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

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: GCST90200145
Name: glycosyl ceramide (d18:1/20:0, d16:1/22:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs12878001

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
14
Beta (Ratio):
-0.222
Position:
64239629
SE (Ratio):
0.022
Effect Allele:
G
Z-score (Ratio):
-10.292
Reference Allele:
T
-log10(P):
-55.531
MAF:
0.165
Beta (Num):
-0.066
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
0.156
SE (Den):
0.020
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs4814176

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
20
Beta (Ratio):
-0.210
Position:
12959398
SE (Ratio):
0.017
Effect Allele:
T
Z-score (Ratio):
-12.637
Reference Allele:
C
-log10(P):
-82.618
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.115
SE (Den):
0.016
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism, ceramide synthesis.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism, glycosphingolipid synthesis.8[1], 9[2], 10[3]

Ratio Explanation:

This ratio reflects the balance between sphingomyelin and glycosylceramide synthesis from a common ceramide precursor pool, potentially modulated by ISM1's metabolic signaling.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variation near the adipokine ISM1 alters its regulation of lipid metabolism.1[1], 2[2] This disrupts the balance of sphingolipids, contributing to dyslipidemia and increasing the risk of cholelithiasis, where abnormal lipid metabolism is a key driver.11[3], 12[4]

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