sphingomyelin (d18:2/23:0, d18:1/23:1, d17:1/24:1)* to sphingomyelin (d18:2/24:1, d18:1/24:2)*

Numerator Metabolite

Metabolite Accession: GCST90200033
Name: sphingomyelin (d18:2/23:0, d18:1/23:1, d17:1/24:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200040
Name: sphingomyelin (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs7157785

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
0.135
Position:
64235556
SE (Ratio):
0.014
Effect Allele:
T
Z-score (Ratio):
9.347
Reference Allele:
G
-log10(P):
-46.152
MAF:
0.166
Beta (Num):
0.131
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
-0.005
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs4814176

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
0.085
Position:
12959398
SE (Ratio):
0.011
Effect Allele:
T
Z-score (Ratio):
7.637
Reference Allele:
C
-log10(P):
-31.434
MAF:
0.386
Beta (Num):
0.018
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
-0.068
SE (Den):
0.014
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

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

Ratio Explanation:

This ratio compares different species of sphingomyelin, lipids integral to cell membranes and lipoproteins. ISM1's role as an adipokine influencing lipid metabolism suggests a potential, though indirect, link to sphingomyelin composition.1[1], 2[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 is an adipokine that influences lipid and glucose metabolism.1[1], 2[2] Alterations in sphingomyelin, a key component of lipoproteins, are associated with disorders of lipoprotein metabolism and cholelithiasis.7[3], 8[4] Therefore, variations in ISM1 function could modulate sphingomyelin profiles, contributing to these phenotypes.

Phenotype Driver:

Gene-centric:ISM1

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