Table 3.

Six SNPs on AGBL1 gene (chromosome 15) significant in GWAS of learning performance. Tests of ${\mathcal{J}}_0^{(g)}$ and ${\mathcal{M}}_0^{(g)}$ were performed for G×R and Main effect models, respectively, for 488,200 SNPs of the learning performance scores over the PING sample (n=479). Both models included covariates for status of learning problem diagnosis and the first two PCs of genotype data. Learning performance scores were, by construction, uncorrelated with age, sex, household income, and parental education. Tests of ${\mathcal{M}}_{0;\mathit{PNC}}^{(g)}$ were performed for main effect models of WRAT scores over the PNC sample (n=2,327). Covariates there included age, sex, status of learning problem diagnosis, and genotyping platform (see Methods section). (a) F-tests of ${\mathcal{J}}_0^{(g)}$ were performed with statistic having 2 and 472 df. F-tests of ${\mathcal{M}}_0^{(g)}$ were performed with statistic having 1 and 474 df. F-tests of ${\mathcal{M}}_{0;\mathit{PNC}}^{(g)}$ were performed with statistic having 1 and 2,322 df. (b) FDR-adjustments were made to the p-values from 976,400 tests performed in the PING sample (n=479). (c) Information gain are for respective G×R and Main effect models over the PING sample (n=479). It represents the increase in adjusted R² for the respective model fit over that of the non-genetic base model including only the covariates. (e) Minor allele frequency is over the PING sample (n=479). (f) SNPs were genotyped with the Illumina Human660W-Quad Beadchip array and their positions correspond to HG build 19. See Supplementary Table 11 for minor alleles for the respective SNPs.

SNP	MAFe (Positionf)	p-valuea (FDRb)			Information gain c		Parameter estimates (standard error)
					Model		G×R model			Main effect model
		${\mathcal{J}}_0^{(g)}$	${\mathcal{M}}_0^{(g)}$	${\mathcal{M}}_{0;\mathit{PNC}}^{(g)}$	G×R	Main	αg	βg	γg	θg	θg;PNC
rs11633708	0.47 (87050708)	3.5E-08 (0.020)	2.3E-06 (0.24)	7.0E-04	7.89	4.27	−0.81 (0.18)	−0.90 (0.22)	0.44 (0.14)	−0.20 (0.04)	−0.100 (0.030)
rs4243100	0.45 (87037559)	4.0E-08 (0.020)	6.5E-05 (0.90)	4.6E-04	7.84	3.01	0.24 (0.17)	1.03 (0.21)	−0.54 (0.13)	0.17 (0.04)	0.102 (0.029)
rs11853362	0.44 (87057124)	1.7E-07 (0.034)	7.7E-05 (0.90)	6.9E-04	7.29	2.95	−0.90 (0.18)	−1.00 (0.22)	0.51 (0.14)	−0.15 (0.04)	−0.100 (0.029)
rs11632104	0.45 (87049894)	2.0E-07 (0.034)	3.0E-04 (0.97)	3.0E-04	7.23	2.44	0.24 (0.17)	1.00 (0.22)	−0.53 (0.13)	0.15 (0.04)	0.105 (0.029)
rs4887473	0.45 (87053206)	2.0E-07 (0.034)	3.0E-04 (0.97)	3.0E-04	7.23	2.44	0.24 (0.17)	1.00 (0.22)	−0.53 (0.13)	0.15 (0.04)	0.106 (0.029)
rs2011905	0.45 (87053846)	2.1E-07 (0.034)	3.1E-04 (0.97)	3.3E-04	7.21	2.42	0.24 (0.17)	1.00 (0.22)	−0.53 (0.13)	0.15 (0.04)	0.105 (0.029)