lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:2/21:0, d16:2/23:0)*

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: GCST90200129
Name: sphingomyelin (d18:2/21:0, d16:2/23:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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):
-0.160
Position:
12959398
SE (Ratio):
0.017
Effect Allele:
T
Z-score (Ratio):
-9.202
Reference Allele:
C
-log10(P):
-44.799
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.066
SE (Den):
0.013
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2], 6[3]

Ratio Explanation:

This ratio reflects the balance of a very-long-chain (lignoceroyl) sphingomyelin to other sphingomyelin species, which may be influenced by overall lipid and ceramide synthesis regulation.4[1]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 suppresses hepatic lipid synthesis.1[1], 7[2], 2[3] Altered ISM1 function could disrupt hepatic lipid homeostasis, including sphingolipid metabolism, potentially contributing to the pro-lithogenic environment of cholelithiasis, a condition linked to altered cholesterol and lipid metabolism.8[4], 9[5], 10[6]

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