sphingomyelin (d18:2/16:0, d18:1/16:1)* to sphingomyelin (d18:1/19:0, d19:1/18:0)*

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: 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

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.247
Position:
8289519
SE (Ratio):
0.020
Effect Allele:
C
Z-score (Ratio):
12.088
Reference Allele:
A
-log10(P):
-75.787
MAF:
0.192
Beta (Num):
0.056
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: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.273
Position:
12962718
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-16.456
Reference Allele:
G
-log10(P):
-138.433
MAF:
0.384
Beta (Num):
-0.074
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.199
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

Denominator Metabolite Explanation:

Sphingolipid metabolism

Ratio Explanation:

The ratio reflects the relative abundance of sphingomyelins with C16 fatty acids versus odd-chain (C19) and very-long-chain odd-chain fatty acids, potentially influenced by substrate availability or enzyme specificity.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variants in SPTLC3 are associated with altered sphingolipid profiles and cholelithiasis risk.5[1], 6[2], 7[3] Reduced SPTLC3 expression, linked to lower ceramide levels, may protect against gallstone formation by altering biliary lipid composition and reducing cholesterol crystallization.5[4], 8[5]

Phenotype Driver:

Gene-centric:SPTLC3

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