Extended Data Fig. 8: An example of a neuron-specific caQTL leading to regulatory mechanisms underlying GWAS loci. | Nature Neuroscience

Extended Data Fig. 8: An example of a neuron-specific caQTL leading to regulatory mechanisms underlying GWAS loci.

From: Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation

Extended Data Fig. 8

a, Numbers of colocalizations between ASCA and GWAS loci. b, The neuron-specific significant caQTL (caSNP: rs9930307; caPeak: chr16: 9,805,221-9,805,420) co-localized with schizophrenia GWAS locus (index SNP: rs7191183). c, Box plot for the caQTL (left, N = 61; P values are estimated by the mixed linear effects model using a two-sided test) and ASCA (right) (caSNP: rs9930307; caPeak: chr16: 9,805,221-9,805,420; P values are estimated by the negative binomial generalized linear models from DESeq2 using a two-sided test62). d, The expression of TFs in which motifs are disrupted by rs9930307. e, The motif logo of TP53 and the position disrupted by rs9930307. f, The box plot for luciferase signal for alleles of rs9930307 in progenitors (N = 8). P value is from two-sided paired student-t tests. (For box plots in (c) and (f), the center of the box is median of the data, the bounds of the box are 25th percentile and 75th percentile of the data, and the whisker boundary is 1.5 times the IQR. Maximum and minimum are the maximum and minimum of the data.).

Back to article page