lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*

Numerator Metabolite

Structure of lignoceroyl sphingomyelin (d18:1/24:0)
Metabolite Accession: GCST90200020
Name: lignoceroyl sphingomyelin (d18:1/24:0)
Hmdb Id: HMDB0011697
Super Pathway: NA
Sub Pathway: NA
Inchikey: QEDPUVGSSDPBMD

Denominator Metabolite

Structure of sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Metabolite Accession: GCST90200017
Name: sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: LQINJRUGTUOHGS

Associated Genomic Regions

Region: rs4814176

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:
20
Beta (Ratio):
-0.178
Position:
12959398
SE (Ratio):
0.017
Effect Allele:
T
Z-score (Ratio):
-10.221
Reference Allele:
C
-log10(P):
-54.794
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.084
SE (Den):
0.015
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.5[1], 6[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.7[1], 8[2]

Ratio Explanation:

This ratio reflects the balance of very long-chain (C24:0) to shorter-chain sphingomyelins, indicating altered acyl-chain composition within the sphingolipid pathway.9[1]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic regulation via ISM1 likely alters hepatic lipid metabolism, influencing sphingomyelin composition.1[1], 4[2] This altered lipid profile, particularly the balance of sphingomyelin species, is linked to cholelithiasis, elevated LDL cholesterol, and ALT, indicating a role in disrupted cholesterol homeostasis.1[3], 10[4], 11[5]

Phenotype Driver:

Metabolite-centric[both]

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