Expressive

rs1029238 (TRIM15): Blood Cell Trait Variant

Key takeaways

  • rs1029238 sits near TRIM15 in the MHC region on chromosome 6p21, one of the most gene-dense stretches of the human genome
  • This variant was assessed in a study of 29 blood cell traits covering 563,085 European-ancestry participants
  • GTEx data links this variant to altered expression of five nearby genes across tissues including skeletal muscle, tibial nerve, tibial artery, adrenal gland, and pituitary gland
  • The specific blood cell trait and effect size for rs1029238 are not detailed in the available study excerpts, so the blood cell association should be treated as preliminary

Key takeaways

  • rs1029238 sits near TRIM15 in the MHC region on chromosome 6p21, one of the most gene-dense stretches of the human genome
  • This variant was assessed in a study of 29 blood cell traits covering 563,085 European-ancestry participants
  • GTEx data links this variant to altered expression of five nearby genes across tissues including skeletal muscle, tibial nerve, tibial artery, adrenal gland, and pituitary gland
  • The specific blood cell trait and effect size for rs1029238 are not detailed in the available study excerpts, so the blood cell association should be treated as preliminary

What the research says A genome-wide association study (GWAS) integrating UK Biobank and international cohort data analyzed 29 blood cell phenotypes - covering red blood cells, white blood cells, and platelets - in 563,085 European-ancestry participants, identifying 5,106 new associated variants and characterizing the genetic architecture of hematopoiesis (the biological process by which blood cells are produced). The study included replication of effect sizes between UK Biobank and the Million Veteran Program, and assessed regulatory noncoding variants and splice-altering changes using tissue-specific hematopoietic profiles. GTEx v11 expression data from 953 donors show that the alternate allele of rs1029238 is linked to altered activity of five nearby MHC-region genes across multiple tissue types, including increased expression of HCG9 in adrenal gland and skeletal muscle, and reduced expression of ENSG00000310496 in tibial nerve, tibial artery, and esophageal junction GTEx Portal.

Reported associations

  • Blood cell phenotypes: rs1029238 was evaluated within a GWAS of 29 blood cell phenotypes in 563,085 European-ancestry participants; the specific trait, p-value, and effect size for this variant individually are not described in the available study excerpts.
  • Gene expression (eQTL): This variant is associated with altered expression of five genes in the surrounding MHC region across multiple tissues, based on GTEx v11 data from 953 donors (FDR less than 0.05) GTEx Portal.

Evidence quality The primary genetic study is a large-scale GWAS (n=563,085) of 29 blood cell phenotypes published in Cell (2021) by Vuckovic et al., representing one of the largest blood trait genetic analyses reported to date. The study compared effect sizes between UK Biobank and the Million Veteran Program, supporting overall methodological rigor. The specific p-value, effect size, and blood cell trait for rs1029238 individually are not available in the provided study text; the blood cell association should therefore be treated as preliminary and the full published results consulted for specifics. No conflicting findings are reported in the provided materials. The GTEx eQTL data are based on 953 donors with FDR less than 0.05, representing a well-powered expression dataset; however, eQTL associations reflect gene expression regulation and do not by themselves establish clinical outcomes.

Tissue-specific expression effects

  • HCG9: Increased expression in adrenal gland and skeletal muscle with the alternate allele GTEx Portal
  • ENSG00000310496: Reduced expression in esophageal gastroesophageal junction, tibial nerve, and tibial artery GTEx Portal
  • RNF39: Increased expression in tibial artery GTEx Portal
  • ENSG00000290870: Reduced expression in tibial nerve GTEx Portal
  • HLA-F-AS1: Reduced expression in pituitary gland GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs1029238?

rs1029238 is a genetic variant located near the TRIM15 gene in the MHC (major histocompatibility complex) region on chromosome 6p21. It was evaluated in a large study examining the genetics of blood cell traits in over 563,000 people.

What does TRIM15 do?

TRIM15 belongs to the tripartite motif (TRIM) protein family, which has roles in immune signaling. It is located in the MHC region, a stretch of chromosome 6 containing hundreds of genes involved in immune function.

Is rs1029238 linked to blood disorders?

rs1029238 was evaluated in a genome-wide association study of 29 blood cell phenotypes in over 563,000 people. The specific blood cell trait and effect size for this variant are not detailed in the available research excerpts, so no firm conclusions can be drawn from the provided data.

Which tissues are affected by rs1029238?

GTEx expression data from 953 donors links this variant to altered activity of five nearby genes in tissues including skeletal muscle, tibial nerve, tibial artery, adrenal gland, esophageal junction, and pituitary gland. These are expression-level findings and their clinical significance is not established.

What is the MHC region?

The major histocompatibility complex (MHC) is a gene-dense region on chromosome 6p21 containing hundreds of genes with roles in immune function. Variants in this region, including rs1029238, often influence expression of multiple neighboring genes.