Table 2 AA (African-American/non-white) population LoF-metabolite relationships at p-value 1e-6 or smaller. Effect sizes measured in standard deviation units to facilitate comparison. The column, “Human phenotypes related to metabolites” was obtained through Human Metabolome database, http://www.hmdb.ca/. LCAC: long-chain acylcarnitine
Gene | SNP | MAF | Metabolite | Path-way | Effect Size (Std.Error) | p-value | Metabolite related human phenotypes | Rep-lication p-value |
|---|---|---|---|---|---|---|---|---|
GPR97 | X16:57707232:G:C | 4 | glycocholenate-sulfate | Lipid | 1.09 (2.34) | 3e-11 | _ | NA |
oleate | Lipid | 1.79 (0.35) | 4e-07 | LCAC accumulation, Inflammation, Schizophrenia, Gestational diabetes | ||||
GGN | X19:38875072:G:A | 8 | androsten-3-beta-17-beta-diol-disulfate 1 | Lipid | 1.68 (0.27) | 1e-09 | – | NA |
xanthine | Nucleotide | 1.63 (0.28) | 4e-09 | Nervous system disorders, Renal failure | ||||
CYP2A13 | X19:41594954:C:T | 6 | pyroglutamine | Amino acid | 1.67 (0.33) | 5e-07 | Nervous system, and Metabolism & nutrition disorders | NA |
hydroxyphenyllactate | Amino acid | 1.87 (0.33) | 2e-08 | Supradiaphragmatic malignancy. Liver dysfunction | ||||
CLDN17 | X21:31538461:G:A | 8 | isoleucine | Amino acid | 1.96 (0.29) | 8e-12 | Heart failure, Leukemia, Maple syrup urine disease | NA |
glycerol | Lipid | 1.72 (0.29) | 2e-09 | Schizophrenia, Diabetes mellitus type 2 | ||||
CYP2A6 | X19:41351363:T:A | 6 | gamma-glutamylleucine | Peptide | 1.92 (0.28) | 1e-11 | NA | NA |
Gamma-glutamylthreonine | Peptide | 1.27 (0.30) | 1e-10 | – | ||||
ZSWIM1 | X20:44511257:G:A | 7 | Phenylacetyl-glutamine | Amino acid | 2.75 (0.35) | 4e-15 | NA | NA |
CRYBB3 | X22:25599863:G:T | 3 | trans-4-hydroxyproline | Amino acid | 2.19 (0.37) | 6e-09 | Renal disorder | NA |
STPG1 | X1:24727815:G:T | 3 | gamma-glutamyl-glutamate | Peptide | 2.49 (0.35) | 1e-12 | NA | NA |
CLSPN | X1:36208741:C:T | 7 | urea | Amino acid | 2.13 (0.28) | 1e-13 | Infection | NA |
CLEC4C | X12:7899913:C:A | 4 | nonadecanoate | Lipid | 2.36 (0.37) | 4e-10 | NA | NA |
BNIPL | X1:151016171:G:A | 3 | decanoylcarnitine | 2.17 (0.35) | 7e-10 | Medium-chain acyl-CoA dehydrogenase deficiency | NA | |
MAP10 | X1:232942469:G:A | 6 | oleate | Lipid | 2.07 (0.35) | 4e-09 | LCAC accumulation, Inflammation, Schizophrenia, Gestational diabetes | NA |
OR11G2 | X14:20666175:C:A | 22 | gamma-glutamylleucine | Peptide | 1.11 (0.18) | 9e-10 | NA | 0.03 |
FAM151A | X1:55075006:G:A | 6 | pregnendiol-disulfate | Lipid | 2.59 (0.35) | 2e-13 | Schizophrenia | NA |
APOA1BP | X1:156563265:C:T | 4 | leucine | Amino acid | 2.51 (0.35) | 9e-13 | Heart failure, Leukemia, Maple syrup urine disease | NA |
KIAA1755 | X20:36869005:G:A | 8 | eicosapentaenoate | Lipid | 2.08 (0.27) | 5e-14 | Essential hypertension | NA |
ELSPBP1 | X19:48523114:G:A | 4 | erythritol | Xenobiotics | 2.52 (0.38) | 2e-11 | Pentose phosphate pathway abnormalities | NA |
COASY | X17:40717487:A:G | 8 | gamma-glutamylglutamate | Peptide | 1.76 (0.29) | 4e-09 | NA | NA |
CD300C | X17:72540958:G:A | 4 | docosahexaenoylglycero-phosphoethanolamine1 | Lysolipid | 2.11 (0.30) | 2e-12 | NA | |
C16orf55 | X16:89724661:G:T | 11 | androsten-3-beta-17-beta-diol-disulfate 2 | Lipid | 1.98 (0.24) | 2e-16 | NA | NA |
C15orf32 | X15:93015466:A:T | 17 | glycerol-3-phosphate | Lipid | 1.11 (0.19) | 4e-09 | NA | 0.9 |
LTK | X15:41799325:G:A | 18 | urea | Amino acid | 1.14 (0.19) | 6e-09 | Infection | 0.6 |
AVEN | X15:34159987:G:A | 4 | urea | Amino acid | 1.71 (0.30) | 2e-08 | Infection | NA |
UPK2 | X11:118827917:G:A | 7 | glycerol | Lipid | 1.89 (0.30) | 3e-10 | Schizophrenia, Diabetes mellitus type2 | NA |
SLC25A27 | X6:46623768:G:A | 21 | – | 1.24 (0.20) | 1e-09 | NA | NA | |
DCLK3 | X3:36756821:A:C | 10 | phenylacetylglutamine | Amino acid | 1.62 (0.28) | 4e-09 | NA | NA |
TMPRSS3 | X21:43792873:A:G | 11 | phenylacetylglutamine | Amino acid | 2.04 (0.25) | 2e-16 | NA | NA |
GUCA1C | X3:108672558:C:A | 6 | glutarylcarnitine | Amino acid | 2.32 (0.35) | 4e-11 | NA | NA |
NWD1 * | X19:16908698:G:A | 22 | carboxy4methyl5propyl2furanpropanoate | Lipid | 0.97 (0.10) | 1e-06 | Psychiatric, kidney, cardiovascular and gastrointestinal disease, seizure | 1e-8 |
POLR1E * | X9:37495945:C:A | 21 | glycerol3phosphate | Lipid | 1.50 (0.23) | 2e-10 | Multi-infarct dementia | 3e-20 |
P2RX7 * | X12:121570899:G:T | 8 | tyrosine | Amino acid | 1.59 (0.32) | 7e-07 | Leukemia, Hypothyroidism, Myocardial infection, Schizophrenia, Epilepsy | 1e-7 |
CAPN11* | X6:44147355:G:A | 14 | aminobutyrate | Amino acid | 1.18 (0.23) | 7e-07 | Metabolism, hepatic disorder, Epilepsy, Aciduria, Febrile seizures, | 1e-7 |
OR11H4 * | X14:20711121:T:A | 22 | catecholsulfate | Xenobiotics | 1.24 (0.19) | 2e-10 | NA | 1e-7 |
C6orf25 * | X6:31692558:C:T | 10 | leucine | Amino acid | 1.85 (0.31) | 7e-09 | Heart failure, Leukemia, Maple syrup urine disease, Schizophrenia, Epilepsy | 8e-13 |
isoleucine | 1.79 (0.27) | 1e-10 | 5e-14 | |||||
valine | 1.72 (0.20) | 3e-09 | 2e-17 |