About 92% of the identified vGWAS SNPs mapped to MHC and the remaining mapped to PTPN22 – both were major RA associated loci in the conventional GWAS that in addition identified TNFAIP3 and TYK2 at the genome-wide significance level (P < 5.0e-08) (Fig. 2). This evidence concerns the gene TNFAIP3 and rheumatoid arthritis.