Table 1. A list of anchor SNPs identified by the p-value combination analysis in GWAS.
| CHR | RS | PP | GI | CLR-NOMINAL | CLR-NOMINAL | CLR-ORDINAL | CLR-ORDINAL |
| −log10(p) | −log10(pFDR) | −log10(p) | −log10(pFDR) | ||||
| 2 | rs6711736 | 34196635 | Hypothetical | 7.48527 | 3.52284 | 9.16600 | 4.68070 |
| rs6729869 | 34196845 | Hypothetical | 7.04924 | 3.16599 | 9.02237 | 4.66200 | |
| rs10495809 | 34216890 | Intergenic | 7.38445 | 3.46342 | 9.46051 | 4.79912 | |
| rs1346007 | 34217210 | Intergenic | 5.79457 | 2.39848 | 7.84643 | 3.82731 | |
| 4 | rs6854244 | 138479489 | Intergenic | 7.76575 | 3.52284 | 8.84525 | 4.65691 |
| rs10519412 | 138487534 | Intergenic | 7.79596 | 3.52284 | 8.51803 | 4.40070 | |
| rs10517739 | 162515975 | Intergenic | 6.43381 | 2.75013 | 7.02313 | 3.10209 | |
| rs1444280 | 162516134 | FSTL5 | 7.88286 | 3.52284 | 8.84119 | 4.65691 | |
| 8 | rs4737649 | 64515583 | IFITM8P | 7.79134 | 3.52284 | 4.31484 | 1.54609 |
| rs1431587 | 64516073 | IFITM8P | 7.70481 | 3.52284 | 3.80069 | 1.31314 | |
| rs1367807 | 64544666 | Intergenic | 6.83890 | 3.05256 | 3.44477 | 1.13168 | |
| rs831738 | 70313702 | Intergenic | 7.49105 | 3.52284 | 3.65335 | 1.23307 | |
| rs705994 | 70313758 | Intergenic | 7.50762 | 3.52284 | 3.61202 | 1.21483 | |
| rs705993 | 70314229 | Intergenic | 7.53247 | 3.52284 | 3.62344 | 1.21852 | |
| 9 | rs945658 | 1606639 | Intergenic | 6.59932 | 2.86734 | 3.9664 | 3.82731 |
| 10 | rs2620887 | 49730508 | WDFY4 | 5.15365 | 1.88658 | 7.04094 | 3.10209 |
| 18 | rs10513909 | 8326569 | Intergenic | 6.98389 | 3.13540 | 4.76805 | 1.76466 |
| rs10513910 | 18326428 | Intergenic | 6.85253 | 3.05256 | 3.96647 | 1.38965 | |
| rs9284423 | 36256475 | Intergenic | 8.48521 | 3.52284 | 9.90126 | 4.93883 | |
| rs9304221 | 36256659 | Intergenic | 6.02669 | 2.40668 | 6.92917 | 3.04592 |
The p-value combination analysis with a window size of 3 identified 20 triplets of SNPs in GWAS. Chromosome (CHR), RS number (RS), physical position (PP) and gene information (GI) of the anchor (central) marker of each SNP triplet are shown. The last four columns represent unadjusted p value (−log10(p)) and adjusted p value (−log10(pFDR)) of the p-value combination analysis based on single-locus p values from a CLR-NOMINAL analysis [model: logit{Prob(Y = YOH|I11,I12)} = a0+a11×I11+a12×I12] and a CLR-ORDINAL analysis [model: logit{Prob(Y = YOH|X)} = a0+a1×X], where Y is YOH status, I1j is an indicator of the three genotypes (j = 1, 2) of a SNP and X is a variable for the number of reference alleles. Anchor markers that had −log10(pFDR)>3 for both tests and were located in known or hypothetical gene regions are highlighted in bold font.