sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)* to glycosyl ceramide (d18:2/24:1, d18:1/24:2)*

Numerator Metabolite

Metabolite Accession: GCST90200013
Name: sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200118
Name: glycosyl ceramide (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs8008068

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):
0.244
Position:
64233717
SE (Ratio):
0.018
Effect Allele:
G
Z-score (Ratio):
13.456
Reference Allele:
A
-log10(P):
-93.366
MAF:
0.166
Beta (Num):
0.222
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
-0.022
SE (Den):
0.020
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

Glycosphingolipid biosynthesis.5[1], 6[2]

Ratio Explanation:

This ratio reflects the balance at a key metabolic branch point from ceramide. ATP10D activity on glycosylceramide may alter this balance.7[1]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variation in ATP10D, a glucosylceramide flippase, likely alters the cellular balance of sphingomyelin and glycosylceramide.8[1], 1[2] This dysregulation of sphingolipid metabolism is linked to disorders of lipoprotein metabolism, triglycerides, and glucose homeostasis (HbA1c), which are observed phenotypes.9[3], 10[4], 11[5]

Phenotype Driver:

Gene-centric:ATP10D

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