using IMPUTE2 with the 1000 Genomes phase 1 v3 European samples as the reference panel, phasing was done with SHAPEIT, and SNPs with imputation quality score (“INFO”) > 0.50 were retained. To replicate the PrediXcan RA findings that meet genome-wide significance, we utilized the DGN whole blood elastic net prediction models (as we had done in the discovery WTCCC data). We estimated the genetically regulated gene expression level GReX^EN in the replication samples and performed logistic regression with disease status.
