sphingomyelin (d18:1/20:0, d16:1/22:0)* to n-palmitoyl-sphinganine (d18:0/16:0)

Numerator Metabolite

Structure of sphingomyelin (d18:1/20:0, d16:1/22:0)*
Metabolite Accession: GCST90200001
Name: sphingomyelin (d18:1/20:0, d16:1/22:0)*
Hmdb Id: HMDB0012102
Super Pathway: NA
Sub Pathway: NA
Inchikey: AADLTHQNYQJHQV

Denominator 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

Associated Genomic Regions

Region: rs7412

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.327
Position:
45412079
SE (Ratio):
0.035
Effect Allele:
T
Z-score (Ratio):
-9.233
Reference Allele:
C
-log10(P):
-45.084
MAF:
0.084
Beta (Num):
-0.192
Novel Locus:
No
SE (Num):
0.027
Beta (Den):
0.136
SE (Den):
0.028
No CNV overlap
rQTL cluster:
8
Reaction Distance:
NA
Closest Genes:
APOE TOMM40 APOC1 PVRL2 APOC4

LLM Analysis

Numerator Metabolite Explanation:

Sphingomyelin biosynthesis, Ceramide metabolism.11[1], 12[2], 13[3], 14[4]

Denominator Metabolite Explanation:

De novo ceramide synthesis, Sphingolipid salvage pathway.15[1], 16[2], 17[3], 18[4], 19[5], 20[6], 21[7], 22[8]

Ratio Explanation:

The ratio reflects the conversion of ceramide (denominator) to sphingomyelin (numerator), a key step in sphingolipid metabolism potentially influenced by APOE's role in lipid transport.8[1], 23[2], 24[3], 25[4], 26[5]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

APOE genotype influences sphingolipid levels and is a major genetic risk factor for coronary atherosclerosis and myocardial infarction, likely through its central role in lipoprotein metabolism.27[1], 28[2], 29[3], 30[4], 31[5], 32[6], 33[7], 34[8], 35[9]

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