A method of identifying mutations in alleles of a gene which may be causative of dysregulation of the expression levels of the alleles of the gene in a target eukaryotic cell, wherein the mutations are in regulatory elements which control the expression of individual alleles of the gene and wherein the regulatory elements are outside the body of the gene, the method comprising the steps of: for a plurality of genes from one or more target eukaryotic cells, (a) obtaining pre-mRNAs of at least two alleles of the genes; and (b) determining the ratios (R i,j) between the amounts of pre-mRNAs of one or more pairs of alleles (i,j) of the genes; wherein when R i,j ≠ 1 for a pair of alleles (i,j) of a gene, or in response to determining that R i,j ≠ 1 for a pair of alleles (i,j) of a gene, the method additionally comprises the steps: (c) determining the nucleotide sequences of that pair of alleles; and (d) comparing the nucleotide sequences of that pair of alleles in order to identify sequence differences between the nucleotide sequences of that pair of alleles; (e) attributing all of the sequence differences to a specific allele to determine allelic skew across the whole gene; wherein the method is performed in a phased genome sequence, and (f) linking these sequence differences with sequence variation in a regulatory element outside the body of the gene. wherein the mutations are in regulatory elements which control the expression of individual alleles of the gene and wherein the regulatory elements are outside the body of the gene, the method comprising the steps of: for a plurality of genes from one or more target eukaryotic cells, (a) obtaining pre-mRNAs of at least two alleles of the genes; and (b) determining the ratios (R i,j) between the amounts of pre-mRNAs of one or more pairs of alleles (i,j) of the genes; wherein when R i,j ≠ 1 for a pair of alleles (i,j) of a gene, or in response to determining that R i,j ≠ 1 for a pair of alleles (i,j) of a gene, the method additionally comprises the steps: (c) determining the nucleotide sequences of that pair of alleles; and (d) comparing the nucleotide sequences of that pair of alleles in order to identify sequence differences between the nucleotide sequences of that pair of alleles; (e) attributing all of the sequence differences to a specific allele to determine allelic skew across the whole gene; wherein the method is performed in a phased genome sequence, and (f) linking these sequence differences with sequence variation in a regulatory element outside the body of the gene. for a plurality of genes from one or more target eukaryotic cells, (a) obtaining pre-mRNAs of at least two alleles of the genes; and (b) determining the ratios (R i,j) between the amounts of pre-mRNAs of one or more pairs of alleles (i,j) of the genes; (a) obtaining pre-mRNAs of at least two alleles of the genes; and (b) determining the ratios (R i,j) between the amounts of pre-mRNAs of one or more pairs of alleles (i,j) of the genes; wherein when R i,j ≠ 1 for a pair of alleles (i,j) of a gene, or in response to determining that R i,j ≠ 1 for a pair of alleles (i,j) of a gene, the method additionally comprises the steps: (c) determining the nucleotide sequences of that pair of alleles; and (d) comparing the nucleotide sequences of that pair of alleles in order to identify sequence differences between the nucleotide sequences of that pair of alleles; (e) attributing all of the sequence differences to a specific allele to determine allelic skew across the whole gene; (c) determining the nucleotide sequences of that pair of alleles; and (d) comparing the nucleotide sequences of that pair of alleles in order to identify sequence differences between the nucleotide sequences of that pair of alleles; (e) attributing all of the sequence differences to a specific allele to determine allelic skew across the whole gene; wherein the method is performed in a phased genome sequence, and (f) linking these sequence differences with sequence variation in a regulatory element outside the body of the gene.