Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant

Rodrigo de Almeida, Isis Ricaño Ponce, Vinod Kumar, Patrick Deelen, Agata Szperl, Gosia Trynka, Javier Gutierrez-Achury, Alexandros Kanterakis, Harm Jan Westra, Lude Franke, Morris A. Swertz, Mathieu Platteel, Jose Ramon Bilbao, Donatella Barisani, Luigi Greco, Luisa Mearin, Victorien M. Wolters, Chris Mulder, Maria Cristina Mazzilli, Ajit SoodBozena Cukrowska, Concepcion Nunez, Riccardo Pratesi, Sebo Withoff, Cisca Wijmenga*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

24 Citations (Scopus)
68 Downloads (Pure)


Using the Immunochip for genotyping, we identified 39 non-human leukocyte antigen (non-HLA) loci associated to celiac disease (CeD), an immune-mediated disease with a worldwide frequency of 1. The most significant non-HLA signal mapped to the intronic region of 70 kb in the LPP gene. Our aim was to fine map and identify possible functional variants in the LPP locus. We performed a meta-analysis in a cohort of 25 169 individuals from six different populations previously genotyped using Immunochip. Imputation using data from the Genome of the Netherlands and 1000 Genomes projects, followed by meta-analysis, confirmed the strong association signal on the LPP locus (rs2030519, P 1.79 10(49)), without any novel associations. The conditional analysis on this top SNP-indicated association to a single common haplotype. By performing haplotype analyses in each population separately, as well as in a combined group of the four populations that reach the significant threshold after correction (P 0.008), we narrowed down the CeD-associated region from 70 to 2.8 kb (P 1.35 10(44)). By intersecting regulatory data from the ENCODE project, we found a functional SNP, rs4686484 (P 3.12 10(49)), that maps to several B-cell enhancer elements and a highly conserved region. This SNP was also predicted to change the binding motif of the transcription factors IRF4, IRF11, Nkx2.7 and Nkx2.9, suggesting its role in transcriptional regulation. We later found significantly low levels of LPP mRNA in CeD biopsies compared with controls, thus our results suggest that rs4686484 is the functional variant in this locus, while LPP expression is decreased in CeD.

Original languageEnglish
Pages (from-to)2481-2489
Number of pages9
JournalHuman Molecular Genetics
Issue number9
Publication statusPublished - 1-May-2014



Cite this