n-palmitoyl-sphinganine (d18:0/16:0) to sphingomyelin (d18:1/19:0, d19:1/18:0)*

Numerator Metabolite

Structure of n-palmitoyl-sphinganine (d18:0/16:0)
Metabolite Accession: GCST90200064
Name: n-palmitoyl-sphinganine (d18:0/16:0)
Hmdb Id: HMDB11760
Super Pathway: NA
Sub Pathway: NA
Inchikey: GCGTXOVNNFGTPQ

Denominator Metabolite

Metabolite Accession: GCST90200131
Name: sphingomyelin (d18:1/19:0, d19:1/18:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs7157785

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.361
Position:
64235556
SE (Ratio):
0.025
Effect Allele:
T
Z-score (Ratio):
-14.500
Reference Allele:
G
-log10(P):
-108.034
MAF:
0.166
Beta (Num):
-0.110
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
0.251
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs7412

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.256
Position:
45412079
SE (Ratio):
0.034
Effect Allele:
T
Z-score (Ratio):
7.573
Reference Allele:
C
-log10(P):
-30.940
MAF:
0.083
Beta (Num):
0.136
Novel Locus:
Yes ✔️
SE (Num):
0.028
Beta (Den):
-0.121
SE (Den):
0.026
No CNV overlap
rQTL cluster:
8
Reaction Distance:
NA
Closest Genes:
APOE TOMM40 APOC1 PVRL2 APOC4

LLM Analysis

Numerator Metabolite Explanation:

Ceramide synthesis, sphingolipid metabolism.7[1], 8[2], 9[3]

Denominator Metabolite Explanation:

Sphingomyelin synthesis, sphingolipid metabolism.10[1], 11[2], 12[3]

Ratio Explanation:

The ratio of precursor n-palmitoyl-sphinganine to product sphingomyelin reflects sphingolipid metabolic efficiency; altered ratios are associated with APOE dysfunction and cardiovascular risk.10[1], 13[2], 14[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

APOE variants alter lipoprotein metabolism, impacting the ceramide/sphingomyelin balance. Elevated ceramides are pro-atherogenic, contributing to dyslipidemia, atherosclerosis, and myocardial infarction, linking the gene to the phenotype.13[1], 15[2], 16[3]

Phenotype Driver:

Gene-centric:APOE

Downloads

Download the full rQTL summary statistics file for this metabolite ratio. Data contains the loci listed here. For each SNP (chromosome, effect_allele, reference_allele, pos_name, position) these columns contain the summary statistics of the ratio (beta, pgain, pval, se, z), the numerator metabolite (beta_1, pval_1, n_iids_1, effect_allele_frequency_1, se_1, z_1) and the denominator metabolite (beta_2, pval_2, n_iids_2, effect_allele_frequency_2, se_2, z_2)

Download rQTL Data