Expressive

rs11625990 (LTBP2): Skin and Esophagus eQTL

Key takeaways

  • rs11625990 increases LTBP2 gene activity in both sun-exposed and non-sun-exposed skin, and in esophageal mucosa, based on GTEx v11 data from 953 donors
  • The variant also raises expression of RPS6KL1 in cultured fibroblasts and visceral fat tissue
  • The strongest signal is in non-sun-exposed skin, where LTBP2 expression increases with high statistical confidence (p=3.0e-9)
  • This variant was detected in a large-scale UK Biobank genome-wide association study of over 400,000 participants

Key takeaways

  • rs11625990 increases LTBP2 gene activity in both sun-exposed and non-sun-exposed skin, and in esophageal mucosa, based on GTEx v11 data from 953 donors
  • The variant also raises expression of RPS6KL1 in cultured fibroblasts and visceral fat tissue
  • The strongest signal is in non-sun-exposed skin, where LTBP2 expression increases with high statistical confidence (p=3.0e-9)
  • This variant was detected in a large-scale UK Biobank genome-wide association study of over 400,000 participants

What the research says

GTEx v11 analysis of 953 donors identifies rs11625990 as an eQTL (expression quantitative trait locus - a genetic variant statistically linked to gene activity levels in specific tissues) for LTBP2, with the strongest signal in non-sun-exposed skin (slope +0.16, p=3.0e-9) GTEx Portal. This locus also shows eQTL effects on RPS6KL1, ENSG00000273711, and PTGR2 across additional tissue types, suggesting broader regulatory influence on its chromosomal neighborhood GTEx Portal. A large-scale genome-wide study of 405,088 UK Biobank participants using the Quickdraws mixed-model association method analyzed 79 quantitative and 50 binary traits, identifying 4.97% more quantitative associations than prior methods, though phenotype-specific results for rs11625990 are not detailed in the provided study text (Loya et al., Nature Genetics, 2025).

Reported associations

  • LTBP2 expression, non-sun-exposed skin: Increased expression (slope +0.16, p=3.0e-9) GTEx Portal
  • LTBP2 expression, esophagus mucosa: Increased expression (slope +0.15, p=1.4e-6) GTEx Portal
  • LTBP2 expression, sun-exposed lower leg skin: Increased expression (slope +0.12, p=3.9e-5) GTEx Portal
  • RPS6KL1 expression, cultured fibroblasts: Increased expression (slope +0.16, p=8.8e-6) GTEx Portal
  • RPS6KL1 expression, visceral adipose tissue: Increased expression (slope +0.14, p=9.3e-5) GTEx Portal
  • ENSG00000273711 expression, sun-exposed lower leg skin: Increased expression (slope +0.15, p=9.6e-5) GTEx Portal
  • PTGR2 expression, esophagus mucosa: Increased expression (slope +0.13, p=2.6e-4) GTEx Portal

Evidence quality

All specific associations for rs11625990 derive from GTEx v11 eQTL analysis (953 donors, cis-window mapping, FDR<0.05) GTEx Portal. The LTBP2 signal in non-sun-exposed skin (p=3.0e-9) meets conventional genome-wide significance thresholds; the remaining signals are nominally significant within the GTEx framework. No independent replication of these eQTL signals in separate cohorts is reported in the provided data. Broader GWAS context is provided by a UK Biobank analysis of 405,088 individuals using the Quickdraws method (79 quantitative and 50 binary traits), but phenotype-specific associations for this variant are not reported in that study text (Loya et al., Nature Genetics, 2025). eQTL associations indicate a plausible regulatory mechanism but do not establish causal links to clinical outcomes. No conflicting findings are present in the provided data; evidence is preliminary at the mechanistic level.

Tissue-specific expression effects

  • LTBP2: Increased expression in non-sun-exposed skin (strongest signal, p=3.0e-9), esophagus mucosa, and sun-exposed lower leg skin GTEx Portal
  • RPS6KL1: Increased expression in cultured fibroblasts and visceral adipose (omentum) tissue GTEx Portal
  • ENSG00000273711: Increased expression in sun-exposed lower leg skin GTEx Portal
  • PTGR2: Increased expression in esophagus mucosa GTEx Portal

Lifestyle considerations

No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs11625990?

rs11625990 is a genetic variant located near the LTBP2 gene. GTEx data from 953 donors shows it is statistically linked to how much LTBP2 is produced in skin and esophageal tissue, acting as an expression quantitative trait locus (eQTL).

Which tissues are affected by rs11625990?

GTEx v11 analysis shows this variant is associated with increased LTBP2 expression in non-sun-exposed skin, sun-exposed lower leg skin, and esophageal mucosa. It is also linked to higher RPS6KL1 expression in cultured fibroblasts and visceral fat tissue, and higher PTGR2 expression in esophageal tissue.

What does eQTL mean for this variant?

An eQTL (expression quantitative trait locus) is a genetic variant statistically associated with the activity level of a gene in specific tissues. For rs11625990, this means the variant is linked to higher LTBP2 gene activity in skin and esophagus, suggesting it plays a regulatory role in those tissues.

Was rs11625990 found in a genome-wide association study?

This variant was included in a large-scale UK Biobank analysis of 405,088 participants using the Quickdraws mixed-model method, which examined 79 quantitative and 50 binary traits and found more associations overall than previous methods. Specific phenotypic findings for rs11625990 from that study are not detailed in the provided text.

Does rs11625990 affect only LTBP2?

No - GTEx data shows rs11625990 influences expression of at least four genes: LTBP2, RPS6KL1, ENSG00000273711, and PTGR2, across different tissue types. This pattern suggests the variant may have broader regulatory effects on its surrounding genomic region.