sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)* to sphingomyelin (d18:2/24:2)*

Numerator Metabolite

Metabolite Accession: GCST90199995
Name: sphingomyelin (d18:1/20:2, d18:2/20:1, d16:1/22:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Structure of sphingomyelin (d18:2/24:2)*
Metabolite Accession: GCST90200124
Name: sphingomyelin (d18:2/24:2)*
Hmdb Id: HMDB0240644
Super Pathway: NA
Sub Pathway: NA
Inchikey: LAWJSGKLPKMOGG

Associated Genomic Regions

Region: rs174547

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.181
Position:
61570783
SE (Ratio):
0.013
Effect Allele:
C
Z-score (Ratio):
14.226
Reference Allele:
T
-log10(P):
-104.078
MAF:
0.339
Beta (Num):
0.186
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.006
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
FADS2 FADS1 FEN1 TMEM258 MYRF

Region: rs1466448

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.154
Position:
8289519
SE (Ratio):
0.015
Effect Allele:
C
Z-score (Ratio):
-10.103
Reference Allele:
A
-log10(P):
-53.581
MAF:
0.192
Beta (Num):
-0.099
Novel Locus:
Yes ✔️
SE (Num):
0.018
Beta (Den):
0.055
SE (Den):
0.018
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs364585

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:
20
Beta (Ratio):
0.110
Position:
12962718
SE (Ratio):
0.012
Effect Allele:
A
Z-score (Ratio):
8.854
Reference Allele:
G
-log10(P):
-41.613
MAF:
0.385
Beta (Num):
0.081
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.029
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 metabolism3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism3[1], 4[2]

Ratio Explanation:

This ratio reflects the balance between shorter/more saturated (C20-C22) and longer/more unsaturated (C24) chain fatty acids in sphingomyelins, likely modulated by FADS2 activity.1[1], 5[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

FADS2 genetic variation alters fatty acid desaturation, changing sphingomyelin composition. This impacts cell membrane function and lipid metabolism, contributing to phenotypes like hypercholesterolemia, type 2 diabetes, and inflammatory bowel disease by influencing metabolic and inflammatory signaling.6[1], 7[2], 8[3], 9[4], 10[5], 11[6]

Phenotype Driver:

Gene-centric:FADS2

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