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Table 3 Examples of hap-ASM DMRs associated with eQTLs and GWAS peaks

From: Genetic–epigenetic interactions in cis: a major focus in the post-GWAS era

Hap-ASM DMR index SNP in haplotype block 5

Regulome-DB score

Genes in 150-kb window

Genes with cis-eQTLs in haplotype block

GWAS index SNPs and disease associations in haplotype block

rs9535274

1b

RCBTB1; ARL11; EBPL

RCBTB1; ARL11; EBPL

rs9568281: multiple sclerosis

rs9330298

2a

S100A* cluster; CHTOP; SNAPIN; ILF2; NPR1; MIR8083

S100A1, S100A13

rs7536700: multiple myelomab

rs12789117

5

JAM3; NCAPD3; VPS26B

JAM3; NCAPD3; VPS26B

rs1267813: schizophrenia

rs11223731: memory performance

rs1031381: neuropsychological test

rs478881: fasting blood insulin

rs2517646

1b

TRIM* cluster

TRIM10

rs2523989: type I diabetes

rs2021722: schizophrenia, bipolar disorder

rs994379

1f

HIST1H* cluster; BTN3A2

HIST1H* cluster; BTN3A2

rs61747867: schizophreniab

rs8176749

5

OBP2B; ABO; SURF6

ABO, SURF6

rs633862: ovarian cancerb

rs495828: thromboembolism

rs8176722, rs8176719: malaria

rs579459: coronary heart disease

rs861855

1b

UBE2L3; YDJC; CCDC116; SDF2L1; MIR301B; MIR130B; PPIL2; YPEL1

CCDC116; YDJC; UBE2L3

rs181359, rs2256609: Crohn’s disease

rs131654: systemic lupus erythematosus

rs2266961: inflammatory bowel disorder

rs2256609: Crohn’s disease

rs4821116: hepatitis B infection rs2298428: celiac diseaseb

rs1627982

4

HLA-H; HCG4B; HLA-A; HCG9; ZNRD1-AS1

HLA-A; HCG9; HCG4; ZNRD1; HLA-H

rs2523809: serum IgE

rs2860580: nasopharyngeal cancer

rs2524005: schizophrenia, bipolar disorder

rs189370103: smoking behavior

rs62396301a

4

UNC5CL; TSPO2; APOBEC2; OARD1; NFYA; ADCY10P1; TREML1; TREM2

NFYA; APOBEC2

rs75932628: Alzheimer’s disease

rs2294693: gastric cancerb

  1. The hap-ASM data are from our published study [49], with confirmation by additional unpublished Methyl-seq data (CD and BT; unpublished data). Of these nine loci, six were also covered and found to have ASM or mQTLs in one or more cell types by Cheung et al. [53]. Regulome-DB scores for the hap-ASM index SNPs are from RegulomeDB (http://www.regulomedb.org/). The scores ranged from 1a to 6, with 1 assigned to putative regulatory SNPs with the highest level of confidence, supported by multiple data types, including eQTLs, TF binding, TF motifs, DNAse footprints, and DNAse hypersensitivity peaks [20]. Cis-eQTLs were downloaded from National Heart, Lung and Blood Institute (NHLBI)-GRASP Build 2.0 [46], only genes with eQTL p value <10−05 are listed. Haplotype blocks were defined using 1000 Genomes project (phase 3) [182] and PLINK (Gabriel’s approach) data [183, 184]. The S100A* cluster includes: S100A4; S100A3; S100A2; S100A16; S100A14; S100A13; and S100A1. The HIST1H* cluster includes: HIST1H1D; HIST1H4F; HIST1H4G; HIST1H3F; HIST1H2BH; HIST1H3G; HIST1H2BI; and HIST1H4H. The TRIM* cluster includes: TRIM10; TRIM15; and TRIM26. Multiple eQTLs have been identified in the haplotype blocks; in the eight first examples, at least one of the eQTLs was also an ASM index SNP, suggesting that these SNPs are regulatory SNPs
  2. aIndex eQTL reported in NHLBI-GRASP is rs6926079, in the same haplotype block as rs62396301 (R2 = 0.975, D′ = 1)
  3. bSub-threshold GWAS peaks (5 × 10–6 < p value < 5 × 10–8)
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Genome Biology

ISSN: 1474-760X

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