sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0) to sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*

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 (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*
Metabolite Accession: GCST90200134
Name: sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: JONXXLXMISNQNG

Associated Genomic Regions

Region: rs2244608

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.121
Position:
121416988
SE (Ratio):
0.014
Effect Allele:
G
Z-score (Ratio):
-8.646
Reference Allele:
A
-log10(P):
-39.775
MAF:
0.317
Beta (Num):
-0.050
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.071
SE (Den):
0.017
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):
0.242
Position:
64239351
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
13.907
Reference Allele:
T
-log10(P):
-99.572
MAF:
0.165
Beta (Num):
0.184
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.058
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 biosynthesis/metabolism.8[1], 9[2], 10[3], 11[4], 12[5], 13[6], 14[7]

Denominator Metabolite Explanation:

Sphingolipid biosynthesis/metabolism.8[1], 9[2], 10[3], 11[4], 12[5], 13[6], 14[7]

Ratio Explanation:

The ratio reflects altered sphingomyelin acyl chain composition, potentially due to HNF1A's influence on enzymes regulating fatty acid elongation or substrate availability.15[1], 16[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Altered HNF1A function likely dysregulates hepatic lipid metabolism, influencing sphingomyelin composition. This altered lipid profile, particularly the balance of different sphingomyelin species, is associated with an increased risk for cholelithiasis and cardiovascular diseases like atherosclerosis and myocardial infarction, which are listed phenotypes.6[1], 17[2], 18[3], 19[4], 20[5], 21[6]

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