rs11164273 (LINC01709): Blood Cell Trait Variant
Key takeaways
- rs11164273 sits near LINC01709, a non-coding RNA gene, and was studied in relation to white blood cell and platelet counts in a multi-ethnic population.
- The PAGE study included over 64,000 participants from African American, Hispanic/Latino, and European ancestry backgrounds - one of the most diverse blood-cell-trait studies to date.
- Evidence for this variant is preliminary: the association reached only suggestive significance (P < 5E-8) and has not yet been independently replicated.
- Genetic effects on blood cell traits are not uniform across ancestry groups, and some previously reported effects were smaller in African American and Hispanic/Latino participants than in European ancestry participants.
Key takeaways
- rs11164273 is located near LINC01709, a long intergenic non-coding RNA (lncRNA) gene, and was examined in the context of white blood cell and platelet traits.
- Evidence comes from a single multi-ethnic genome-wide association study (GWAS) in the PAGE study, which included up to 64,784 participants across African American, Hispanic/Latino, and European ancestry groups.
- Associations identified as novel in this study reached only suggestive significance (P < 5E-8), below the genome-wide threshold used by the authors (P < 2E-9), and require independent replication to be considered established.
- Genetic effects on blood cell traits can differ across ancestry groups; previously reported variant effects tended to be attenuated in African American and Hispanic/Latino populations compared to European ancestry participants.
What the research says rs11164273 is located near LINC01709 (a long intergenic non-coding RNA, sometimes abbreviated lncRNA) and was examined as part of a large multi-ethnic GWAS of eight white blood cell and platelet traits in the Population Architecture using Genomics and Epidemiology (PAGE) study, which enrolled up to 64,784 participants: 16,201 African Americans, 21,347 Hispanic/Latinos, and 27,236 European ancestry individuals. The PAGE study identified six novel findings at suggestive significance (P < 5E-8) requiring confirmation, and independent signals at six previously established regions at genome-wide significance (P < 2E-9). Effect estimates for variants at previously reported loci were attenuated in African American and Hispanic/Latino participants relative to European ancestry participants, underscoring the importance of ancestrally diverse study populations.
Reported associations
- White blood cell and platelet traits: This variant was examined in the context of a study assessing white blood cell count, basophil count, eosinophil count, lymphocyte count, monocyte count, neutrophil count, platelet count, and mean platelet volume; novel findings in this study reached only suggestive significance (P < 5E-8), and specific effect sizes for this locus are not reported in the available study text.
Evidence quality The PAGE study enrolled up to 64,784 participants (16,201 African Americans, 21,347 Hispanic/Latinos, and 27,236 European ancestry individuals), representing one of the more ancestrally diverse blood-cell-trait GWAS published to date. Trait heritability for the studied phenotypes ranges from approximately 13.8% for basophil count to over 50% for platelet count and mean platelet volume, indicating a meaningful genetic component. However, associations reported as novel in this study, which would include any signal at the LINC01709 locus, reached only suggestive significance (P < 5E-8) and did not clear the genome-wide significance threshold the authors applied (P < 2E-9), making these findings preliminary and in need of independent replication. Genomic inflation factors across all ancestry groups and traits ranged from 0.936 to 1.150, suggesting minimal systematic bias in the analysis. No specific p-value, odds ratio, or beta coefficient for rs11164273 is reported in the available study text, so effect-size interpretation is not possible from this source alone.
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is LINC01709?
LINC01709 is a long intergenic non-coding RNA (lncRNA) gene. Unlike protein-coding genes, it produces RNA molecules that do not make proteins but may help regulate the activity of nearby genes.
What traits is rs11164273 associated with?
rs11164273 has been studied in the context of white blood cell and platelet traits, including total white blood cell count, individual white blood cell subtypes such as lymphocytes and neutrophils, platelet count, and mean platelet volume.
How strong is the evidence linking rs11164273 to blood cell traits?
The evidence is preliminary. The association was identified at suggestive significance (P < 5E-8) in one study but did not reach the stricter genome-wide significance threshold (P < 2E-9) used by the researchers. Independent replication in other studies is needed before this can be considered a confirmed finding.
Does rs11164273 have the same effect in all ethnic groups?
Research from the PAGE study suggests genetic effects on blood cell traits can vary across ancestry groups. Some previously reported variant effects were attenuated in African American and Hispanic/Latino populations relative to European ancestry populations, which is one reason diverse study designs matter in genetic research.
What is the PAGE study?
PAGE stands for Population Architecture using Genomics and Epidemiology. It is a large genetic study funded by the National Human Genome Research Institute and the National Institute on Minority Health and Health Disparities, designed to study complex traits in racially and ethnically diverse populations in the United States.