Table 2.

Novel independent loci for combined intracranial volume and head circumference

Variant	Chr:Pos (b37)	EA: EAF	ICV		HC (Pediatric + adult)		ICV + HC (Pediatric + adult)		N Total
			β* (SE)	p	β* (SE)	p	β* (SE)	p	N
rs2168812	1: 243777066	A: 0.18	0.05 (0.01)	9.0×10−6	0.06 (0.01)	1.5×10−5	0.05 (0.01)	2.3×10−9	45,458
rs4513262	2: 10181457	T: 0.21	0.05 (0.01)	7.7×10−7	0.04 (0.01)	2.3×10−3	0.05 (0.01)	2.9×10−8	45,336
rs41288837	2: 85531116	T: 0.03	−0.10 (0.03)	1.0×10−4	−0.15 (0.03)	1.6×10−6	−0.11 (0.02)	7.2×10−9	43,916
rs429150a	6: 32075563	T: 0.52	0.04 (0.01)	3.1×10−5	0.04 (0.01)	1.0×10−4	0.04 (0.01)	3.9×10−8	43,122
rs9271147b	6: 32577385	T: 0.17	0.06 (0.02)	4.3×10−4	0.07 (0.01)	6.5×10−8	0.07 (0.01)	4.4×10−10	30,057
rs11154343	6: 126412953	T: 0.31	−0.05 (0.01)	1.7×10−8	−0.03 (0.01)	1.2×10−2	−0.04 (0.01)	1.0×10−8	45,458
rs7808664a	7: 32917550	A: 0.37	−0.04 (0.01)	1.2×10−6	−0.03 (0.01)	2.0×10−3	−0.04 (0.01)	3.6×10−8	45,458
rs148974918	10: 112033051	T: 0.05	−0.08 (0.02)	9.4×10−5	−0.1 (0.02)	1.6×10−5	−0.08 (0.02)	2.4×10−8	45,458
rs3217870	12: 4400111	T: 0.62	−0.03 (0.01)	1.0×10−4	−0.05 (0.01)	7.0×10−7	−0.04 (0.01)	3.1×10−9	45,458
rs2066827	12: 12871099	T: 0.77	0.05 (0.01)	3.9×10−6	0.05 (0.01)	9.3×10−5	0.05 (0.01)	5.4×10−9	38,871
rs78378222c	17: 7571752	G: 0.02	0.15 (0.04)	1.4×10−5	0.21 (0.04)	1.5×10−7	0.17 (0.03)	7.9×10−11	41,371

Genome-wide combined meta-analysis of intracranial volume and head circumference scores as described in Fig. 1b; Evidence for association was assessed using Z-weighted meta-analysis. Standardized estimates were derived as described in the Methods. Only independent variants (Linkage disequilibrium (LD)-r² < 0.2 within ±500 kb) reaching nominal evidence for genome-wide significance (p < 5.0 × 10⁻⁸) are shown. The adjusted threshold for genome-wide significance is 3.3×10⁻⁸, accounting for multiple testing. Detailed meta-analysis information can be found in Supplementary Data 11. Detailed SNP and gene information is given in Supplementary Data 16 and 17

ICV—intracranial volume (ICV) meta-analysis of ENIGMA2 and CHARGE samples, N ≤ 26,577

HC (Pediatric + adult)—combined pediatric and adult head circumference meta-analysis, N ≤ 18,881

Position base pair position, EA effect allele, EAF effect allele frequency, β* standardized effect estimate, SE standard error, p p-value, N sample size

^aPasses a nominal threshold for genome-wide significance only (p < 5.0 × 10⁻⁸)

^brs9271147 is in linkage disequilibrium with rs9268812 (r² = 0.41), a novel GWAS signal from HC (Pediatric + adult) (Table 1, Supplementary Data 3)

^crs78378222 is in linkage disequilibrium with rs35850753 (r² = 0.56), a novel GWAS signal from HC (Pediatric + adult) (Table 1, Supplementary Data 3)