sphingomyelin (d17:2/16:0, d18:2/15:0)* to sphingomyelin (d18:1/19:0, d19:1/18:0)*

Numerator Metabolite

Metabolite Accession: GCST90200125
Name: sphingomyelin (d17:2/16:0, d18:2/15:0)*
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: rs1466448

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.230
Position:
8289519
SE (Ratio):
0.014
Effect Allele:
C
Z-score (Ratio):
16.666
Reference Allele:
A
-log10(P):
-141.922
MAF:
0.192
Beta (Num):
0.039
Novel Locus:
No
SE (Num):
0.017
Beta (Den):
-0.191
SE (Den):
0.018
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):
-0.174
Position:
12962718
SE (Ratio):
0.011
Effect Allele:
A
Z-score (Ratio):
-15.548
Reference Allele:
G
-log10(P):
-123.841
MAF:
0.385
Beta (Num):
0.025
Novel Locus:
No
SE (Num):
0.014
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 metabolism4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism4[1], 5[2], 6[3]

Ratio Explanation:

The ratio reflects the relative activity of ceramide synthases; CERS4 may favor the synthesis of the denominator's longer-chain sphingomyelins over the numerator's shorter/odd-chain species.1[1], 2[2], 3[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

CERS4 variants are associated with altered sphingomyelin levels and cholelithiasis.7[1], 8[2] Altered sphingomyelin profiles are linked to cholelithiasis, potentially through effects on bile composition and cholesterol crystallization, and are also associated with elevated ALT and LDL-C, further connecting to liver pathology and gallstone risk.9[3], 10[4], 11[5], 12[6]

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