sphingomyelin (d18:2/14:0, d18:1/14:1)* to sphingomyelin (d18:1/19:0, d19:1/18:0)*

Numerator Metabolite

Metabolite Accession: GCST90199975
Name: sphingomyelin (d18:2/14:0, d18:1/14:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200131
Name: sphingomyelin (d18:1/19:0, d19:1/18:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1871194

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.188
Position:
8283819
SE (Ratio):
0.014
Effect Allele:
C
Z-score (Ratio):
13.541
Reference Allele:
A
-log10(P):
-94.517
MAF:
0.461
Beta (Num):
0.034
Novel Locus:
No
SE (Num):
0.013
Beta (Den):
-0.153
SE (Den):
0.015
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.212
Position:
12962718
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-15.755
Reference Allele:
G
-log10(P):
-127.100
MAF:
0.385
Beta (Num):
-0.013
Novel Locus:
No
SE (Num):
0.013
Beta (Den):
0.199
SE (Den):
0.015
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

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

Ratio Explanation:

The ratio reflects relative ceramide synthase activities; genetic variant-driven CERS4 expression likely alters the ceramide pool used for synthesizing different sphingomyelin species.

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variation likely alters CERS4 expression, changing the sphingomyelin acyl-chain profile.2[1], 6[2] This dysregulation of sphingolipid metabolism, particularly in the liver, may promote cholelithiasis by altering cholesterol homeostasis and bile composition, and is also associated with polyneuropathies and gout.2[3], 7[4], 8[5], 9[6], 10[7]

Phenotype Driver:

Gene-centric:CERS4

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