sphingomyelin (d18:2/24:1, d18:1/24:2)* to sphingomyelin (d18:2/21:0, d16:2/23:0)*

Numerator Metabolite

Metabolite Accession: GCST90200040
Name: sphingomyelin (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200129
Name: sphingomyelin (d18:2/21:0, d16:2/23:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs11666866

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.133
Position:
8285607
SE (Ratio):
0.014
Effect Allele:
A
Z-score (Ratio):
-9.605
Reference Allele:
G
-log10(P):
-48.623
MAF:
0.413
Beta (Num):
-0.064
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.070
SE (Den):
0.014
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs4814175

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.134
Position:
12959094
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-9.969
Reference Allele:
T
-log10(P):
-52.230
MAF:
0.386
Beta (Num):
-0.068
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.066
SE (Den):
0.013
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2], 6[3]

Ratio Explanation:

The ratio reflects the relative activity of ceramide synthases, where CERS4 contributes to the synthesis of ceramides that are precursors to the numerator sphingomyelins.1[1], 2[2]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4 variants may alter sphingomyelin composition, influencing lipid metabolism.7[1], 8[2] Altered sphingomyelin profiles have a protective association with cholelithiasis, potentially mediated by LDL cholesterol levels, and are linked to ALT levels, suggesting a role in liver health.9[3], 10[4]

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