rs10838801 (PTPRJ): Multi-Tissue Expression Variant
Key takeaways
- The alternative allele at rs10838801 reduces PTPRJ expression in at least seven different tissues, most strongly in the pancreas
- C1QTNF4 expression in heart atrial appendage tissue is also reduced by this allele
- This variant appears in two large genome-wide association studies covering circulating lipid species and adult height
- All observed PTPRJ tissue expression effects point in the same direction, indicating a consistent functional role for this variant
Key takeaways
- The alternative allele at rs10838801 reduces PTPRJ expression in at least seven different tissues, most strongly in the pancreas
- C1QTNF4 expression in heart atrial appendage tissue is also reduced by this allele
- This variant appears in two large genome-wide association studies covering circulating lipid species and adult height
- All observed PTPRJ tissue expression effects point in the same direction, indicating a consistent functional role for this variant
What the research says rs10838801 functions as a cis-eQTL (a variant that alters nearby gene expression) for PTPRJ (protein tyrosine phosphatase receptor J) across at least seven tissues, with the alternative allele consistently associated with reduced expression GTEx Portal. The same allele separately reduces C1QTNF4 expression in heart atrial appendage tissue, with all effects exceeding a strict false discovery rate threshold (FDR<0.05) GTEx Portal. Two large GWAS studies - one of 970 circulating lipid species (discovery n=6,096, replicated in two independent cohorts) and one of adult height (n=183,727 across 46 studies) - provide genomic context for this locus, though the provided study excerpts do not specify per-variant effect estimates for rs10838801 within those analyses.
Reported associations
- PTPRJ expression - pancreas: The alternative allele is linked to reduced expression; the largest eQTL effect across all tissues examined (slope -0.41, p=1.3e-22) GTEx Portal
- PTPRJ expression - esophagus (three subtypes): Reduced expression in muscularis (slope -0.28, p=5.5e-18), gastroesophageal junction (slope -0.25, p=1.4e-9), and mucosa (slope -0.25, p=4.0e-17) GTEx Portal
- PTPRJ expression - subcutaneous adipose, tibial nerve, and sun-exposed skin: Reduced expression in each tissue (slopes -0.20 to -0.21) GTEx Portal
- C1QTNF4 expression - heart atrial appendage: Reduced expression with the alternative allele (slope -0.29, p=4.6e-8) GTEx Portal
Evidence quality The expression QTL evidence for rs10838801 is statistically robust: associations with the gene are replicated across seven tissues at FDR<0.05 in GTEx v11 (953 donors), with p-values from 1.3e-22 (pancreas) to 1.4e-9 (esophageal gastroesophageal junction) GTEx Portal. All seven tissue associations point in the same direction (reduced expression), strengthening confidence in the finding. The C1QTNF4 heart association (p=4.6e-8) is observed in one tissue only, which warrants caution. Two GWAS studies supply additional genomic context: a population-based lipid GWAS (Rhineland Study n=6,096, validated in FinnGen n=7,266 and EPIC-Potsdam n=1,188) that identified 217 loci across 970 lipid species, and a height meta-analysis (n=183,727, 180 genome-wide significant loci explaining approximately 10.5% of height variance). The provided text excerpts from those studies do not confirm specific effect estimates for rs10838801, and no conflicts between available data sources are evident.
Tissue-specific expression effects
- PTPRJ: Reduced expression in pancreas, esophagus muscularis, esophageal gastroesophageal junction, esophagus mucosa, subcutaneous adipose, tibial nerve, and sun-exposed lower leg skin - all tissues show the same direction of effect with the alternative allele GTEx Portal
- C1QTNF4: Reduced expression in heart atrial appendage tissue GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What does rs10838801 do?
rs10838801 is a genetic variant linked to reduced expression of the PTPRJ gene across at least seven tissues, including the pancreas, esophagus, subcutaneous fat, tibial nerve, and skin. It also reduces C1QTNF4 expression in heart tissue.
What is the PTPRJ gene?
PTPRJ encodes protein tyrosine phosphatase receptor type J. Carriers of the alternative allele at rs10838801 tend to show lower PTPRJ expression across multiple body tissues, with the pancreas showing the largest reduction.
Is rs10838801 linked to lipid levels or height?
This variant has been studied in the context of genome-wide association studies of circulating lipid species and adult height. However, specific effect sizes for rs10838801 within those studies are not confirmed from the available study text.
How strong is the evidence for rs10838801 affecting gene expression?
The GTEx v11 dataset (953 donors) shows associations between rs10838801 and reduced PTPRJ expression across seven tissues, all passing a strict false discovery rate threshold. The pancreas association has a p-value of 1.3e-22, among the most significant eQTL effects in the dataset.
Which tissues are most affected by rs10838801?
The pancreas shows the strongest PTPRJ expression reduction. Other affected tissues include three esophageal subtypes, subcutaneous adipose, tibial nerve, and sun-exposed skin. The heart atrial appendage shows a separate reduction in C1QTNF4 expression.