Figure 4: 3C Analysis at the 2q31 locus.

We systematically tested for interactions between the HOXD9 promoter and risk SNPs. We identified an interaction between a region containing rs2857532 and the HOXD9 promoter. (a) Map of the genomic region, showing the HOXD gene cluster and the fine mapped risk SNPs. (b) The interaction was verified by sequencing. (c) Agarose gel electrophoresis of ligation products. There was no ligation product in the absence of ligase (Lg). M, 100-bp molecular weight marker. (d) Quantification of 3C interaction frequencies between a constant fragment containing the HOXD9 promoter and each target fragment. In both cell lines, a peak of interaction is observed with the fragment containing the rs2857532 variant located 48 kb away from the constant fragment. The y axis refers to semi-quantitative PCR products from 3C libraries in both cell lines normalized by each interrogated ligation PCR product using BAC control template. The error bars represent the s.e.m.