Fig. 6

Genetic polymorphisms have an effect on XCI status of variably escaping genes. a The number of genes with each XCI status call in the TCGA dataset made using Xi/Xa expression or DNAme, as compared to meta-status calls. Many of the genes escaping XCI by DNAme became variably escaping genes when the threshold for variable escape was lowered to 100 or more samples with each XCI status. b–i The percent of samples with each allele that were found with each XCI status at the most significant loci for our association analyses. The chromosomal location below the gene name is for the locus associated with the XCI status of the gene and is the location in hg38. The top row of graphs are the most significant loci associated with Xi/Xa-based XCI status calls from the autosomes (b) and X (c), along with the top loci associated with DNAme-based XCI status calls from the autosomes (d) and X (e). The second row is the most significant DNAmeQTL (f) and the three DNAmeQTL that are in the range to change XCI status (g–i). j–l DNAme values split by sex and allele for top loci by association with DNAme-based XCI status calls (j), the most significant DNAmeQTL (k), and the DNAmeQTLs in the range to change XCI status (l)