Table 2. Collapsing methods results for most significant loci in stage 2.
| Locus, (GWAS gene) | Stage 1 | Stage 2 | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Threshold | P-value | Threshold | All variants | Independent variants | ||||||
| Number of variants | Number of alternative allele counts | P-value | Number of variants | Number of alternative allele counts | P-value | P-value after permutations | ||||
| chr3:25633833–25636833, (RARB) | 5.81x10−4 | 9.43x10−7 | 1.25x10−2 | 3 | 363 | 5.32x10−2 | 3 | 363 | 5.32x10−2 | 6.25x10−2 |
| chr3:169238286–169241286, (MECOM) | 1.87x10−4 | 1.46x10−5 | 8x10−3 | 2 | 573 | 2.94x10−3 | 2 | 573 | 2.94x10−3 | 1.92x10−2 |
| chr4:145293600–145296600, (HHIP) | 2.76x10−4 | 1.11x10−5 | 1.25x10−2 | 2 | 167 | 4.16x10−2 | 2 | 167 | 4.16x10−2 | 6.19x10−2 |
| NPNT (chr4:106816596–106892828), (GSTCD) | 1.25x10−2 | 1.81x10−3 | 2.5x10−2 | 9 | 1400 | 5.25x10−2 | 3 | 422 | 5.1x10−1 | 4.07x10−1 |
| TNXB (chr6:32008931–32077151), (AGER) | 7.14x10−3 | 6.91x10−3 | 5x10−2 | 37 | 8086 | 6.08x10−2 | 11 | 1752 | 4.73x10−2 | 6.69x10−2 |
| C10orf11 (chr10:77542518–78317126) (C10orf11) | 5x10−2 | 3.95x10−18 | 5x10−2 | 304 | 39634 | 4.03x10−2 | 124 | 15529 | 2.77x10−2 | 5x10−1 |
“GWAS gene” presents the gene previously reported for lung function [9] for each of the 26 regions. The most significant stage 1 P-values across the three algorithms for the analysis only including independent variants are presented here; for full results see S7 Table. Stage 2 P-values that meet the threshold are shown in bold.