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. 2023 Aug 28;3(9):100399. doi: 10.1016/j.xgen.2023.100399

Figure 1.

Figure 1

Allele-specific open chromatin (ASoC) mapping in NGN2-Glut identifies strong ASoC at the SZ-associated VPS45 locus

(A) The strategy of generating NGN2-glutamatergic excitatory neurons from hiPSCs for bulk ATAC-seq and RNA-seq analysis.

(B) Circus plot showing SZ-credible-risk SNPs that exhibited ASoC (FDR <0.05) in NGN2-Glut, iN-Glut, or both.

(C) Allelic ratio correlation of SZ-associated ASoC SNPs (FDR <0.05) in iN-Glut and NGN2-Glut, n = 26.

(D) Cell-type-specific and allele-specific ATAC-seq read pile-ups flanking ASoC SNP rs2027349 at the SZ-associated VPS45 locus. The top track shows the PGC3 SZ GWAS probabilities of all the SNPs in this region. Aquamarine, total reads that contain rs2027349; dark blue, reads containing reference allele (G); dark red, reads containing alternative allele (A).