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

  1. The most significant variant at each locus for each phenotype is shown. βM – βP represents difference in parental effect size