Table 2 COJO genetic variants that explain association between local ancestry regions and metabolites
From: Ancestry-driven metabolite variation provides insights into disease states in admixed populations
Metabolite | Chr | LA ID | COJO rsID | Gene | Gene function | Driving ancestry (MAF) | AM joint P-value | Conditional joint P-value |
|---|---|---|---|---|---|---|---|---|
Alliin | 2 | 1579 | rs10189885 | ALMS1P1 | Intronic | EUR (—) | 2.77 × 10−10 | 9.00 × 10−2 |
N-acetylkynurenine (2) | 2 | 1579 | rs10189885a | ALMS1P1 | Intronic | AFR (—) | 4.13 × 10−12 | 2.87 × 10−1 |
N2-acetyllysine | 2 | 1579 | rs12620091 | ALMS1P1 | Intronicb | AFR (0.17) | 2.87 × 10−17 | 1.19 × 10−3 |
N-acetylglutamine | 2 | 1579 | rs13431529 | ALMS1P1 | Intronicb | AFR (0.6) | 6.05 × 10−12 | 6.29 × 10−1 |
N2-acetyllysine | 2 | 1579 | rs1881244 | ALMS1 | Intronic | AFR (0.85) | 2.87 × 10−17 | 3.47 × 10−3 |
N-acetylarginine | 2 | 1579 | rs1881244 | ALMS1 | Intronic | AFR (0.85) | 4.85 × 10−25 | 3.75 × 10−3 |
N-acetylasparagine | 2 | 1579 | rs1881244 | ALMS1 | Intronic | AFR (0.85) | 1.74 × 10−22 | 7.78 × 10−4 |
N-acetylglutamine | 2 | 1579 | rs1881244 | ALMS1 | Intronic | AFR (0.85) | 6.05 × 10−12 | 1.42 × 10−2 |
N-acetylleucine | 2 | 1579 | rs1881244 | ALMS1 | Intronic | AFR (0.85) | 2.07 × 10−19 | 1.52 × 10−4 |
N-acetyltyrosine | 2 | 1579 | rs1881244 | ALMS1 | Intronic | AFR (0.85) | 1.73 × 10−14 | 1.04 × 10−1 |
N-delta-acetylornithine | 2 | 1579 | rs28525015 | ALMS1P1 | Intronicb | AFR (0.61) | 6.15 × 10−24 | 3.17 × 10−4 |
N-acetylleucine | 2 | 1579 | rs28879089 | ALMS1 | Intronic | AFR (—) | 2.07 × 10−19 | 6.41 × 10−3 |
N-acetyltyrosine | 2 | 1579 | rs6546854 | ALMS1 | Intronic | AFR (0.62) | 1.73 × 10−14 | 1.86 × 10−1 |
2-Aminooctanoic acid | 2 | 1581 | rs72903325 | ACTG2 | Intronic | AFR (0.35) | 6.26 × 10−11 | 1.73 × 10−4 |
Androstenediol (3alpha, 17alpha) monosulfate (3) | 4 | 3592 | rs138040976 | GNRHR | Intronic | AFR (—) | 4.07 × 10−11 | 3.10 × 10−4 |
3-aminoisobutyrate | 5 | 4386 | rs191679549 | AGXT2 | Intronic | NAM (—) | 7.11 × 10−29 | 6.87 × 10−3 |
Betaine | 5 | 4546 | rs7736027 | DMGDH | Intronic | AFR (0.66) | 2.16 × 10−11 | 2.12 × 10−2 |
N-acetylglucosaminylasparagine | 6 | 5848 | rs2346120a | UNC93A | Intronic | NAM (—) | 3.20 × 10−9 | 1.67 × 10−2 |
S-1-pyrroline-5-carboxylate | 8 | 7373 | rs2242090 | PYCR3 | Exonicc | EUR (0.52) | 1.43 × 10−24 | 1.01 × 10−1 |
6-oxopiperidine-2-carboxylate | 8 | 7376 | rs11993782 | PLEC | Intronic | AFR (0.83) | 2.24 × 10−10 | 9.18 × 10−2 |
2′-O-methyluridine | 9 | 7977 | rs56023505 | PHYHD1 | UTR5 | AFR (0.44) | 3.35 × 10−10 | 4.56 × 10−3 |
Carnitine | 10 | 8412 | rs12415764 | ARID5B | Intergenic | NAM (0.24) | 2.32 × 10−11 | 5.37 × 10−5 |
N-methylpipecolate | 10 | 8587 | rs2147896 | PYROXD2 | Exonicc | EUR (0.35) | 2.02 × 10−46 | 1.39 × 10−3 |
MG 20:4 | 11 | 9120 | rs102274 | TMEM258 | Intronic | NAM (0.59) | 2.15 × 10−37 | 5.72 × 10−3 |
PC 16:0/18:2 | 11 | 9120 | rs11320420 | MYRF | Intronic | NAM (—) | 1.53 × 10−15 | 6.34 × 10−2 |
Stearidonic acid | 11 | 9120 | rs174556 | FADS1 | Intronic | NAM (0.57) | 1.30 × 10−19 | 3.60 × 10−4 |
1-arachidonoyl-GPC (20:4n6)b | 11 | 9120 | rs174562 | FADS2 | Intronic | NAM (0.59) | 7.02 × 10−76 | 1.02 × 10−4 |
PC 16:0/20:4 | 11 | 9120 | rs174562 | FADS2 | Intronic | NAM (0.59) | 1.04 × 10−69 | 1.72 × 10−4 |
Arachidonoylcholine | 11 | 9120 | rs174567 | FADS2 | Intronic | NAM (0.61) | 8.82 × 10−28 | 9.13 × 10−3 |
PC 18:2/18:2 | 11 | 9120 | rs3834458 | FADS2 | Intronic | NAM (0.58) | 5.97 × 10−26 | 4.87 × 10−3 |
LPC 18:2/0:0 | 11 | 9120 | rs3834458 | FADS2 | Intronic | NAM (0.58) | 8.16 × 10−11 | 1.23 × 10−1 |
Sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)b | 11 | 9120 | rs3834458 | FADS2 | Intronic | NAM (0.58) | 2.24 × 10−10 | 1.61 × 10−2 |
PE 16:0/18:2 | 11 | 9120 | rs5792235 | FADS2 | Intronic | NAM (0.59) | 5.40 × 10−29 | 4.02 × 10−2 |
PC 18:0/18:2 | 11 | 9120 | rs5792235 | FADS2 | Intronic | NAM (0.59) | 3.80 × 10−11 | 1.43 × 10−1 |
PE 18:0/18:2 | 11 | 9120 | rs5792235 | FADS2 | Intronic | NAM (0.59) | 2.32 × 10−22 | 7.67 × 10−2 |
LPC P-16:0 or LPC O-16:1 | 11 | 9121 | rs11230873 | FTH1 | Intergenic | NAM (0.26) | 1.60 × 10−10 | 9.49 × 10−5 |
MG 20:4 | 11 | 9149 | rs142021492 | — | — | NAM (—) | 2.93 × 10−9 | 2.21 × 10−3 |
3beta-hydroxy-5-cholestenoate | 11 | 9317 | chr11:110244360 | RDX | — | NAM (—) | 6.11 × 10−26 | 4.75 × 10−2 |
Ethylmalonate | 12 | 10132 | chr12:121176083 | ACADS | Exonicc | AFR (—) | 5.72 × 10−13 | 1.41 × 10−1 |
Ethylmalonate | 12 | 10,132 | rs73415734 | — | — | AFR (—) | 5.72 × 10−13 | 1.82 × 10−2 |
LPE 16:0/0:0 | 15 | 11487 | rs1077834 | LIPC | Intronicc | NAM (0.43) | 2.32 × 10−14 | 2.90 × 10−3 |
LPE 18:0/0:0 | 15 | 11487 | rs1077834 | LIPC | Intronicc | NAM (0.43) | 1.85 × 10−11 | 4.26 × 10−2 |
PE 16:0/20:4 | 15 | 11487 | rs2070895 | LIPC | Intronic | NAM (—) | 5.53 × 10−18 | 3.20 × 10−2 |
PE 18:0/20:4 | 15 | 11487 | rs2070895 | LIPC | Intronic | NAM (—) | 5.10 × 10−13 | 1.98 × 10−1 |
Cys-gly, oxidized | 16 | 12348 | chr16:89909429 | SPIRE | Intronic | NAM (—) | 1.46 × 10−29 | 4.68 × 10−2 |
Cysteinylglycine | 16 | 12348 | rs62068366 | SPATA2L | Intronic | NAM (0.28) | 8.45 × 10−10 | 3.14 × 10−2 |