Table 3.

Characteristics of High-Confidence Associations: Highly Significant, Colocalized, and Potentially Causal Features

Location	Gene	SNP Weight Set	TWAS z	TWAS p	Novela	Colocalization PP4b	FOCUS PIPc
chr1:71861623-72748417	NEGR1	GTEx whole blood	8.76	1.94 × 10−18	No	.99	1.00
chr5:87988462-87989789	CTC-467M3.3	GTEx frontal cortex	−7.09	1.33 × 10−12	No	.85	.84
chr7:12250867-12282993	TMEM106B	GTEx whole blood	5.53	3.18 × 10−8	Yes (GWAS)	.99	.61
chr14:42076773-42373752	LRFN5	GTEx cerebellum	5.60	2.17 × 10−8	No	.96	.50
chr14:64550950-64770377	ESR2	GTEx pituitary	−5.98	2.20 × 10−9	No	.86	.59
chr14:75319736-75330537	PROX2	GTEx thyroid	−5.76	8.51 × 10−9	Yes (TWAS)	.96	.72

Chr, chromosome; GTEx, Genotype-tissue expression; GWAS, genome-wide association study; PIP, posterior inclusion probability; PP, posterior probability; SNP, single nucleotide polymorphism; TWAS, transcriptome-wide association study.

^aGenes are novel compared with GWAS if >500 kb away from a lead GWAS variant and if their predicted expression is not correlated with GWAS variant (R² < .1). Genes are novel compared with previous TWASs of major depression if these did not identify them as statistically significant.

^bPP of colocalization.

^cPIP estimate of causality.