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

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

Structure of sphingomyelin (d18:2/23:1)*
Metabolite Accession: GCST90200126
Name: sphingomyelin (d18:2/23:1)*
Hmdb Id: HMDB0240668
Super Pathway: NA
Sub Pathway: NA
Inchikey: PUTLJICFLAOKRD

Associated Genomic Regions

Region: rs7157785

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.162
Position:
64235556
SE (Ratio):
0.014
Effect Allele:
T
Z-score (Ratio):
-11.851
Reference Allele:
G
-log10(P):
-72.926
MAF:
0.166
Beta (Num):
-0.005
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.158
SE (Den):
0.018
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs364585

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.128
Position:
12962718
SE (Ratio):
0.011
Effect Allele:
A
Z-score (Ratio):
-12.154
Reference Allele:
G
-log10(P):
-76.584
MAF:
0.384
Beta (Num):
-0.068
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.060
SE (Den):
0.014
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid biosynthesis

Denominator Metabolite Explanation:

Sphingolipid biosynthesis

Ratio Explanation:

This ratio contrasts sphingomyelins with even very-long-chain fatty acids (C24) against those with odd-chain fatty acids (C23), likely reflecting ceramide synthase specificity.

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetically-driven variation in SPTLC3 expression alters *de novo* sphingolipid synthesis.4[1], 5[2] This change, reflected in the sphingomyelin profile, impacts lipoprotein metabolism and cholesterol homeostasis, increasing the risk of dyslipidemia and cholelithiasis.6[3], 7[4]

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