n-stearoyl-sphingosine (d18:1/18:0)* to sphingomyelin (d18:0/20:0, d16:0/22:0)*

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

Metabolite Accession: GCST90200123
Name: sphingomyelin (d18:0/20:0, d16:0/22:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs7310409

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.181
Position:
121424861
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-10.451
Reference Allele:
G
-log10(P):
-57.189
MAF:
0.382
Beta (Num):
-0.083
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.098
SE (Den):
0.016
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):
0.203
Position:
64239351
SE (Ratio):
0.022
Effect Allele:
C
Z-score (Ratio):
9.074
Reference Allele:
T
-log10(P):
-43.614
MAF:
0.166
Beta (Num):
0.132
Novel Locus:
Yes ✔️
SE (Num):
0.020
Beta (Den):
-0.071
SE (Den):
0.020
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid biosynthesis/metabolism.7[1], 8[2], 9[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.7[1], 8[2], 9[3], 10[4]

Ratio Explanation:

An elevated ratio of n-stearoyl-sphingosine to sphingomyelin may indicate a disruption in sphingolipid metabolism, potentially influenced by HNF1A, where ceramide synthesis or sphingomyelin degradation is altered.4[1], 11[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

HNF1A regulates genes in sphingolipid metabolism.4[1], 5[2], 6[3] Altered HNF1A function can disrupt the balance between ceramide (a precursor to n-stearoyl-sphingosine) and sphingomyelin, which is associated with cholelithiasis and cardiovascular phenotypes like myocardial infarction.12[4], 13[5], 14[6], 11[7], 15[8]

Phenotype Driver:

Gene-centric:HNF1A

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