lignoceroyl sphingomyelin (d18:1/24:0) to n-stearoyl-sphinganine (d18:0/18:0)*

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 n-stearoyl-sphinganine (d18:0/18:0)*
Metabolite Accession: GCST90200448
Name: n-stearoyl-sphinganine (d18:0/18:0)*
Hmdb Id: HMDB0011761
Super Pathway: NA
Sub Pathway: NA
Inchikey: KZTJQXAANJHSCE

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):
-0.208
Position:
12962718
SE (Ratio):
0.023
Effect Allele:
A
Z-score (Ratio):
-9.111
Reference Allele:
G
-log10(P):
-43.956
MAF:
0.384
Beta (Num):
-0.093
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.115
SE (Den):
0.018
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid de novo biosynthesis.3[1], 5[2]

Ratio Explanation:

The ratio reflects altered sphingolipid metabolism, where higher levels of very-long-chain sphingomyelin and lower levels of a dihydroceramide may indicate shifts in ceramide synthesis or breakdown.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Altered ISM1 function may influence sphingolipid metabolism, contributing to changes in bile composition and increased LDL-cholesterol, thus promoting cholelithiasis.6[1], 7[2]

Phenotype Driver:

Gene-centric:ISM1

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