5alpha-pregnan-3beta,20alpha-diol disulfate to 3b-hydroxy-5-cholenoic acid

Numerator Metabolite

Structure of 5alpha-pregnan-3beta,20alpha-diol disulfate
Metabolite Accession: GCST90199838
Name: 5alpha-pregnan-3beta,20alpha-diol disulfate
Hmdb Id: HMDB0094650
Super Pathway: NA
Sub Pathway: NA
Inchikey: LSQGWMYMIHQKSA

Denominator Metabolite

Structure of 3b-hydroxy-5-cholenoic acid
Metabolite Accession: GCST90199933
Name: 3b-hydroxy-5-cholenoic acid
Hmdb Id: HMDB0000308
Super Pathway: NA
Sub Pathway: NA
Inchikey: HIAJCGFYHIANNA

Associated Genomic Regions

Region: rs62129966

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:
19
Beta (Ratio):
-0.439
Position:
48374950
SE (Ratio):
0.030
Effect Allele:
A
Z-score (Ratio):
-14.811
Reference Allele:
C
-log10(P):
-112.602
MAF:
0.161
Beta (Num):
-0.277
Novel Locus:
No
SE (Num):
0.021
Beta (Den):
0.161
SE (Den):
0.023
No CNV overlap
rQTL cluster:
7
Reaction Distance:
NA
Closest Genes:
SULT2A1 TPRX2P CRX TPRX1 SEPW1

LLM Analysis

Numerator Metabolite Explanation:

Steroid hormone biosynthesis5[1], 6[2]

Denominator Metabolite Explanation:

Bile acid biosynthesis7[1], 8[2]

Ratio Explanation:

The ratio reflects SULT2A1 activity; higher activity increases sulfation of the pregnanediol (numerator) and bile acid precursor (denominator), altering their balance.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variants in SULT2A1, a gene involved in steroid and bile acid sulfation, are associated with cholelithiasis.1[1], 9[2], 10[3] Altered SULT2A1 activity likely modifies bile acid metabolism, a key factor in gallstone formation, and is also linked to changes in ALP and cholecystitis.

Phenotype Driver:

Gene-centric:SULT2A1

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