Table 2.

List of Independent Transcriptome-wide Significant Loci

Locationa	MinP (TWAS)b	MinP (GWAS)c	MinP (MAGMA)d	Variance Explained (%)e	Jointly Significantf	Marginally Significantg
chr2:10923518-10952970	1.8 × 10−6	1.3 × 10−4	4.3 × 10−4	94.2	PDIA6	PDIA6
chr8:8998934-9002945	3.3 × 10−7	1.8 × 10−6	6.6 × 10−7	76.5	RP11-10A14.3	RP11-10A14.3
chr8:11700033-11725646	2.0 × 10−6	3.3 × 10−6	1.1 × 10−6	96.2	CTSB	CTSB
chr17:44344403-44346060	5.0 × 10−7	4.4 × 10−6	1.6 × 10−7	99.9	RP11-259G18.1	ARHGAP27, CRHR1-IT1, DND1P1, KANSL1, KANSL1-AS1, LRRC37A, LRRC37A4P, MAPT, RN7SL739P, RP11-259G18.1
chr20:21283941-21370463	1.8 × 10−8	2.0 × 10−9	1.9 × 10−9	84.5	XRN2	XRN2

GWAS, genome-wide association study; SNP, single nucleotide polymorphism; TWAS, transcriptome-wide association study.

^aChromosome and start/stop coordinates of the jointly significant gene.

^bMinimum p value across SNP weight sets for the jointly significant gene.

^cThe p value for top SNP association ±500 kb of the jointly significant gene.

^dThe p value of most significant gene in MAGMA analysis ±500 kb of the jointly significant gene.

^eProportion of the MinP (GWAS) association explained by the most significant TWAS feature in the region, calculated as 1 – (χ²-conditioned GWAS association/χ²-unconditioned GWAS association).

^fGenes that remain significant after accounting for variance explained by all nearby marginally significant genes.

^gGenes that are no longer significant after accounting for variance explained by surrounding jointly significant genes; associations are considered to be dependent if they are with 1 Mb of each other.