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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

From: Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics

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 O-sulfo L-tyrosine 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
  1. The last column represents the p-value in the replication analysis. Genes with asterisk are replicated