lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:0/20:0, d16:0/22:0)*

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

Metabolite Accession: GCST90200123
Name: sphingomyelin (d18:0/20:0, d16:0/22:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs364585

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):
-0.387
Position:
12962718
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-23.838
Reference Allele:
G
-log10(P):
-287.534
MAF:
0.384
Beta (Num):
-0.093
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.294
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 biosynthesis

Denominator Metabolite Explanation:

Sphingolipid biosynthesis

Ratio Explanation:

This ratio may reflect the relative activity of different SPTLC-containing enzyme complexes, influencing the fatty acid chain composition of sphingomyelins.

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

SPTLC3 genetic variants are associated with altered sphingolipid metabolism.1[1] Altered sphingomyelin levels, in turn, are linked to cholelithiasis, potentially through modulation of LDL-cholesterol.5[2], 6[3], 7[4] Higher total sphingomyelin levels have been associated with a protective effect against cholelithiasis, a relationship that appears to be mediated by LDL.5[5], 6[6], 7[7]

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