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In vivo characterization of regulatory polymorphisms is a key requirement for next-generation human genetic analysis. Here we describe haploChIP, a method that uses chromatin immunoprecipitation (ChIP) and mass spectrometry to identify differential protein-DNA binding in vivo associated with allelic variants of a gene. We demonstrate this approach with the imprinted gene SNRPN. HaploChIP showed close correlation between the level of bound phosphorylated RNA polymerase II at the SNRPN locus and allele-specific expression. Application of the approach to the TNF/LTA locus identified functionally important haplotypes that correlate with allele-specific transcription of LTA. The haploChIP method may be useful in high-throughput screening for common DNA polymorphisms that affect gene regulation in vivo.

Original publication




Journal article


Nature genetics

Publication Date





469 - 475


Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.


Cell Line, Chromatin, Humans, RNA Polymerase II, Ribonucleoproteins, Small Nuclear, Autoantigens, Mass Screening, Precipitin Tests, Genetic Techniques, Transcription, Genetic, Genomic Imprinting, Protein Binding, Phosphorylation, Genotype, Haplotypes, Polymorphism, Genetic, Alleles, Models, Genetic, Time Factors, Mass Spectrometry, snRNP Core Proteins