Characteristics of the top non-HLA SNPs from GWAS of ACPA-positive versus ACPA-negative RA for EIRA in comparison with NARAC and WTCCC studies
| EIRA ACPA-positive versus ACPA-negative | EIRA ACPA positive RA | EIRA ACPA negative RA | NARAC | WTCCC | Genotyping status* | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Reference sequence | Chromosome | ACPA positive | ACPA negative | p Value* | Minor allele | Allelic frequency in cases | Allelic frequency in controls | p Value† | Allelic frequency in cases | Allelic frequency in controls | p Value† | Allelic frequency in cases | Allelic frequency in controls | p Value† | Allelic frequency in cases | Allelic frequency in controls | p Value | EIRA | NARAC | WTCCC |
| rs4305317 | 2 | 777/1499 | 384/1132 | 3.86E-08 | T‡ | 0.34 | 0.33 | 0.453 | 0.25 | 0.33 | 2.32E-06 | 0.46 | 0.46 | 0.7962 | 0.48 | 0.45 | 0.008084 | gen | imp | imp |
| rs6448119 | 4 | 283/2007 | 116/1420 | 7.27E-06 | T | 0.12 | 0.12 | 0.5 | 0.08 | 0.12 | 8.98E-05 | 0.03 | 0.03 | 0.8406 | 0.03 | 0.02 | 0.5038 | gen/imp | imp | imp |
| rs2961663 | 5 | 237/2051 | 238/1308 | 4.37E-06 | T | 0.10 | 0.13 | 0.004487 | 0.15 | 0.13 | 0.05238 | 0.10 | 0.10 | 0.9345 | 0.09 | 0.10 | 0.127 | gen | gen | imp |
↵* Genotyping status referred as directly genotyped (‘gen’) or imputed (‘imp’).
↵† Cochran–Armitage trend test.
↵‡ Genotyping frequency for ACPA-negative RA group presented for opposite allele due to different direction of association.
ACPA, antibodies to citrullinated peptide antigens; EIRA, Swedish Epidemiological Investigation of Rheumatoid Arthritis; GWAS, genome-wide association studies; NARAC, North American RA Consortium; RA, rheumatoid arthritis; SNP, single nucleotide polymorphism; WTCCC, Wellcome Trust Case–Control Consortium.