Extended Data Fig. 4: Features of caQTLs. | Nature Neuroscience

Extended Data Fig. 4: Features of caQTLs.

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

Extended Data Fig. 4

a, Flowchart for caQTL data analysis. b, PCA plot for ATAC-seq data on sex chromosomes (chrX and chrY), colored by sex from genotype data, showing sex could be called using ATAC-seq data. c, MDS plot for genotype data of HapMap3 and donors in this study, colored by populations from HapMap3 data. ASW: African ancestry in Southwest USA; CEU: Utah residents with Northern and Western European ancestry from the CEPH collection; CHB: Han Chinese in Beijing, China; CHD: Chinese in Metropolitan Denver, Colorado; GIH: Gujarati Indians in Houston, Texas; JPT: Japanese in Tokyo, Japan; LWK: Luhya in Webuye, Kenya; MEX: Mexican ancestry in Los Angeles, California; MKK: Maasai in Kinyawa, Kenya; TSI: Toscans in Italy; YRI: Yoruba in Ibadan, Nigeria. d, Neuron and progenitor caPeaks enrichment at epigenetically annotated regulatory elements from fetal brain (Epigenetics Roadmap ID = E081). e, Comparison of percent variance explained (r2) for shared neuron/progenitor caQTLs and fetal brain eQTLs (subset to the same sample size). P values are estimated by two-sided paired student-t tests. 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.

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