Analysis is made on the DNA methylation of the region (including a promoter region) upstream from the translation initiation point of a rheumatoid arthritis-associated gene DR3 in human genome. As a result, it is found out that an allele-specific methylation occurs in a CpG sequence located about −380 to −180 bp upstream from translation initiation point (ATG) of the gene DR3. It is further found out that the CpG sequences downstream therefrom of the genes DR3 originating in healthy subjects are all in the unmethylated state, while methylated and unmethylated sequences are both observed in the genes DR3 originating in RA patients.