sphingomyelin (d18:1/18:1, d18:2/18:0) to 5-dodecenoylcarnitine (c12:1)

Numerator Metabolite

Structure of sphingomyelin (d18:1/18:1, d18:2/18:0)
Metabolite Accession: GCST90199878
Name: sphingomyelin (d18:1/18:1, d18:2/18:0)
Hmdb Id: HMDB0012101
Super Pathway: NA
Sub Pathway: NA
Inchikey: NBEADXWAAWCCDG

Denominator Metabolite

Metabolite Accession: GCST90200151
Name: 5-dodecenoylcarnitine (c12:1)
Hmdb Id: HMDB13326
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs603424

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:
10
Beta (Ratio):
0.212
Position:
102075479
SE (Ratio):
0.024
Effect Allele:
A
Z-score (Ratio):
8.769
Reference Allele:
G
-log10(P):
-40.856
MAF:
0.176
Beta (Num):
0.078
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
-0.134
SE (Den):
0.020
No CNV overlap
rQTL cluster:
67
Reaction Distance:
NA
Closest Genes:
PKD2L1 BLOC1S2 SCD CWF19L1 CHUK

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism, fatty acid biosynthesis.4[1], 5[2]

Denominator Metabolite Explanation:

Fatty acid beta-oxidation.6[1], 7[2]

Ratio Explanation:

The ratio likely reflects the balance between sphingomyelin synthesis, influenced by SCD-mediated oleic acid (18:1) production, and incomplete fatty acid beta-oxidation.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variation near SCD likely alters its activity, modifying lipid composition. This dyslipidemia is a known contributor to atherosclerosis, hypercholesterolemia, and myocardial infarction risk.8[1], 9[2]

Phenotype Driver:

Gene-centric:SCD

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