stearoyl sphingomyelin (d18:1/18:0) to sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*

Numerator Metabolite

Structure of stearoyl sphingomyelin (d18:1/18:0)
Metabolite Accession: GCST90200335
Name: stearoyl sphingomyelin (d18:1/18:0)
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

Denominator Metabolite

Structure of sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*
Metabolite Accession: GCST90200134
Name: sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: JONXXLXMISNQNG

Associated Genomic Regions

Region: rs2244608

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.143
Position:
121416988
SE (Ratio):
0.018
Effect Allele:
G
Z-score (Ratio):
-8.118
Reference Allele:
A
-log10(P):
-35.282
MAF:
0.318
Beta (Num):
-0.072
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.071
SE (Den):
0.017
No CNV overlap
rQTL cluster:
49
Reaction Distance:
NA
Closest Genes:
HNF1A AC079602.1 C12orf43 OASL SPPL3

Region: rs12897637

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
0.234
Position:
64239351
SE (Ratio):
0.022
Effect Allele:
C
Z-score (Ratio):
10.671
Reference Allele:
T
-log10(P):
-59.536
MAF:
0.165
Beta (Num):
0.176
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.058
SE (Den):
0.021
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs2336168

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.284
Position:
8288542
SE (Ratio):
0.021
Effect Allele:
C
Z-score (Ratio):
-13.615
Reference Allele:
T
-log10(P):
-95.521
MAF:
0.197
Beta (Num):
-0.230
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.055
SE (Den):
0.020
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism, Ceramide synthesis.3[1], 6[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism, Ceramide synthesis.3[1], 7[2], 8[3]

Ratio Explanation:

This ratio likely reflects the activity of CERS4, which produces C18:0 ceramide (a precursor to the numerator), relative to enzymes producing very-long-chain ceramide precursors.3[1], 9[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variants impacting CERS4 function can alter the composition of sphingomyelin species, which are critical for cell membrane structure and signaling.10[1], 11[2] This dysregulation is a plausible mechanism contributing to associated phenotypes like coronary atherosclerosis and hypercholesterolemia.11[3], 12[4], 13[5]

Phenotype Driver:

Gene-centric:CERS4

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