Table 4 Significant secondary associations identified around selected prostate cancer CpGs through conditional analysis of predictor meQTL SNPs.

From: Integrative multi-omic analysis identifies genetically influenced DNA methylation biomarkers for breast and prostate cancers

CpG

Chr

Location (bp)

Cytoband

meQTL SNP

Location (bp)

Effect allele

Prostate cancer GWAS results

Conditional analysis, LD from 1000 G phase 3 (EUR)

Frequency

β

PGWAS

Pcond*

cg14752965, cg14720773, cg27208169, cg06775073, cg17844831, cg19447962, cg10870160, cg08129017

17

17579346, 17603531, 17603584, 17603749, 17604146, 17628656, 17695459, 17728660

 

rs9899634

17727943

A

0.637

−0.040

9.47 × 10−7

–

 

rs55888125

18505676

T

0.519

−0.024

7.41 × 10−3

6.79 × 10−3

 

rs7225876

17178553

T

0.658

−0.019

2.97 × 10−2

3.96 × 10−3

17p11.2

rs75534953

17300299

A

0.053

−0.046

3.60 × 10−2

7.91 × 10−3

 

rs4641803

16936194

T

0.124

−0.025

5.83 × 10−2

3.20 × 10−3

 

rs77287723

17508656

C

0.081

0.018

2.26 × 10−1

2.05 × 10−2

 

rs8079130

16884960

T

0.142

0.029

1.13 × 10−2

3.99 × 10−2

  1. Chr chromosome.
  2. *At each CpG site, the Pcond for a meQTL SNP is the association significance after conditioning on all the meQTL SNPs present in the rows above. For example, the Pcond of rs4641803 is calculated after conditioning on rs9899634, rs55888125, rs7225876 and rs75534953.
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