Expressive

rs11628318 (LINC02323): Platelet Trait Variant

Key takeaways

  • The LINC02323 region was identified in a study of ~67,000 people as one of 68 genome locations associated with platelet count and size
  • Those 68 loci collectively account for about 5% of platelet count variation and 10% of platelet volume variation
  • Carrying the alternate allele at rs11628318 is associated with lower LINC02323 expression in at least 8 tissues, including skin, thyroid, and fat tissue
  • The platelet associations held up directionally in South Asian and Japanese populations, not only in Europeans
  • LINC02323 encodes a non-coding RNA with no known protein product; how it connects to platelet biology is not yet established

Key takeaways

  • The LINC02323 region was identified in a study of ~67,000 people as one of 68 genome locations associated with platelet count and size.
  • Those 68 loci collectively account for about 5% of platelet count variation and 10% of platelet volume variation.
  • Carrying the alternate allele at rs11628318 is associated with lower LINC02323 expression in at least 8 tissues, including skin, thyroid, and fat tissue.
  • The platelet associations held up directionally in South Asian and Japanese populations, not only in Europeans.
  • LINC02323 encodes a non-coding RNA with no known protein product; how it connects to platelet biology is not yet established.

What the research says A meta-analysis of genome-wide association studies in up to 66,867 individuals of European ancestry identified 68 genomic loci at genome-wide significance (P ≤ 5 × 10^-8) associated with platelet count (PLT) and mean platelet volume (MPV), with those loci collectively explaining 4.8% of PLT variance and 9.9% of MPV variance. The LINC02323 locus - home to rs11628318 - was among the regions identified in that analysis as associated with platelet traits, and cross-ancestry replication in South Asian and Japanese cohorts showed 82-87% directional concordance across the 68 loci. In GTEx v11 eQTL data (953 donors, FDR < 0.05), the alternate allele at rs11628318 is associated with reduced LINC02323 expression in eight tissues, most markedly in sun-exposed skin (slope −0.49, p = 1.6 × 10^-²^7) GTEx Portal.

Reported associations

  • Platelet count (PLT): the LINC02323 region is among 68 loci associated with PLT in up to 66,867 individuals of European ancestry; across all 68 loci, the average per-allele effect is approximately 2.57 × 10^9 cells/L.
  • Mean platelet volume (MPV): the same 68-locus panel includes associations with MPV; those loci collectively explain 9.9% of MPV variance, with an average per-allele effect of approximately 0.10 fL.

Evidence quality The platelet-trait evidence derives from a large meta-analysis (up to 66,867 European-ancestry individuals) applying genome-wide significance thresholds (P ≤ 5 × 10^-8) with a two-stage discovery-plus-replication design. Directional consistency was confirmed in South Asian (n up to 8,295 for PLT) and Japanese (n up to 14,697 for PLT) cohorts - a level of cross-ancestry concordance assessed as highly unlikely to arise by chance. The specific per-allele effect size for rs11628318 individually is not available in the provided evidence; the figures reported (approximately 2.57 × 10^9 cells/L for PLT and 0.10 fL for MPV per allele) are averages across all 68 loci, not variant-level estimates. LINC02323 is a long intergenic non-coding RNA (lncRNA) - it produces no known protein product - and the biological mechanism linking this locus to platelet biology remains uncharacterized. The GTEx eQTL data (n = 953 donors, FDR < 0.05) show consistent expression reduction across all eight reported tissues, supporting a regulatory role for rs11628318, but eQTL effects describe gene regulation rather than clinical outcomes and should not be interpreted as such.

Tissue-specific expression effects

  • LINC02323: reduced expression across eight tissues - sun-exposed skin (strongest effect), thyroid, non-sun-exposed skin, testis, subcutaneous adipose tissue, breast mammary tissue, esophageal mucosa, and transverse colon; all effects are directionally consistent (decreased expression) GTEx Portal.

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is LINC02323?

LINC02323 is a long intergenic non-coding RNA (lncRNA) gene - it produces an RNA molecule but does not code for a protein. Its biological role, including any connection to blood cell formation, is not yet fully established.

Is rs11628318 linked to platelet disorders?

A large genetic study found the LINC02323 region associated with normal variation in platelet count and mean platelet volume across roughly 67,000 people. This reflects variation within the normal physiological range rather than a clinical disease association.

What does eQTL mean, and why does it matter for this variant?

An eQTL (expression quantitative trait locus) is a genetic variant that influences how much a nearby gene is expressed. GTEx data show that the alternate allele at rs11628318 consistently reduces LINC02323 expression across at least eight tissues, suggesting the variant acts by altering the level of this lncRNA.

How strong is the genetic evidence for the platelet association?

The platelet associations come from a genome-wide-significant analysis (P ≤ 5 × 10^-8) in up to 66,867 people, with directional replication in South Asian and Japanese cohorts. The specific effect size for rs11628318 individually was not reported; the average across all 68 discovered loci was small, roughly 2.57 billion platelets per liter per allele copy.

Which tissues show reduced LINC02323 expression for this variant?

According to GTEx eQTL data, the alternate allele reduces LINC02323 expression in sun-exposed skin, thyroid, non-sun-exposed skin, testis, subcutaneous fat, breast tissue, esophageal mucosa, and the transverse colon - with the strongest effect observed in skin.