Skip to main content

Table 2 Selected mQTL and their associated CpG sites

From: Mediation by differential DNA methylation of known associations between single nucleotide polymorphisms and bladder cancer risk

SNP SNP Location RA (RAF) CpG CpG Location CpG Gene CpG Gene Groupa Relation to CpG Islandb ARIES Directionc ARIES Effect Sized
rs798766 chr4:1734239 T (0.23) cg00006948 chr4:1768889    Island + 0.004
rs401681 chr5:1322087 C (0.53) cg27028750 chr5:1349422    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
  1. 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
  2. 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
  3. cDirection of association between mQTL and CpG site reported in the ARIES mQTL database
  4. dEffect size (defined as the difference in median proportion methylated between homozygote groups) between mQTL and CpG site reported in the ARIES mQTL database
  5. Abbreviations: RA Risk allele; RAF Risk allele frequency