Table 3.
Genome-wide significant (p<5x10-8) LD independent loci from the VITL-VITE-MG meta-analysis.
| SNP | Locus | Nearest genes (<20kb) | P-meta | OR | SE | Top SNP VITE | P-VITE | Top SNP VITL | P-VITL | Top SNP MG | P-MG |
|---|---|---|---|---|---|---|---|---|---|---|---|
| rs9981704 | chr21:43831955-43867059 | TMPRSS3 UBASH3A | 6.09x10-19 | 1.31 | 0.03 | – | 4.30x10-4 | rs12482396 | 4.06x10-20 | – | 3.60x10-3 |
| rs60946162 | chr3:188084682-188133518 | LPP | 1.78x10-15 | 0.8 | 0.03 | – | 2.43x10-7 | rs13098877 | 2.62x10-11 | – | 1.17x10-3 |
| rs7137828 | chr12:111833788-112037526 | ATXN2 SH2B3 | 1.70x10-13 | 0.82 | 0.03 | – | 7.31x10-5 | rs10774624 | 8.28x10-9 | – | 1.26x10-3 |
| rs8088891 | chr18:60007263-60029292 | TNFRSF11A | 3.51x10-13 | 1.22 | 0.03 | – | 9.89x10-4 | – | 1.14x10-3 | rs4369774 | 1.09x10-13 |
| rs1951459 | chr6:167370353-167455629 | FGFR1OP MIR3939 RNASET2 | 3.61x10-13 | 0.81 | 0.03 | rs2247315 | 3.48x10-9 | rs366938 | 1.14x10-8 | – | 9.53x10-4 |
| rs64547 | chr22:37575469-37595156 | C1QTNF6 SSTR3 | 8.14x10-13 | 0.82 | 0.03 | rs229528 | 2.09x10-8 | rs229527 | 1.55x10-12 | – | 7.33x10-3 |
| rs831071 | chr3:71426419-71430389 | FOXP1 | 1.01x10-10 | 1.2 | 0.03 | – | 2.11x10-3 | rs60135207 | 3.14x10-9 | – | 3.40x10-6 |
| rs3116513 | chr2:204694611-204792732 | CTLA4 ICOS | 1.42x10-10 | 1.19 | 0.03 | – | 2.25x10-2 | – | 5.64x10-5 | – | 2.65x10-6 |
| rs644515 | chr11:128589472-128617231 | FLI1 | 1.44x10-9 | 1.17 | 0.03 | – | 2.89x10-5 | – | 2.89x10-5 | – | 1.24x10-2 |
The column SNP contains the top SNP in each locus. The columns P, OR and SE correspond to the top SNP in each locus. The autoimmune disorder specific Top SNP column contains the top genome-wide significant SNP in the locus that was available in the input dataset. The autoimmune disorder specific P column contains the lowest p-value in the locus that was available in the input dataset.