sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0) to sphingomyelin (d18:0/18:0, d19:0/17:0)*

Numerator Metabolite

Metabolite Accession: GCST90200047
Name: sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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: rs17101394

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):
0.265
Position:
64232386
SE (Ratio):
0.023
Effect Allele:
A
Z-score (Ratio):
11.552
Reference Allele:
G
-log10(P):
-69.404
MAF:
0.164
Beta (Num):
0.187
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.079
SE (Den):
0.021
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism, de novo lipogenesis.5[1], 6[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.7[1], 8[2]

Ratio Explanation:

This ratio reflects altered fatty acid precursor availability for ceramide synthesis, likely due to HNF1A dysregulation impacting de novo fatty acid synthesis and sphingolipid metabolism.9[1], 10[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

The HNF1A missense variant likely dysregulates hepatic lipid metabolism, altering sphingolipid composition.10[1], 3[2] This contributes to hypercholesterolemia, cholelithiasis, and atherosclerosis, which are observed associated phenotypes.11[3], 12[4], 13[5]

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