sphingomyelin (d18:2/16:0, d18:1/16:1)* to glycosyl ceramide (d18:1/20:0, d16:1/22:0)*

Numerator Metabolite

Metabolite Accession: GCST90199947
Name: sphingomyelin (d18:2/16:0, d18:1/16:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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: rs1871194

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.222
Position:
8283819
SE (Ratio):
0.016
Effect Allele:
C
Z-score (Ratio):
13.537
Reference Allele:
A
-log10(P):
-94.457
MAF:
0.462
Beta (Num):
0.038
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.184
SE (Den):
0.016
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs686548

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.190
Position:
12973521
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-11.790
Reference Allele:
T
-log10(P):
-72.199
MAF:
0.387
Beta (Num):
-0.075
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 synthesis/metabolism.3[1], 4[2]

Denominator Metabolite Explanation:

Glycosphingolipid biosynthesis.5[1], 6[2], 7[3]

Ratio Explanation:

This ratio reflects the metabolic fate of ceramides produced by CERS4, indicating a shift toward sphingomyelin synthesis over glycosylceramide production from shared precursors.2[1], 4[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetically driven CERS4 expression alters the balance of sphingomyelin and glycosylceramide.2[1], 8[2] This dysregulation of sphingolipid metabolism is a known contributor to cholelithiasis (gallstones), gout, and altered liver enzymes by affecting bile composition and inflammatory processes.9[3], 10[4], 11[5], 12[6], 13[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