sphingomyelin (d18:2/16:0, d18:1/16:1)* to glycosyl-n-behenoyl-sphingadienine (d18:2/22:0)*

Numerator Metabolite

Metabolite Accession: GCST90199947
Name: sphingomyelin (d18:2/16:0, d18:1/16:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200105
Name: glycosyl-n-behenoyl-sphingadienine (d18:2/22:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs686548

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.109
Position:
12973521
SE (Ratio):
0.014
Effect Allele:
A
Z-score (Ratio):
-7.812
Reference Allele:
T
-log10(P):
-32.814
MAF:
0.387
Beta (Num):
-0.075
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.034
SE (Den):
0.016
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

Region: rs35818294

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:
4
Beta (Ratio):
-0.302
Position:
47545141
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
-16.953
Reference Allele:
C
-log10(P):
-146.759
MAF:
0.177
Beta (Num):
-0.002
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.300
SE (Den):
0.020
No CNV overlap
rQTL cluster:
126
Reaction Distance:
NA
Closest Genes:
ATP10D CORIN COMMD8 GABRB1 NFXL1

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

Glycosphingolipid metabolism.6[1], 7[2], 5[3]

Ratio Explanation:

The ratio compares two sphingolipids derived from ceramide, potentially reflecting a shift in lipid metabolism influenced by ATP10D's role in lipid transport.8[1], 9[2], 3[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered ATP10D flippase activity likely modifies hepatic lipid composition and metabolism, including hexosylceramides, impacting bile constituents and cholesterol solubility, which elevates the risk for cholelithiasis and alters liver enzymes (ALT) and LDL-cholesterol.10[1], 11[2], 12[3], 13[4]

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