SNP | SNP Location | RA (RAF) | CpG | CpG Location | CpG Gene | CpG Gene Groupa | Relation to CpG Islandb | ARIES Directionc | ARIES Effect Sized |
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rs798766 | chr4:1734239 | T (0.23) | cg00006948 | chr4:1768889 | Â | Â | Island | + | 0.004 |
rs401681 | chr5:1322087 | C (0.53) | cg27028750 | chr5:1349422 | Â | Â | S_Shelf | + | 0.059 |
cg26209169 | chr5:1316264 |  |  |  | – | 0.038 |
rs2294008 | chr8:143761931 | T (0.49) | cg06565975 | chr8:143823917 | SLURP1 | TSS200 | S_Shelf | – | 0.041 |
cg03405983 | chr8:143858548 | LYNX1 | 5’UTR/TSS200/1stExon | Island | – | 0.009 |
cg24023258 | chr8:143781297 | LY6K | TSS1500 | N_Shore | + | 0.004 |
cg17888033 | chr8:143858414 | LYNX1 | 5’UTR/1stExon | Island | – | 0.020 |
cg17252645 | chr8:143867129 | LY6D | Body |  | – | 0.042 |
rs8102137 | chr19:30296853 | C (0.32) | cg16836589 | chr19:30303674 | CCNE1 | 1stExon/Body | Island | – | 0.011 |
cg27475126 | chr19:30303651 | CCNE1 | 1stExon/Body | Island | – | 0.049 |
- aFunctional region of gene as indicated in v1.2 Illumina annotation: TSS1500 = 200–1500 bases upstream of the transcription start site; TSS200 = 0–200 bases upstream of the transcription start site; 5’UTR = 5 prime untranslated region; 1stExon = First segment of gene coding for peptide sequence; Body = Between ATG and stop codon; 3’UTR = Between stop codon and poly A signal; Multiple listings indicate locus is in a region with multiple splice variants
- bPosition relative to CpG island as indicated in v1.2 Illumina annotation: Island = CpG island (CG content > 50%, Obs/Exp CpG ratio > 0.60, and length > 200 bps); OpeanSea = Non-island region; Shore = 0–2 kb flanking CpG island; Shelf = 2–4 kb flanking CpG island
- cDirection of association between mQTL and CpG site reported in the ARIES mQTL database
- dEffect size (defined as the difference in median proportion methylated between homozygote groups) between mQTL and CpG site reported in the ARIES mQTL database
- Abbreviations: RA Risk allele; RAF Risk allele frequency