Table 3.
Discovery GWAS, replication and combined meta-analysis results for LOMG
| Nearest gene | Index SNP | CHR | BP (GRCh37) | A1/A2 | FRQ case | FRQ control | Proxy | P | OR | SE | P-rep | OR-rep | SE-rep | P-comb | OR-comb | SE-comb |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PTPN22 | rs2476601a | 1 | 114377568 | A/G | 0.141 | 0.132 | same | 9.26e−15 | 1.47669 | 0.0503 | 3.92e−14 | 1.311637 | 0.035159 | 5.11e−27 | 1.3637 | 0.0288 |
| CTLA4 | rs231779a,b | 2 | 204734487 | C/T | 0.572 | 0.515 | rs231770 | 2.66e−06 | 0.85172 | 0.0342 | 2.37e−05 | 0.910374 | 0.024511 | 4.99e−09 | 0.89003 | 0.0199 |
| MHC | rs72848204a | 6 | 32594073 | G/T | 0.749 | 0.697 | same | 1.20e−23 | 1.50953 | 0.0411 | 2.37e−02 | 1.049218 | 0.024296 | 1.04e−11 | 1.15281 | 0.0209 |
| TNFRSF11A | rs7239261a | 18 | 60005046 | A/C | 0.492 | 0.368 | same | 1.56e−14 | 1.29576 | 0.0337 | 4.43e−04 | 1.079214 | 0.022905 | 1.50e−12 | 1.14339 | 0.0189 |
The table presents the results from the discovery-, replication-, and combined inverse-variance-weighted fixed-effects meta-analyses.
BP (GRCh37) Base Pair position on Genome Reference Consortium Human Build 37, CHR chromosome, comb combined meta-analysis of discovery and control GWAS results, FRQ frequency.
aPreviously published as genome-wide significant locus.
bWould not withstand a multiple testing correction for 13 million tests (P < 3.85e−9), accounting for the leave-one-out GWAS.