Table 2 Genome-wide significant loci for EduYears in cross-ancestry meta-analysis combining EAS and EUR populations

From: Shared genetic architectures of educational attainment in East Asian and European populations

Chr

Start

End

Credible set ID

Credible set size

Total PIP

N of significant variantsa,*

SNP with maximum PIP

Maximum PIP

A1

Effect size (EAS)

A1 Freq (EAS)

Marginal P value (EAS)

Effect size (EUR)

A1 Freq (EUR)

Marginal P value (EUR)

Gene

Annotation

2

161,721,597

162,351,261

1

2

0.99

2

rs11678980

0.93

A

−0.020

0.39

4.19 × 10−9

−0.017

0.43

3.69 × 10−24

NA

NA

4

180,613,679

181,136,169

1

4

0.99

4

rs4861427

0.38

C

0.020

0.47

6.81 × 10−9

0.005

0.48

3.66 × 10−3

NA

NA

5

93,838,858

94,392,030

1

15

0.95

14

rs255338

0.18

C

0.022

0.73

1.11 × 10−8

0.007

0.90

6.08 × 10−3

MCTP1

Intron

5

106,947,725

107,455,182

1

2

0.95

2

rs7708343

0.51

A

−0.021

0.32

4.46 × 10−9

−0.012

0.11

2.28 × 10−6

FBXL17

Intron

5

106,947,725

107,455,182

2

15

0.96

2

rs6868799

0.17

A

0.009

0.36

9.40 × 10−3

0.009

0.35

3.13 × 10−8

FBXL17

Intron

6

27,515,505

29,611,229

1

3

0.96

3

rs9461540

0.39

G

−0.027

0.17

6.19 × 10−10

NA

NA

NA

GABBR1

Upstream gene

6

27,515,505

29,611,229

2

35

0.96

25

rs112644424

0.13

T

−0.022

0.28

2.33 × 10−9

−0.014

0.08

2.45 × 10−6

NA

NA

10

103,385,878

104,057,295

1

26

0.96

26

rs3758551

0.07

G

−0.013

0.77

1.06 × 10−3

−0.012

0.60

6.24 × 10−14

GBF1, PITX3

Upstream gene

10

103,385,878

104,057,295

2

4

0.98

4

rs11191193

0.70

G

−0.021

0.23

6.89 × 10−8

−0.017

0.34

5.89 × 10−23

C10orf76

Intron

10

103,385,878

104,057,295

3

3

0.98

0

rs11598489

0.54

T

NA

NA

NA

0.023

0.04

2.65 × 10−7

NA

NA

17

42,899,988

43,438,117

1

2

0.97

1

rs2867316

0.90

T

0.004

0.62

2.84 × 10−1

−0.010

0.32

2.32 × 10−8

MAP3K14

Intron

17

42,899,988

43,438,117

2

7

0.97

6

rs12948326

0.71

G

−0.020

0.53

4.90 × 10−9

−0.004

0.39

1.04 × 10−2

NMT1, PLCD3

Downstream gene

17

42,899,988

43,438,117

3

3

1.00

3

rs11871429

0.51

G

−0.005

0.33

1.45 × 10−1

−0.014

0.21

1.73 × 10−12

HIGD1B

Upstream gene

  1. Abbreviations: A1 Freq, frequency of A1; A1, effect allele; Chr, chromosome; N, number; NA, not available. Gene symbols are italicized.
  2. aNumber of genome-wide significant variants with P value of a two-sided test <5 × 10−8. *at least in one population.
  3. Base pair position is based on the human genome assembly GRCh37 (hg19).
  4. ‘Credible set ID’: the ID of credible sets used to identify different credible sets in the same region.
  5. ‘Gene’: the genes affected by the variant using the Variant Effect Predictor tool.
  6. ‘Annotation’: the consequence of variants on the protein sequence using the Variant Effect Predictor tool.
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