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Table 1 Enrichment analysis for mechanistically relevant features reveals similarities between normal and cancer ASM

From: Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs

Parameter

Normal ASMa

(N = 13,069)

OR (p value)

Cancer ASMb

(N = 4361)

OR (p value)

Same direction in cancer vs normal ASM?

Enrichment strength in cancer vs. normal

OR (p value)

ASM SNP is an ASB SNP

14.5 (< 1 × 10−999)

5 (3.1 × 10−32)

Yes: enriched

0.3 (2.8 × 10− 13)

Poised promoter

5.1 (< 1 × 10− 999)

5.6 (< 1 × 10− 999)

Yes: enriched

1.1 (0.069)

Polymorphic TFBS motifc

4.9 (2 × 10− 184)

2 (3.7 × 10− 34)

Yes: enriched

0.4 (6.4 × 10−28)

Weak promoter

4.4 (< 1 × 10− 999)

3.5 (3 × 10− 290)

Yes: enriched

0.8 (5.9 × 10−10)

Active promoter

4.1 (< 1 × 10− 999)

3.9 (2 × 10− 238)

Yes: enriched

1 (0.44)

Correlated polymorphic TF binding motifc

3.7 (< 1 × 10−999)

0.8 (0.3 × 10−4)

NO

0.2 (3 × 10− 106)

Weak/poised enhancer

2.7 (< 1 × 10−999)

1.5 (8.9 × 10− 45)

Yes: enriched

0.6 (1.4 × 10− 58)

Repetitive sequences

2.2 (3.8 × 10− 76)

1.9 (9.6 × 10− 16)

Yes: enriched

0.9 (0.083)

ASM SNP is eqtl SNP

2.2 (1.2 × 10−92)

1.9 (4.7 × 10−21)

Yes: enriched

0.9 (0.11)

Strong enhancer

2.2 (< 1 × 10−999)

1.3 (1.1 × 10−14)

Yes: enriched

0.6 (6.1 × 10−34)

ASM SNP is GWAS peak SNP

2 (2.2 × 10−32)

2 (9.1 × 10−12)

Yes: enriched

1 (0.97)

Insulator element

2 (5 × 10−214)

1.5 (9 × 10−19)

Yes: enriched

0.7 (5.11 × 10−11)

Polycomb repressed

2 (< 1 × 10−999)

1.9 (2 × 10−103)

Yes: enriched

1 (0.22)

ASM SNP in stringent block with GWAS peak SNP (autoimmune/inflammatory)

1.5 (1.7 × 10−17)

1.3 (0.0043)

Yes: enriched

0.9 (0.13)

ASM SNP in stringent block with GWAS peak SNP (cancers)

1.5 (3.8−15)

1.6 (9.5 × 10−9)

Yes: enriched

1.1 (0.39)

ASM SNP is GWAS peak or LD Rsq > =0.8

1.5 (3.7 × 10−40)

1.4 (2.1 × 10−9)

Yes: enriched

0.9 (0.2)

Active transcriptional state (txn)

1.3 (9.1 × 10−47)

1 (0.18)

No

0.7 (1.1 × 10−17)

ASM SNP in stringent block with GWAS peak SNP (all diseases/phenotype)

1.2 (1.7 × 10−13)

1.1 (0.0019)

Weak

1 (0.34)

Quiescent chromatind

0.3 (3 × 10− 274)

0.6 (9.5 × 10−35)

Yes: depleted

1.9 (2.1 × 10−30)

Chromatin deserte

0.2 (< 1 × 10−999)

0.5 (3.3 × 10−82)

Yes: depleted

3.1 (4 × 10−124)

  1. a“Normal ASM” is ASM in at least one non-cancer sample, allowing ASM in cancer samples
  2. b“Cancer ASM” is ASM present in cancer samples (including GM12878 LCL), but not in any normal sample
  3. cEnriched and correlated motifs determined on the complete set of ASM SNPs
  4. dHeterochromatin in at least one cell lines and no other states observed in the other cells
  5. eChromatin desert defined in the “Materials and methods” section