Table 2 Significant opposite parent-of-origin effect GWAS associations
From: Parent-of-origin effects on quantitative phenotypes in a large Hutterite pedigree
Phenotype | rsid | chr:loc | Variant location | Nearest gene | MAF | βM – βP (SE) | Opposite effect GWAS | Paternal GWAS | Maternal GWAS | Standard GWAS p-value | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
p-value | Beta (SE) | p-value | Beta (SE) | |||||||||
Age of menarche | rs57878386 | 16:62201228 | Intergenic | CDH8 | 0.17 | −0.654 (0.109) | 5.27E–09 | 5.20E–06 | 0.391 (0.085) | 1.85E–05 | −0.368 (0.085) | 8.68E–01 |
BMI | rs77785972 | 5:97415767 | Intergenic | LINC01340 (noncoding RNA gene) | 0.025 | 0.154 (0.025) | 5.12E–10 | 5.84E–07 | −0.094 (0.019) | 1.58E–05 | 0.081 (0.019) | 5.39E–01 |
rs17605739 | 6:22962798 | Intronic | RP1-209A6.1 (noncoding RNA gene) | 0.17 | 0.053 (0.010) | 3.01E–08 | 6.99E–05 | −0.032 (0.008) | 1.42E–06 | 0.034 (0.007) | 1.56E–01 | |
Eosinophil count | rs2355879 | 1:18732860 | Intergenic | IGSF21 | 0.14 | 0.091 (0.016) | 1.69E–08 | 5.83E–08 | −0.065 (0.012) | 5.59E–04 | 0.043 (0.012) | 2.53E–01 |
FEV1 | rs12714812 | 3:74813002 | Intergenic | CNTN3 | 0.45 | −0.119 (0.021) | 4.52E–08 | 1.78E–03 | 0.052 (0.017) | 6.35E–06 | −0.073 (0.016) | 9.58E–01 |
LDL | rs1032596 | 16:86281537 | Intronic | LINC01081 (noncoding RNA gene) | 0.30 | −0.310 (0.056) | 3.69E–08 | 1.05E–06 | 0.201 (0.041) | 4.56E–04 | −0.148 (0.042) | 2.71E–01 |
LVMI | rs16853098 | 2:168013281 | Intronic | XIRP2 | 0.12 | −0.091 (0.053) | 4.18E–08 | 5.29E–06 | 0.064 (0.014) | 2.04E–04 | −0.048 (0.013) | 9.26E–01 |
Neutrophil count | rs142030841 | 18:34371947 | Intronic | TPGS2 | 0.042 | −0.224 (0.041) | 4.40E–08 | 2.25E–03 | 0.078 (0.025) | 1.30E–07 | −0.188 (0.035) | 5.77E–01 |
Triglycerides | rs7525463 | 1:218860879 | Intronic | MIR548F3 (noncoding RNA gene) | 0.16 | −0.401 (0.071) | 2.51E–08 | 1.14E–03 | 0.195 (0.060) | 5.52E–08 | −0.267 (0.049) | 2.84E–02 |
Total cholesterol | rs7033776 | 9:36704465 | Intergenic | MELK | 0.41 | 0.230 (0.041) | 4.12E–08 | 5.60E–08 | −0.183 (0.034) | 2.28E–03 | 0.099 (0.032) | 6.70E–02 |