Table 1.

Significant Association in the SLIC Association Screen

SNP	Chromosome Position (bp – B36)	Gene	Alleles (A1/A2)	A1 CEPH Frequency	Typed Strand	p Quant	Effect Size	Heritability	p Emp QTDT	p Case-Cont	Frequency of A1 Cases	Frequency of A1 Controls	Odds ratio (95% CI)	p Emp PLINK
rs8051754	78,554,834	intergenic	T/C∗	0.46	−	0.0931	−0.28 ± 0.11	0.019	0.0892	0.0007∗	0.64	0.85	3.1 (1.6–6.0)	0.0018∗
rs4417561	78,568,860	intergenic	G∗/C	0.26	−	0.0244	−0.30 ± 0.11	0.022	0.0252	0.0004∗	0.37	0.15	3.2 (1.7–6.3)	0.0011∗
rs2316184	79,204,885	CDYL2	G/A∗	0.14	+	0.0032∗	-0.48 ± 0.12∗	0.045	0.0034∗	0.0096∗	0.15	0.30	2.5 (1.2–4.9)	0.0126
rs12927866	80,209,823	CMIP	A/G∗	0.47	−	0.4104	−0.27 ± 0.10	0.019	0.3581	0.0003∗	0.29	0.49	2.4 (1.5–3.9)	0.0004∗
rs4265801	80,222,553	CMIP	T∗/G	0.43	+	0.3446	−0.09 ± 0.09	0.030	0.5065	4 × 10−5∗	0.61	0.29	3.9 (2.0–7.6)	0.0393∗
rs7201632	80,234,949	CMIP	C/T∗	0.49	+	0.8966	−0.25 ± 0.09	0.017	0.7975	0.0004∗	0.36	0.56	2.3 (1.4–3.7)	0.0004∗
rs3785054	82,918,978	WFDC1	C∗/T	0.36	−	0.0044∗	−0.29 ± 0.10∗	0.019	0.0033∗	0.0089∗	0.34	0.20	2.0 (1.2–3.4)	0.0102
rs8053211	83,011,254	ATP2C2	A∗/G	0.46	+	5 × 10−5∗	−0.38 ± 0.09∗	0.040	3 × 10−5∗	0.0014∗	0.61	0.43	2.1 (1.3–3.3)	0.0029∗
rs11860694	83,014,948	ATP2C2	C∗/G	0.54	−	2 × 10−5∗	−0.37 ± 0.09∗	0.039	9 × 10−6∗	0.0018∗	0.61	0.43	2.1 (1.3–3.3)	0.0027∗
rs16973771	83,018,079	ATP2C2	G/A∗	0.48	−	0.0003∗	−0.35 ± 0.09∗	0.034	0.0006∗	0.0025∗	0.34	0.51	2.0 (1.3–3.2)	0.0036∗
rs2875891	83,021,410	ATP2C2	T/C∗	0.44	+	0.0057∗	−0.34∗ ± 0.10∗	0.031	0.0063∗	0.0022∗	0.30	0.47	2.1 (1.3–3.4)	0.0026∗
rs8045507	83,022,078	ATP2C2	T/C∗	0.48	−	0.0017∗	−0.33 ± 0.09∗	0.029	0.0020∗	0.0022∗	0.34	0.51	2.1 (1.3–3.3)	0.0028∗

Three significant SNPs fell within the CMIP gene, and five fell within ATP2C2. The remaining four significant SNPs were either intergenic or isolated signals of association. SNP alleles are given with the minor allele in the SLIC sample first. Putative risk alleles are marked with an asterisk. P Quant gives the p value for the quantitative, family-based analysis. p case-cont gives the p value for the case-control analysis. p values <0.01 are marked with an asterisk. The odds ratios indicate the ratio of case/control odds for each additional copy of the putative risk allele. Odds ratios were calculated within PLINK. The effect size is the estimated effect of each risk allele on the nonword repetition score (in SD ± SE). Effect sizes were calculated with MERLIN. Heritability gives the proportion of total variance explained by the SNP. Heritability estimates were calculated with MERLIN. The p Emp column gives empirical p values for the given SNP; these values were derived from permutations within QTDT or PLINK.