1-palmitoyl-2-docosahexaenoyl-gpc (16:0/22:6) to sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)*

Numerator Metabolite

Structure of 1-palmitoyl-2-docosahexaenoyl-gpc (16:0/22:6)
Metabolite Accession: GCST90200043
Name: 1-palmitoyl-2-docosahexaenoyl-gpc (16:0/22:6)
Hmdb Id: HMDB0007991
Super Pathway: NA
Sub Pathway: NA
Inchikey: IESVDEZGAHUQJU

Denominator 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

Associated Genomic Regions

Region: rs174546

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
-0.245
Position:
61569830
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
-12.331
Reference Allele:
C
-log10(P):
-78.771
MAF:
0.339
Beta (Num):
-0.166
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.079
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
FADS2 FADS1 FEN1 TMEM258 MYRF

Region: rs964184

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.221
Position:
116648917
SE (Ratio):
0.028
Effect Allele:
G
Z-score (Ratio):
7.925
Reference Allele:
C
-log10(P):
-33.715
MAF:
0.131
Beta (Num):
0.119
Novel Locus:
Yes ✔️
SE (Num):
0.022
Beta (Den):
-0.102
SE (Den):
0.021
No CNV overlap
rQTL cluster:
248
Reaction Distance:
NA
Closest Genes:
ZNF259 BUD13 APOA5 APOA4 APOC3

LLM Analysis

Numerator Metabolite Explanation:

Phosphatidylcholine biosynthesis5[1]

Denominator Metabolite Explanation:

Sphingolipid biosynthesis6[1], 7[2], 8[3]

Ratio Explanation:

The ratio reflects FADS enzyme activity, where higher activity increases the numerator's DHA component, set against the baseline synthesis of sphingomyelin.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

FADS1/FADS2 variants influence desaturase activity, altering levels of the PC (16:0/22:6) numerator and impacting lipid metabolism.9[1], 10[2], 11[3] This dyslipidemia is strongly associated with increased risk for cholelithiasis and cardiovascular diseases like coronary artery disease and myocardial infarction.12[4], 13[5], 14[6], 15[7]

Phenotype Driver:

Gene-centric:FADS1/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