Table 3.
GTEx and RegulomeDB data on SNPs under positive selection in European populations (GBR, TSI, FIN). Given is also a summary of reported traits from the NHGRI-EBI GWAS catalogue. GTEx eQTLs–eGene interaction with p < 0.0001. RegulomeDB rank: 2b: TF binding + any motif + DNase Footprint + DNase peak; 3a: TF binding + any motif + DNase peak; 4–5: TF binding + DNase peak; 6: motif hit. The RegulomeDB probability score ranges from 0 to 1, with 1 being most likely to be a regulatory variant (for further details see54). Transcription factor HNF4A, an important regulatory element of the ALDH2 gene expression, is given in bold.
| GTEx | RegulomeDB | GWAS reported traits | ||||
|---|---|---|---|---|---|---|
| eQTL | eGene | Rank | Score | Chromatin state | Motif | |
| rs3184504 | ALDH2, LINC01405, TMEM116 | 3a | 0.67022 | Strong transcription; enhancers | MTF1 | Cardiovascular disease, blood pressure, ischemic stroke, glaucoma, rheumatoid arthritis, cancer, celiac disease, type I diabetes mellitus, parental longevity, inflammatory bowel disease, multiple sclerosis, blood cell count, hypothyroidism, haemoglobin measurement |
| rs4766578 | ALDH2, TMEM116 | 2b | 0.63936 | Strong transcription; enhancers | ESRRA, ESRRB, HNF4A, NR6A1 | Sjögren's syndrome, reticulocyte fraction of red cells, arthritis, vitiligo, HDL cholesterol, smoking status, coronary artery disease |
| rs10774625 | ALDH2, ADAM1B, TMEM116 | 5 | 0 | Strong transcription; enhancers | FOXJ2, FOXQ1 | Hypertension, myocardial infarction, coronary artery disease, asthma, cholesterol levels, systemic lupus erythematosus, urate measurement, life span, systolic blood pressure, hypothyroidism, glomerular filtration rate |
| rs597808 | ALDH2, LINC01405, ADAM1B | 5 | 0.13454 | Strong transcription | – | Systolic blood pressure, alcohol drinking, diastolic blood pressure, cholesterol levels, apolipoprotein B levels, colorectal cancer, allergic diseases, haematocrit, systemic lupus erythematosus, allergy |
| rs653178 | ALDH2, LINC01405 | 4 | 0.60906 | Active TSS; strong transcription; enhancers | – | Allergic disease, asthma, celiac disease, cholesterol level, eczema, Crohn's disease, chronic kidney disease, blood pressure, eosinophil counts, inflammatory bowel disease, type 1 diabetes, urate level |
| rs847892 | ALDH2, TMEM116, NAA25 | 6 | 0.20016 | Active TSS; strong transcription; enhancers | HNF4A | No data |
| rs2013002 | ALDH2, ADAM1B | 6 | 0.55195 | Active TSS; enhancers | MAFB, MAFK | Alcohol drinking and blood pressure |