Table 2.
Information for the 21 Analyzed SNPs Within and Adjacent to the RTP3 Gene and Their Association Results in GWAS Analysis Using EIGENSTRAT
| SNP ID | Name | Position | Gene | Role | Allelea | MAFb | MAFc | P value for BR | P value for CT |
|---|---|---|---|---|---|---|---|---|---|
| 1 | rs2269436 | 46462257 | LTF | Intron | G/A | 0.042 | 0.042 | 2.38 × 10−1 | 2.87 × 10−1 |
| 2 | rs17141154 | 46462271 | LTF | Intron | A/G | 0.167 | 0.167 | 1.74 × 10−3 | 6.21 × 10−4 |
| 3 | rs17078863 | 46473920 | LTF | Intron | C/T | 0.045 | 0.042 | 5.02 × 10−1 | 3.05 × 10−1 |
| 4 | rs7629657 | 46474176 | LTF | Intron | T/C | 0.048 | 0.042 | 4.89 × 10−1 | 2.95 × 10−1 |
| 5 | rs9862388 | 46479320 | LTF | Intron | G/A | 0.300 | 0.267 | 2.38 × 10−1 | 2.87 × 10−1 |
| 6 | rs1520483 | 46485213 | RTP3 | Promoter | T/C | 0.350 | 0.374 | 1.81 × 10−4 | 7.14 × 10−4 |
| 7 | rs7639243 | 46488981 | LTF | Promoter | A/C | 0.400 | 0.333 | 2.32 × 10−1 | 2.21 × 10−1 |
| 8 | rs7641783 | 46489276 | RTP3 | Promoter | T/C | 0.273 | 0.258 | 4.06 × 10−4 | 6.56 × 10−5 |
| 9 | rs883739 | 46513022 | RTP3 | Promoter | A/C | 0.352 | 0.375 | 4.99 × 10−5 | 8.87 × 10−5 |
| 10 | rs7430431 | 46516151 | RTP3 | Intron | C/T | 0.494 | 0.483 | 1.61 × 10−7 | 1.92 × 10−6 |
| 11 | rs11130094 | 46516507 | RTP3 | Intron | A/G | 0.404 | 0.364 | 1.03 × 10−3 | 2.49 × 10−4 |
| 12 | rs10514713 | 46518621 | RTP3 | 3′ UTR | A/C | 0.380 | 0.381 | 2.68 × 10−4 | 3.09 × 10−4 |
| 13 | rs7371865 | 46524192 | RTP3 | 3′ UTR | A/C | 0.105 | 0.075 | 2.49 × 10−1 | 1.93 × 10−1 |
| 14 | rs1879328 | 46543161 | LRRC2 | Intron | G/A | 0.167 | 0.140 | 8.10 × 10−1 | 8.40 × 10−1 |
| 15 | rs6791703 | 46544725 | LRRC2 | Intron | G/T | 0.498 | 0.500 | 8.69 × 10−7 | 1.80 × 10−4 |
| 16 | rs939421 | 46551085 | LRRC2 | Intron | G/A | 0.300 | 0.225 | 4.90 × 10−2 | 1.60 × 10−1 |
| 17 | rs11705987 | 46559076 | LRRC2 | Intron | C/A | 0.210 | 0.246 | 7.54 × 10−2 | 5.40 × 10−2 |
| 18 | rs9810340 | 46559176 | LRRC2 | Intron | T/A | 0.450 | 0.458 | 5.33 × 10−7 | 7.70 × 10−5 |
| 19 | rs9846026 | 46563817 | LRRC2 | Intron | A/C | 0.100 | 0.078 | 2.86 × 10−2 | 3.90 × 10−1 |
| 20 | rs9808967 | 46564298 | LRRC2 | Intron | T/A | 0.050 | 0.076 | 3.03 × 10−3 | 9.17 × 10−2 |
| 21 | rs11919651 | 46568910 | LRRC2 | Intron | C/A | 0.180 | 0.158 | 3.71 × 10−2 | 4.60 × 10−2 |
Note: The RTP3 gene is located in 3p21.31. MAF = minor allele frequency; BR = buckling ratio; CT = cortical thickness.
a
The former allele represents the minor allele of each locus.
b
Minor allele frequency calculated in our own Caucasian sample.
c
Minor allele frequency reported for Caucasians in the public database such as Hap Map or dbSNP.
d
P values were calculated using EIGENSTRAT analyses. Significant results at the GWAS level are labeled in bold.