sphingomyelin (d18:1/18:1, d18:2/18:0) to alpha-hydroxyisovalerate

Numerator Metabolite

Structure of sphingomyelin (d18:1/18:1, d18:2/18:0)
Metabolite Accession: GCST90199878
Name: sphingomyelin (d18:1/18:1, d18:2/18:0)
Hmdb Id: HMDB0012101
Super Pathway: NA
Sub Pathway: NA
Inchikey: NBEADXWAAWCCDG

Denominator Metabolite

Structure of alpha-hydroxyisovalerate
Metabolite Accession: GCST90199736
Name: alpha-hydroxyisovalerate
Hmdb Id: HMDB0000407
Super Pathway: NA
Sub Pathway: NA
Inchikey: NGEWQZIDQIYUNV

Associated Genomic Regions

Region: rs2393791

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

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
12
Beta (Ratio):
-0.203
Position:
121423956
SE (Ratio):
0.021
Effect Allele:
C
Z-score (Ratio):
-9.559
Reference Allele:
T
-log10(P):
-48.182
MAF:
0.382
Beta (Num):
-0.087
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.116
SE (Den):
0.015
No CNV overlap
rQTL cluster:
49
Reaction Distance:
NA
Closest Genes:
HNF1A AC079602.1 C12orf43 OASL SPPL3

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

Leucine, isoleucine, and valine metabolism.7[1], 8[2], 9[3]

Ratio Explanation:

HNF1A regulates lipid and amino acid metabolism; altered levels of sphingomyelin and alpha-hydroxyisovalerate may reflect its dysregulation.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

HNF1A variants are associated with cholelithiasis and myocardial infarction.10[1], 11[2], 12[3], 13[4], 14[5] Dysregulation of HNF1A may alter sphingomyelin and alpha-hydroxyisovalerate levels, contributing to the pathogenesis of these conditions through effects on lipid metabolism and inflammation.

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