Table 5 Top ten SNPs with the strongest effects from whole-genome/methylome prediction using Bayes-B and fitting all SNPs as random effects.
SNP name | Chromosome: base pair | Alleles | Major allele | MAFa | Gene nameb | Distance from gene | Effect |
|---|---|---|---|---|---|---|---|
rs1004664 | 14: 24424005 | G/T | T | 0.3756 | KH and NYN domain containing (KHNYN) | Body | −0.00016 |
rs513203 | 12: 63545960 | A/G | A | 0.4643 | A ncRNA class with ensemble code ID LOC105369797 | Body | −0.00015 |
rs2077507 | 3: 11576994 | A/G | A | 0.2875 | Vestigial-like family member 4 (VGLL4) | Body | −0.00014 |
rs11179382 | 12: 72820377 | C/T | T | 0.2686 | A lncRNA with ensemble code ID ENSG00000258235 | 91.53 Kb downstream | −0.00014 |
rs2911738 | 8: 71674057 | A/C | A | 0.3361 | A lincRNA with ensemble code ID ENSG00000254277 | 1.24 Kb upstream | −0.00013 |
rs2395175 | 6: 32437249 | A/G | G | 0.0982 | Major histocompatibility complex, class II, DR alpha (HLA-DRA) | 2.59 Kb upstream | −0.00013 |
rs8049226 | 16: 52423230 | A/G | G | 0.3672 | An uncategorized gene with ensemble code ID ENSG00000279427 | 13.54 Kb upstream | −0.00013 |
rs1364616 | 8: 71654009 | G/T | G | 0.3321 | A lincRNA with ensemble code ID ENSG00000254277 | 21.29 Kb upstream | −0.00012 |
rs6797550 | 3: 76747494 | A/G | G | 0.3281 | Sapiens roundabout guidance receptor 2 (ROBO2) | Body | −0.00012 |
rs2595415 | 11: 6897324 | C/T | C | 0.2821 | A ncRNA LOC107984019 (uncharacterized) | Body | −0.00012 |
