tricosanoyl sphingomyelin (d18:1/23:0)* to sphingomyelin (d18:1/19:0, d19:1/18:0)*

Numerator Metabolite

Structure of tricosanoyl sphingomyelin (d18:1/23:0)*
Metabolite Accession: GCST90200034
Name: tricosanoyl sphingomyelin (d18:1/23:0)*
Hmdb Id: HMDB0012105
Super Pathway: NA
Sub Pathway: NA
Inchikey: SXZWBNWTCVLZJN

Denominator Metabolite

Metabolite Accession: GCST90200131
Name: sphingomyelin (d18:1/19:0, d19:1/18:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1466448

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:
19
Beta (Ratio):
0.246
Position:
8289519
SE (Ratio):
0.016
Effect Allele:
C
Z-score (Ratio):
15.063
Reference Allele:
A
-log10(P):
-116.386
MAF:
0.192
Beta (Num):
0.055
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
-0.191
SE (Den):
0.018
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

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):
-0.248
Position:
12959398
SE (Ratio):
0.013
Effect Allele:
T
Z-score (Ratio):
-18.603
Reference Allele:
C
-log10(P):
-176.182
MAF:
0.386
Beta (Num):
-0.048
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.200
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.3[1], 4[2]

Denominator Metabolite Explanation:

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

Ratio Explanation:

The ratio of tricosanoyl sphingomyelin (d18:1/23:0) to another long-chain sphingomyelin reflects altered ceramide synthase activity, specifically influencing the production of sphingomyelins with different fatty acid chain lengths.2[1]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variants near CERS4 and SPTLC3 alter the balance of sphingomyelin species by affecting the acyl-chain composition during synthesis.5[1], 2[2] This dysregulation impacts biliary lipid composition and liver function (ALT levels), which increases the risk for cholelithiasis, a phenotype with strong colocalization and MR evidence.6[3], 7[4], 8[5]

Phenotype Driver:

Metabolite-centric[tricosanoyl sphingomyelin (d18:1/23:0)* to sphingomyelin (d18:1/19:0, d19:1/18:0)*]

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