Table 2.
Prioritized chromosome 5q positional candidate SNPs tested in the Australian and Norwegian preeclampsia cohorts.
| Gen | SNP | Function | Aust/NZ cohort | Norwegian cohort | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GoldenGate genotyping | SNPlex genotyping | iPLEX Gold genotyping | |||||||||||||
| Allele (frequency) | MG Puncorr |
MG Pcorr |
QTDT Puncorr |
QTDT Pcorr |
Allele (frequency) | MG Puncorr |
Allele (frequency) | MG Puncorr |
MG Pcorr |
||||||
| CRHBP | rs32897 | Intronic | A (0.849) | G (0.151) | 0.914 | 0.993 | A (0.818) | G (0.182) | 0.947 | ||||||
| rs6453267 | Intronic | Excludeda | Excludedb | ||||||||||||
| rs7721519 | Intronic | C (0.618) | T (0.382) | 0.117 | NS | 0.075 | NS | C (0.620) | T (0.380) | 0.016 | C (0.627) | T (0.373) | 0.038 | 0.083 | |
| rs1875999 | 3’UTR | A (0.665) | G (0.335) | 0.062 | NS | 0.065 | NS | A (0.648) | G (0.352) | 0.052 | A (0.650) | G (0.350) | 0.030 | 0.065 | |
| ERAP1 | rs27980 | 3’UTR | A (0.690) | C (0.310) | 1.000 | 0.378 | A (0.660) | C (0.340) | 0.540 | ||||||
| rs27582 | 3’UTR | G (0.697) | A (0.303) | 0.700 | 0.149 | G (0.660) | A (0.340) | 0.514 | |||||||
| rs17481856 | Synonymous | G (0.874) | A (0.126) | 0.374 | 0.365 | G (0.869) | A (0.131) | 0.676 | |||||||
| rs27044 | Missense | C (0.709) | G (0.291) | 0.252 | 0.188 | Failed genotyping | |||||||||
| rs469783 | Synonymous | T (0.559) | C (0.441) | 0.477 | 0.094 | T (0.563) | C (0.437) | 0.762 | |||||||
| rs10050860 | Missense | C (0.781) | T (0.219) | 0.951 | 0.720 | C (0.804) | T (0.196) | 0.088 | C (0.800) | T (0.200) | 0.066 | NS | |||
| rs30187 | Missense | C (0.680) | T (0.320) | 0.533 | 0.377 | C (0.661) | T (0.339) | 0.558 | |||||||
| rs27529 | Synonymous | G (0.678) | A (0.322) | 0.418 | 0.571 | G (0.660) | A (0.340) | 0.499 | |||||||
| rs2287987 | Missense | Failed assay design | T (0.794) | C (0.206) | 0.075 | T (0.801) | C (0.199) | 0.063 | NS | ||||||
| rs26618 | Missense | T (0.777) | C (0.223) | 0.933 | 0.352 | T (0.773) | C (0.227) | 0.752 | |||||||
| rs26653 | Missense | G (0.735) | C (0.265) | 0.628 | 0.953 | G (0.710) | C (0.290) | 0.062 | Failed assay design | ||||||
| rs3734016 | Missense | G (0.960) | A (0.040) | 0.078 | NS | 0.009 | 0.074 | G (0.944) | A (0.056) | 0.196 | |||||
| rs34750 | Intronic | C (0.736) | G (0.264) | 0.595 | 0.881 | C (0.709) | G (0.291) | 0.071 | C (0.709) | G (0.291) | 0.011 | 0.082 | |||
| ERAP2 | rs3733905 | Missense | C (0.995) | T (0.005) | 0.633 | 1.000 | C (0.997) | T (0.003) | 0.368 | ||||||
| rs2549782 | Missense | T (0.572) | G (0.428) | 0.015 | NS | 0.004 | 0.018 | T (0.494) | G (0.506) | 0.480 | |||||
| rs2548538 | Synonymous | T (0.572) | A (0.428) | 0.015 | NS | 0.004 | 0.018 | T (0.493) | A (0.507) | 0.372 | |||||
| rs2287988 | Synonymous | A (0.572) | G (0.428) | 0.015 | NS | 0.004 | 0.018 | A (0.493) | G (0.507) | 0.514 | |||||
| rs17408150 | Missense | T (0.963) | A (0.037) | 0.614 | 0.675 | T (0.961) | A (0.039) | 0.044 | T (0.958) | A (0.042) | 0.009 | 0.039 | |||
| rs1056893 | Synonymous | T (0.572) | C (0.428) | 0.014 | NS | 0.004 | 0.018 | T (0.491) | C (0.509) | 0.624 | |||||
| rs2255546 | Synonymous | A (0.573) | G (0.427) | 0.015 | NS | 0.004 | 0.018 | A (0.492) | G (0.508) | 0.513 | |||||
| LNPEP | rs3797799 | Missense | NP | NP | |||||||||||
| rs12520455 | Missense | NP | NP | ||||||||||||
| rs2303138 | Missense | G (0.918) | A (0.089) | NS | NS | G (0.922) | A (0.078) | NS | |||||||
| rs17087233 | Missense | NP | NP | ||||||||||||
| rs11746232 | Missense | A (0.909) | G (0.091) | NS | NS | A (0.903) | G (0.097) | NS | |||||||
| rs2287927 | Synonymous | NP | NP | ||||||||||||
| LVRN | rs10062297 | Synonymous | T (0.820) | C (0.180) | NS | NS | T (0.830) | C (0.170) | NS | ||||||
| rs12520255 | Missense | C (0.820) | T (0.180) | NS | NS | C (0.832) | T (0.168) | NS | |||||||
| rs1445708 | Synonymous | C (0.597) | T (0.403) | NS | NS | C (0.573) | T (0.427) | NS | |||||||
| rs17482536 | Synonymous | C (0.981) | T (0.019) | NS | NS | C (0.977) | T (0.023) | NS | |||||||
| rs7724126 | Missense | Excludeda | NP | ||||||||||||
| rs7712021 | Synonymous | T (0.656) | C (0.344) | NS | NS | T (0.652) | C (0.348) | NS | |||||||
| rs1560079 | Missense | NP | NP | ||||||||||||
| rs17138632 | Missense | G (0.971) | T (0.029) | NS | NS | G (0.959) | T (0.041) | NS | |||||||
| rs17138681 | Missense | NP | NP | ||||||||||||
| rs1508886 | 3’UTR | A (0.506) | G (0.494) | NS | NS | A (0.540) | G (0.460) | NS | |||||||
| IL3 | rs40401 | Missense | C (0.790) | T (0.210) | NS | NS | C (0.772) | T (0.228) | NS | ||||||
| CSF2 | rs2069625 | Synonymous | Excludeda | NP | |||||||||||
| rs25882 | Missense | T (0.806) | C (0.194) | NS | NS | T (0.791) | C (0.209) | NS | |||||||
| IL5 | rs2069818 | Synonymous | NP | NP | |||||||||||
| rs1800474 | Synonymous | NP | NP | ||||||||||||
| IL13 | rs1295687 | Intronic | C (0.941) | G (0.059) | NS | NS | C (0.915) | G (0.085) | NS | ||||||
| rs3212145 | Intronic | NP | NP | ||||||||||||
| rs2069744 | Intronic | C (0.991) | T (0.009) | NS | NS | C (0.995) | T (0.005) | NS | |||||||
| rs2069747 | Intronic | NP | NP | ||||||||||||
| rs1295686 | Intronic | G (0.826) | A (0.174) | NS | NS | G (0.793) | A (0.207) | NS | |||||||
| rs20541 | Missense | C (0.823) | T (0.177) | NS | NS | C (0.794) | T (0.206) | NS | |||||||
| rs848 | 3’UTR | G (0.826) | T (0.174) | NS | NS | G (0.795) | T (0.205) | NS | |||||||
| IL4 | rs17772853 | 5’UTR | C (0.995) | T (0.005) | NS | NS | Failed genotyping | ||||||||
| rs2070874 | 5’UTR | C (0.858) | T (0.142) | NS | NS | C (0.844) | T (0.156) | NS | |||||||
| rs4986964 | Missense | Excludeda | NP | ||||||||||||
Abbreviations: QTDT, quantitative transmission disequilibrium test; MG, measured genotype test; Puncorr, uncorrected p-value; Pcorr, corrected p-value; NP, non-polymorphic; NS, not significant.
a
NP excluded from statistical analysis (observed minor allele count < 5).
b
NP excluded from statistical analysis (individual genotype success rate = 14.8%).