n-stearoyl-sphingosine (d18:1/18:0)* to sphingomyelin (d18:0/18:0, d19:0/17:0)*

Numerator Metabolite

Structure of n-stearoyl-sphingosine (d18:1/18:0)*
Metabolite Accession: GCST90200341
Name: n-stearoyl-sphingosine (d18:1/18:0)*
Hmdb Id: HMDB0004950
Super Pathway: NA
Sub Pathway: NA
Inchikey: VODZWWMEJITOND

Denominator Metabolite

Structure of sphingomyelin (d18:0/18:0, d19:0/17:0)*
Metabolite Accession: GCST90200056
Name: sphingomyelin (d18:0/18:0, d19:0/17:0)*
Hmdb Id: HMDB0012087
Super Pathway: NA
Sub Pathway: NA
Inchikey: JCELSEVNSMXGKA

Associated Genomic Regions

Region: rs2393791

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.154
Position:
121423956
SE (Ratio):
0.015
Effect Allele:
C
Z-score (Ratio):
-10.407
Reference Allele:
T
-log10(P):
-56.727
MAF:
0.382
Beta (Num):
-0.082
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.071
SE (Den):
0.016
No CNV overlap
rQTL cluster:
49
Reaction Distance:
1.0
Closest Genes:
HNF1A AC079602.1 C12orf43 OASL SPPL3

Region: rs8012828

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:
14
Beta (Ratio):
0.210
Position:
64233980
SE (Ratio):
0.019
Effect Allele:
T
Z-score (Ratio):
11.021
Reference Allele:
C
-log10(P):
-63.361
MAF:
0.166
Beta (Num):
0.132
Novel Locus:
Yes ✔️
SE (Num):
0.020
Beta (Den):
-0.078
SE (Den):
0.020
No CNV overlap
rQTL cluster:
47
Reaction Distance:
1.0
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

Sphingolipid metabolism, sphingomyelin synthesis.7[1], 8[2], 9[3]

Ratio Explanation:

This ratio reflects the balance between ceramide and its conversion to sphingomyelin. Increased SGPP1 activity can elevate the ceramide precursor, potentially raising the ratio.1[1], 10[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variation in SGPP1 may alter sphingolipid metabolism, increasing the ceramide/sphingomyelin ratio. Elevated ceramides are linked to lipotoxicity, promoting dyslipidemia, inflammation, and increasing risk for cholelithiasis and myocardial infarction.11[1], 12[2], 13[3], 14[4], 15[5]

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