sphingomyelin (d18:0/18:0, d19:0/17:0)* to n-stearoyl-sphingadienine (d18:2/18:0)*

Numerator 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

Denominator Metabolite

Structure of n-stearoyl-sphingadienine (d18:2/18:0)*
Metabolite Accession: GCST90200111
Name: n-stearoyl-sphingadienine (d18:2/18:0)*
Hmdb Id: HMDB0240362
Super Pathway: NA
Sub Pathway: NA
Inchikey: LBBFOWQGVUEADU

Associated Genomic Regions

Region: rs2257962

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:
12
Beta (Ratio):
0.145
Position:
121445808
SE (Ratio):
0.018
Effect Allele:
C
Z-score (Ratio):
7.874
Reference Allele:
T
-log10(P):
-33.302
MAF:
0.356
Beta (Num):
0.067
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
-0.078
SE (Den):
0.017
No CNV overlap
rQTL cluster:
49
Reaction Distance:
NA
Closest Genes:
C12orf43 HNF1A OASL AC079602.1 SPPL3

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid biosynthesis, ceramide synthesis.11[1], 12[2], 13[3], 14[4]

Denominator Metabolite Explanation:

Sphingolipid biosynthesis.11[1], 13[2], 14[3], 15[4]

Ratio Explanation:

The ratio may reflect altered sphingolipid metabolism due to HNF1A dysfunction, a transcription factor that influences lipid homeostasis, though a direct regulatory link is not established.16[1], 17[2], 18[3], 19[4], 20[5]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

HNF1A variants impact lipid metabolism and increase the risk for type 2 diabetes and related conditions like cholelithiasis and altered cholesterol levels.16[1], 18[2], 21[3], 22[4], 23[5], 24[6], 25[7], 26[8], 27[9], 28[10], 29[11], 30[12], 31[13], 32[14], 33[15] This altered metabolism, potentially reflected in the sphingolipid ratio, contributes to the observed phenotypes.

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