sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)* to n-palmitoyl-sphinganine (d18:0/16:0)

Numerator Metabolite

Metabolite Accession: GCST90200053
Name: sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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: rs7157785

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
0.419
Position:
64235556
SE (Ratio):
0.024
Effect Allele:
T
Z-score (Ratio):
17.344
Reference Allele:
G
-log10(P):
-153.486
MAF:
0.166
Beta (Num):
0.309
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
-0.110
SE (Den):
0.020
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):
-0.252
Position:
45412079
SE (Ratio):
0.033
Effect Allele:
T
Z-score (Ratio):
-7.674
Reference Allele:
C
-log10(P):
-31.723
MAF:
0.084
Beta (Num):
-0.117
Novel Locus:
Yes ✔️
SE (Num):
0.026
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:

Sphingolipid metabolism; Sphingomyelin synthesis.6[1], 7[2], 8[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism; Ceramide synthesis.6[1], 9[2], 10[3]

Ratio Explanation:

This ratio reflects the conversion of ceramide to sphingomyelin, a key step in sphingolipid metabolism, likely modulated by APOE-mediated transport of these lipids.7[1], 11[2]

Ratio Evidence:

canonical reaction, not mediated by an associated enzyme

Gene Ratio Phenotype Relationship:

APOE variants alter systemic lipid transport, reflected in the sphingomyelin/ceramide ratio; this dysregulation contributes to atherosclerosis and ischemic heart disease.12[1], 13[2], 14[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