Table 1 Selected examples of replicated 3-SNP haplotypes.
From: Genome-wide haplotype association analysis of primary biliary cholangitis risk in Japanese
Chr | 3-SNP haplotype or logic tree | Gene analytic windows with 3-SNP haplotype | # SNPs in gene windows | Discovery (N = 1,937) | Replication (N = 949) | Combined (N = 2,886) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Permutation-based selection statistic | OR | P | OR | P | OR | P | # with 0 haplotype copies (% cases) | # with 1 haplotype copy (% cases) | # with 2 haplotype copies (% cases) | ||||
6 | (rs3129881 = C) or ((rs375244 = A) and (rs3132947 = G)) | CFB; NELFE; C2; C2-AS1 | 153–163 | −69.730 | 4.937 | 1.8 × 10−20 | 2.324 | 1.6 × 10−5 | 3.665 | 2.3 × 10−24 | 17 (17.6%) | 360 (21.7%) | 2,509 (51.8%) |
6 | ((rs9268831 = T) or (rs9269190 = T)) or (rs9270652 = C) | ATF6B; FKBPL; PPT2; PPT2-EGFL8; AGPAT1 | 158–169 | −43.565 | 3.640 | 3.2 × 10−23 | 2.315 | 1.9 × 10−7 | 3.075 | 7.3 × 10−29 | 46 (15.2%) | 496 (26.0%) | 2,344 (53.1%) |
6 | (rs9295704 = C) and ((rs2451752 = A) and (rs2575174 = C))a | BTN3A2; BTN2A2 | 46–52 | −12.263 | 0.362 | 1.7 × 10−10 | 0.374 | 1.3 × 10−5 | 0.365 | 8.9 × 10−15 | 2,571 (50.4%) | 304 (27.3%) | 11 (9.1%) |
7 | ((rs12671658 = T) or (rs12702656 = A)) and (rs11768586 = G)a | GLCCI1; LOC100505921; ICA1; COL28A1; MIOS; RPA3; LOC100505938; UMAD1; LOC101927391 | 204–292 | −16.424 | 0.040 | 8.7 × 10−6 | 0.112 | 3.6 × 10−4 | 0.066 | 3.9 × 10–9 | 2,802 (49.1%) | 84 (6.0%) | 0 (NA) |
9 | (rs4979484 = C) or ((rs13300483 = T) and (rs7028891 = G))a | LOC100505478; TNFSF15; C9orf91; TNFSF8 | 121–156 | −28.431 | 1.746 | 4.2 × 10−17 | 1.528 | 8.6 × 10−6 | 1.672 | 3.0 × 10−21 | 775 (35.4%) | 1,434 (48.7%) | 677 (60.4%) |
