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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