Extended Data Fig. 1: Highlighted Regional Miami plots of GWAS and TWAS results.
corresponding to the genomic region of (a) GABRA1, (b) CYP7B1, (c) DCC, (d) CTTNBP2, (e) FURIN and (f) GIGYF2 genes/transcripts (1Mbp window from start site). Top panels: GWAS results (dots colored according to European ancestry linkage disequilibrium r2 with top SNP): The x-axis shows genomic position, and the y axis shows significance as –log10(P) of z statistics (two-sided nominal P values); blue line corresponds to P = 1 × 10−5, orange line to P = 5 × 10−8 (genome-wide significance). Bottom panels: TWAS results: The x-axis shows genomic position. The y axis shows significance as –log10(P) of z statistics (two-sided nominal P values) for genes represented by both gene expression and isoform expression. Black triangles facing upwards or downwards for a positive or negative association z-score (Wald test; two-sided P values) respectively (up- or down-regulation); transcripts with Bonferroni-adjusted (for all reliably imputed transcripts) P value < 0.1 are labeled; orange line corresponds to Bonferroni-adjusted P = 0.05. Each Bonferroni-significant transcript is connected with lines to the SNPs contributing to its transcriptomic imputation model; lines are gray when the SNPs have a P>1 × 10−5, blue when P < 1 × 10−5 but orange when P < 5 × 10−8. The SNPs that are above the blue line and contribute to the transcriptomic imputation models of significant transcripts are labeled. See Supplementary Fig. 10-1 to 10-88 and Supplementary Table 10.
