sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)* to sphingomyelin (d18:1/25:0, d19:0/24:1, d20:1/23:0, d19:1/24:0)*

Numerator Metabolite

Structure of sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Metabolite Accession: GCST90200017
Name: sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: LQINJRUGTUOHGS

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):
-0.111
Position:
121416988
SE (Ratio):
0.014
Effect Allele:
G
Z-score (Ratio):
-7.799
Reference Allele:
A
-log10(P):
-32.706
MAF:
0.317
Beta (Num):
-0.040
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: rs8012828

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
0.389
Position:
64233980
SE (Ratio):
0.018
Effect Allele:
T
Z-score (Ratio):
22.152
Reference Allele:
C
-log10(P):
-248.673
MAF:
0.166
Beta (Num):
0.332
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.057
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 and metabolism.8[1], 9[2], 10[3]

Denominator Metabolite Explanation:

Sphingolipid biosynthesis and metabolism.8[1], 9[2], 10[3]

Ratio Explanation:

The ratio reflects altered sphingolipid acyl chain length homeostasis, potentially due to HNF1A's regulatory role, which influences sphingolipid metabolism and is linked to cardiovascular risk.4[1], 6[2], 7[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

HNF1A variants are associated with altered sphingolipid profiles and an increased risk for coronary atherosclerosis and hypercholesterolemia.6[1], 7[2] This suggests that HNF1A's regulatory effects on lipid metabolism, including sphingomyelins, contribute to the development of cardiovascular and lipid-related disorders.4[3], 11[4], 12[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