sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)* to sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Metabolite Accession: GCST90200010
Name: sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Hmdb Id: HMDB0012104
Super Pathway: NA
Sub Pathway: NA
Inchikey: VBFKEZGCUWHGSK

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: rs1169284

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.122
Position:
121419926
SE (Ratio):
0.016
Effect Allele:
C
Z-score (Ratio):
-7.617
Reference Allele:
T
-log10(P):
-31.280
MAF:
0.314
Beta (Num):
-0.057
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.065
SE (Den):
0.017
No CNV overlap
rQTL cluster:
49
Reaction Distance:
NA
Closest Genes:
HNF1A AC079602.1 C12orf43 OASL SPPL3

Region: rs12897637

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):
0.263
Position:
64239351
SE (Ratio):
0.020
Effect Allele:
C
Z-score (Ratio):
13.262
Reference Allele:
T
-log10(P):
-90.762
MAF:
0.165
Beta (Num):
0.205
Novel Locus:
No
SE (Num):
0.019
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:

Sphingomyelin synthesis and degradation pathways.10[1], 11[2], 12[3], 13[4]

Denominator Metabolite Explanation:

Sphingomyelin synthesis and degradation pathways.10[1], 11[2], 12[3], 13[4]

Ratio Explanation:

The ratio likely reflects altered sphingolipid metabolism, potentially influenced by HNF1A's regulatory role, affecting the balance between different chain-length sphingomyelins, which have varied associations with cardiovascular health.14[1], 15[2], 16[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

HNF1A variants alter its transcriptional control over genes involved in lipid metabolism, including sphingolipids.8[1], 15[2] This dysregulation, reflected in the sphingomyelin ratio, contributes to phenotypes like hypercholesterolemia and atherosclerosis, as different sphingomyelin species have distinct roles in cardiovascular health.14[3], 17[4], 18[5], 19[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