Table 1 Summary of nominally significant burden results

Case–control	Trait	SNP subset	Test	Average excess of variants in cases	Optimised MAF threshold (N. SNP)	P-value
	rMDD	RegPot	BURDEN	1.39	—	0.044
	rMDD	PhastCon	VTTEST	1.20	0.0018 (31)	0.022
Quantitative traits	Trait	SNP subset	Test	Effect size (beta)	Optimised MAF threshold (N. SNP)	P-value
	Symptoms of depression^a	TFBS	BURDEN	0.062	—	0.032
	Moray House Test at age 70^b	PhastCon	VTTEST	−0.074	0.0013 (21)	0.030
	Moray House Test at age 70 adjusted for the Moray House Test score at age 11^b	CpG	VTTEST	−0.064	0.00060 (2)	0.047
	Moray House Test at age 11^b	Coding	VTTEST	−0.101	0.00070 (12)	0.028
	Moray House Test at age 11^b	CpG	VTTEST	−0.097	0.31(3)	0.040

Abbreviations: MAF, minor allele frequency; rMDD, recurrent major depressive disorder; SNPs, single-nucleotide polymorphisms.
See main text for trait descriptions and Supplementary Table S8 for results on all diagnoses and traits. Quantitative trait analysis was one-tailed under the hypothesis that an increased burden of minor alleles would reduce scores for cognitive traits and increase scores for anxiety, depression and neuroticism.
References for all quantitative traits are available in the open-access Lothian Birth Cohort protocol paper (Deary et al.⁶⁰). Coding: SNPs in protein-coding regions of exons including both synonymous and non-synonymous SNPs. PCon, SNPs within regions of conservation in placental mammals (PhastCon, UCSC). RegPot: SNPs with putative regulatory potential (UCSC, 7 x regulatory potential). CpG: SNPs in CpG islands commonly associated with promoter regions.
^aTested using the Hospital Anxiety Depression Scales.
^bThe Moray House Test is the general cognitive test—mostly a verbal reasoning, IQ-type test—that was used in the Scottish Mental Survey 1947.

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