Table 1 Genomic loci significantly associated with lipid species.
From: An Amish founder population reveals rare-population genetic determinants of the human lipidome
SNP | Position | A1/A2 | A2_Freq_Amish | A2_Freq_Eur | Top associated trait | Effecta | P-value | Gene | Type | GOLDN effecta | GOLDN P-value |
|---|---|---|---|---|---|---|---|---|---|---|---|
Rare-population Amish-enriched loc | |||||||||||
rs5742904 | 2:21006288 | C/T | 0.0634 | 0.0004 | SM(d34:1) | 1.22 | 7.89E-25 | APOB | missense | - | - |
rs7863920 | 9:115987317 | G/A | 0.0433 | 0.0169 | GlcCer(d42:2) | −1.14 | 6.22E-18 | LINC00474 | intergenic | - | - |
rs76353203 | 11:116830637 | C/T | 0.0219 | 0.0008 | PE(36:2) | −1.45 | 6.29E-13 | APOC3 | nonsense | - | - |
rs147698408 | 12:50001009 | T/C | 0.0447 | 0.0159 | SM(d32:2) | −1.06 | 1.79E-14 | RACGAP1 | intronic | - | - |
rs536055318 | 17:4790207 | G/A | 0.0762 | 0.0014 | SM(d40:0) | −0.76 | 1.14E-12 | GLTPD2 | missense | - | - |
Common known loci | |||||||||||
rs887829 | 2:233759924 | C/T | 0.4194 | 0.3272 | androstenediol | 0.44 | 1.23E-15 | UGT1A,3,10 | intronic | −0.02 | 7.25E-01 |
rs3778167 | 6:11033235 | T/C | 0.2771 | 0.4233 | PC(42:5) | −0.40 | 3.65E-10 | ELOVL2 | intronic | −0.24 | 3.78E-06 |
rs174578 | 11:61838027 | T/A | 0.2515 | 0.3552 | PC(37:4) | −0.78 | 6.33E-36 | FADS2 | intronic | −0.43 | 2.32E-14 |
rs184061227 | 11:63073643 | A/G | 0.0555 | 0.0714 | estriol | 0.98 | 1.05E-15 | SLC22A24 | intergenic | −0.22 | 2.70E-02 |
rs10468017 | 15:58386313 | C/T | 0.2621 | 0.2869 | PE(36:4) | 0.48 | 7.32E-15 | LIPC | intergenic | 0.28 | 2.76E-07 |
rs1321940 | 20:12979237 | A/G | 0.5239 | 0.6014 | Cer(d43:1) | −0.69 | 3.37E-32 | LOC101929486 | intergenic | −0.45 | 2.95E-19 |
rs360525 | 20:13020644 | G/A | 0.0728 | 0.1240 | Cer(d43:1) | 0.86 | 5.34E-15 | SPTLC3 | intronic | 0.19 | 7.58E-03 |
