Identifying the impact of intergenic variants from meta-GWAS of Rheumatoid Arthritis

We performed an analysis of 489 GWAS variants that are associated with RA disease or are markers of RA drug efficacy. These variants were analyzed for: 1) their spatial interactions in three-dimensions, as captured by proximity ligation; 2) chromatin markers of regulatory functions (DNAse Hypersensitivity Sites, transcription factor binding site motifs, luciferase allele-specific SNP enhancer activity); and 3) their ability to affect linked gene expression (i.e. act as an eQTL). SNPs rs3184504, rs653178, and rs11545078 show evidence of differential long distance spatial associations in HL-60/S4 cells in undifferentiated versus differentiated cell states. RA associated variants at the SH2B3 locus (rs3184504/rs653178)) have a spatially-reinforced eQTL with BAZ2A, ~60Mb away, which affects platelet formation. Similarly, a variant at the GGH locus, which is associated with methotrexate toxicity, forms an inter-chromosomal spatially-reinforced eQTL with MGEA5, which is overexpressed in peripheral blood mononuclear cells. Overall design: Hi-C library preparation was adapted from Lieberman-Aiden et al. 2009. Genome-wide Hi-C analysis and contact maps were generated for each of the three cell types. The analysis pipeline included three programs for sequence alignment and analysis. The raw sequence files were aligned using bowtie and analyzed using HiCup v0.5.826 to produce a filtered set of mapped chromosome interactions. Following alignment, HOMER was used to identify significant structural interactions in each of the three cell types for both 75- and 500-kb bin sizes (both intra- and inter-chromosomal interactions).