within risk loci based on pair-wise LD (Supplementary Table 8), COJO26 analysis of each locus conditional on the leading variants suggested that only one locus carried a conditionally independent GWS SNP (rs3132388 on chromosome 6, P = 2.86 × 10−9). This locus however, is in the MHC region, whose complicated linkage disequilibrium (LD) structure27 may not be accurately captured by reference panels.
