Table 1.
Results of the 27 SNPs with P values < 5 × 10–6 in the discovery phase
| 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 |
Bolded P values indicate genome-wide significance in the combined analysis
CHR chromosome, EA effect allele, EAF effect allele frequency, SE standard error
*Genome-wide suggestive loci
aFrom combined analysis
bLocus previously reported for infant head circumference [11]
cLocus previously reported for adult intracranial volume [7, 9]
dLocus previously reported for adult head brain volume [8]
eLocus previously reported for childhood and adult head circumference and intracranial volume [10]