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Table 1 Results of the 27 SNPs with P values < 5 × 10–6 in the discovery phase

From: Genetics of early-life head circumference and genetic correlations with neurological, psychiatric and cognitive outcomes

SNP

CHR

Position

Nearest gene

EA/non_EA

P value discovery

P value replication

EAFa

Beta (SE) combined

P value combined

Heterogeneity I2 combined analysis

rs8756b, c, d

12

66,359,752

HMGA2

C/A

5.18 × 10–12

4.62 × 10–3

0.50

0.065 (0.009)

1.84 × 10–13

0

rs9795522b

12

123,730,935

C12orf65

C/A

3.20 × 10–9

3.86 × 10–5

0.23

0.072 (0.010)

7.37 × 10–12

0

rs10883848d

10

104,973,061

NT5C2

A/G

3.06 × 10–6

0.03

0.35

0.058 (0.010)

9.99 × 10–10

54.8

rs6095360

20

47,532,536

ARFGEF2

G/A

3.53 × 10–8

6.19 × 10–4

0.32

0.055 (0.009)

4.39 × 10–9

36.6

rs3134614

1

40,363,054

MYCL1

C/G

4.31 × 10–6

7.75 × 10–4

0.88

0.075 (0.013)

1.43 × 10–8

0

rs6016511

20

39,709,255

TOP1

T/C

4.55 × 10–7

0.02

0.68

0.052 (0.010)

4.02 × 10–8

0

rs7792211d

7

50,707,141

GRB10

G/A

7.62 × 10–7

0.01

0.42

0.051 (0.009)

4.43 × 10–8

11.3

rs1490384c, d

6

126,851,160

CENPW

T/C

5.46 × 10–8

0.14

0.51

0.049 (0.009)

5.70 × 10–8*

43.9

rs116536930

17

43,855,156

CRHR1

G/T

4.19 × 10–8

0.53

0.51

0.055 (0.011)

2.27 × 10–7*

40.1

rs72952297

2

180,379,814

ZNF385B

T/G

2.07 × 10–6

0.11

0.93

0.087 (0.018)

9.19 × 10–7*

0

rs12350281

9

20,637,773

MLLT3

G/A

4.22 × 10–6

0.03

0.05

0.152 (0.031)

9.98 × 10–7*

43.1

rs7658192

4

140,023,559

ELF2

T/G

2.29 × 10–7

0.46

0.33

0.046 (0.010)

1.70 × 10–6*

62.9

rs143094271e

17

7,463,102

TNFSF12-TNFSF13

A/G

5.96 × 10–7

0.44

0.02

0.133 (0.028)

2.02 × 10–6*

33.7

rs1014098

1

119,458,215

TBX15

C/T

2.67 × 10–6

0.17

0.79

0.051 (0.011)

2.05 × 10–6*

30.3

rs77690628

8

26,189,223

PPP2R2A

A/T

1.02 × 10–6

0.31

0.07

0.080 (0.017)

3.26 × 10–6*

24.6

rs9853018

3

141,101,961

ZBTB38

T/C

5.41 × 10–7

0.62

0.45

0.040 (0.009)

5.30 × 10–6

38.4

rs4674101

2

217,487,622

RPL37A

A/G

8.66 × 10–7

0.57

0.31

0.043 (0.010)

6.56 × 10–6

65.3

rs150266910

1

23,442,265

LUZP1

C/T

1.42 × 10–6

0.65

0.83

0.052 (0.012)

1.04 × 10–5

58.2

rs13067734

3

141,963,015

GK5

A/C

2.83 × 10–6

0.55

0.52

0.037 (0.009)

1.22 × 10–5

26.5

rs17223831

14

90,601,920

KCNK13

A/G

1.24 × 10–6

0.18

0.14

0.067 (0.015)

1.30 × 10–5

67.6

rs62580922

9

125,631,594

RC3H2

C/T

1.13 × 10–8

0.35

0.07

0.072 (0.017)

1.52 × 10–5

77.8

rs2448415

1

93,469,310

FAM69A

A/G

1.97 × 10–6

0.81

0.47

0.037 (0.009)

2.56 × 10–5

60.7

rs261752

5

39,328,506

C9

A/G

1.39 × 10–6

0.70

0.55

0.035 (0.009)

7.63 × 10–5

63.7

rs72979897

6

140,881,181

MIR3668

T/A

4.13 × 10–6

0.88

0.04

0.100 (0.025)

8.26 × 10–5

50.6

rs503783

6

161,959,649

PARK2

T/C

2.98 × 10–6

0.66

0.27

0.037 (0.010)

1.59 × 10–4

74.3

rs113397574

5

31,968,320

PDZD2

T/C

4.56 × 10–6

0.61

0.02

0.118 (0.032)

2.40 × 10–4

58.5

rs77535478

9

77,533,287

TRPM6

A/G

1.28 × 10–6

0.39

0.04

0.081 (0.026)

2.05 × 10–3

75.4

  1. Bolded P values indicate genome-wide significance in the combined analysis
  2. CHR chromosome, EA effect allele, EAF effect allele frequency, SE standard error
  3. *Genome-wide suggestive loci
  4. aFrom combined analysis
  5. bLocus previously reported for infant head circumference [11]
  6. cLocus previously reported for adult intracranial volume [7, 9]
  7. dLocus previously reported for adult head brain volume [8]
  8. eLocus previously reported for childhood and adult head circumference and intracranial volume [10]