Table 1. SNPs with statistically significant results in EPICOLON stage 1 in the candidate-gene approach for regions 9q22 and 3q22.
SNP_ID | Gene | Location/relevance | Alleles | MAF cases | MAF controls | Test | GT counts cases | GT counts controls | OR (95% CI) | P-value |
---|---|---|---|---|---|---|---|---|---|---|
rs4149338 | ABCA1 | 9q22/intron, triplex, mcons | C/T | 0.241 | 0.285 | Dom | 201/280 | 248/252 | 0.73 (0.57–0.94) | 0.0141 |
rs2515618 | ABCA1 | 9q22/intron, triplex, mcons | G/A | 0.255 | 0.278 | Dom | 213/287 | 250/260 | 0.77 (0.60–0.99) | 0.0406 |
rs4149339 | ABCA1 | 9q22/miss, ESE, mcons | C/T | 0.217 | 0.278 | Dom | 183/300 | 247/257 | 0.63 (0.49–0.82) | 0.00043 |
rs10991898 | AUH | 9q22/intron, triplex, mcons | C/T | 0.095 | 0.119 | Dom | 87/394 | 117/386 | 0.73 (0.53–0.99) | 0.0493a |
rs589362 | C9ORF102 | 9q22/3′UTR, ESE, mcons | C/G | 0.320 | 0.358 | Dom | 257/223 | 306/198 | 0.75 (0.58–0.96) | 0.0230 |
rs10123342 | NOL8 | 9q22/promoter, mcons | T/G | 0.343 | 0.394 | Rec | 52/433 | 86/407 | 0.57 (0.39–0.82) | 0.0025 |
rs11466445 | TGFBR1 | 9q22/3 AA deletion (GGCGGCGGC), mcons | 3AA/- | 0.084 | 0.109 | Dom | 77/406 | 105/399 | 0.72 (0.52–0.99) | 0.0491a |
rs12236219 | ZNF169 | 9q22/miss, ESE, mcons | C/T | 0.031 | 0.068 | Allelic | 30/940 | 69/939 | 0.43 (0.28–0.67) | 0.00012a |
rs2246945 | A4GNT | 3q22/miss, ESE, mcons | A/C | 0.289 | 0.325 | Rec | 37/430 | 59/431 | 0.63 (0.40–0.97) | 0.0340 |
rs2346747 | A4GNT | 3q22/promoter, mcons | G/A | 0.317 | 0.352 | Rec | 46/434 | 69/417 | 0.64 (0.43–0.95) | 0.0268 |
rs329387 | ARMC8 | 3q22/intron, triplex, mcons | G/A | 0.450 | 0.502 | Dom | 317/151 | 377/124 | 0.69 (0.52–0.91) | 0.0095 |
rs939453 | ARMC8 | 3q22/triplex, mcons | C/A | 0.422 | 0.484 | Allelic | 404/554 | 484/516 | 0.78 (0.65–0.93) | 0.0056 |
rs13088006 | CDV3 | 3q22/intron, triplex, mcons | T/C | 0.232 | 0.256 | Rec | 22/458 | 40/448 | 0.54 (0.31–0.92) | 0.0217 |
rs1673607 | CEP70 | 3q22/miss, ESE, ESS, mcons | A/G | 0.472 | 0.501 | Rec | 108/388 | 140/367 | 0.73 (0.55–0.97) | 0.0321 |
rs811322 | FAIM | 3q22/synon, ESE | A/G | 0.456 | 0.485 | Rec | 98/389 | 128/373 | 0.73 (0.54–0.99) | 0.0423 |
rs108858 | IL20RB | 3q22/3′UTR, ESE | A/G | 0.433 | 0.475 | Dom | 313/161 | 362/136 | 0.73 (0.56–0.96) | 0.0243 |
rs3738000 | NEK11 | 3q22/miss, mcons | T/A | 0.273 | 0.301 | Dom | 218/262 | 261/239 | 0.76 (0.59–0.98) | 0.0337 |
rs10934954 | PIK3R4 | 3q22/synon, ESS | C/T | 0.242 | 0.204 | Rec | 33/446 | 19/481 | 1.87 (1.05–3.34) | 0.0311 |
rs2071387 | RBP1 | 3q22/intron, mcons | T/C | 0.170 | 0.177 | Rec | 8/475 | 22/478 | 0.37 (0.16–0.83) | 0.0124 |
rs1131597 | SLCO2A1 | 3q22/3′UTR, mcons | G/A | 0.303 | 0.379 | Allelic | 289/665 | 380/622 | 0.71 (0.59–0.86) | 0.00038 |
rs1444601 | TOPBP1 | 3q22/synon, mcons | A/G | 0.238 | 0.281 | Allelic | 231/739 | 282/720 | 0.80 (0.65–0.98) | 0.0284 |
Abbreviations: AA=amino acid; CI=confidence interval; Dom=dominant; ESE=exonic splicing enhancer; ESS=exonic splicing silencer; GT=genotype; MAF=minor allele frequency; mcons=conserved in mouse; miss=missense; Rec=recessive; SNP_ID=SNP identification; synon=synonymous; intron=intronic; UTR=untranslated region.
Results are shown according to the best fitting-model.
If one of the genotypes had a frequency <5, then Fisher's exact test was used.