rs1071664 (TK1): Blood Cell and Gene Expression
Key takeaways
- rs1071664 is a variant in the TK1 gene region, identified in a large blood cell traits study of more than 563,000 people.
- The alternate allele reduces SYNGR2 expression in the pituitary, salivary gland, pancreas, and thyroid.
- This variant raises AFMID expression in whole blood but lowers it in thyroid and sun-exposed skin - opposite directions in the same gene.
- In tibial artery tissue, the alternate allele is linked to increased TK1 expression.
- All associations are from population-level data and do not indicate individual clinical outcomes.
Key takeaways
- rs1071664 is a variant in the TK1 gene region, identified in a large blood cell traits study of more than 563,000 people.
- The alternate allele reduces SYNGR2 expression in the pituitary, salivary gland, pancreas, and thyroid.
- This variant raises AFMID expression in whole blood but lowers it in thyroid and sun-exposed skin - opposite directions in the same gene.
- In tibial artery tissue, the alternate allele is linked to increased TK1 expression.
- All associations are from population-level data and do not indicate individual clinical outcomes.
What the research says A genome-wide association study (GWAS) integrating data from the UK Biobank and a large international collaborative effort, encompassing 563,085 participants of European ancestry, identified 5,106 new genetic variants independently associated with 29 blood cell phenotypes, providing the population-genetic context within which rs1071664 was characterized. Expression quantitative trait locus (eQTL) analyses from GTEx v11 (953 donors) - studies that examine how genetic variants relate to nearby gene activity - show that the alternate allele at this locus is associated with reduced SYNGR2 (synaptogyrin-2) expression in the pituitary, minor salivary gland, pancreas, and thyroid GTEx Portal. The same alternate allele increases AFMID (arylformamidase) expression in whole blood while reducing it in thyroid and sun-exposed skin, and is also linked to increased TK1 expression in tibial artery GTEx Portal.
Reported associations
- Blood cell phenotypes: rs1071664 was identified in the context of a GWAS covering 29 blood cell phenotypes in 563,085 European ancestry participants; the study excerpt provided does not specify which individual phenotype this variant is primarily associated with.
- SYNGR2 expression - pituitary: the alternate allele is associated with reduced SYNGR2 expression in the pituitary gland, representing the strongest signal across all tested tissues for this gene GTEx Portal.
- SYNGR2 expression - salivary gland, pancreas, thyroid: the alternate allele is associated with reduced SYNGR2 expression in minor salivary gland, pancreas, and thyroid, with smaller effect sizes than in pituitary GTEx Portal.
- AFMID expression - whole blood: the alternate allele is associated with increased AFMID expression in whole blood GTEx Portal.
- AFMID expression - thyroid and skin: the alternate allele is associated with reduced AFMID expression in thyroid and sun-exposed lower-leg skin, the opposite direction from the whole blood finding GTEx Portal.
- TK1 expression - tibial artery: the alternate allele is associated with increased TK1 expression in tibial artery tissue GTEx Portal.
Evidence quality The blood cell trait GWAS integrated data from the UK Biobank and an international cohort totaling 563,085 European ancestry participants and identified 5,106 new variants across 29 phenotypes; this represents a large-scale effort but the specific effect size and p-value for rs1071664 in any blood cell phenotype were not available in the provided study excerpt. The eQTL evidence is drawn from GTEx v11 (953 donors) using a cis-window approach at FDR less than 0.05, meaning the false discovery rate - a statistical measure controlling how many reported associations are likely to be spurious - is held below 5% across all tests. The SYNGR2 eQTL signals are directionally consistent across all four tissues tested, lending confidence to that finding. However, AFMID shows directionally opposite effects in whole blood versus thyroid and sun-exposed skin; this explicit conflict suggests tissue-specific regulatory mechanisms rather than a uniform effect of the variant, and the biological basis of this divergence is not established from the available data. All eQTL associations describe population-level gene expression differences and do not establish functional or clinical consequences for any individual.
Tissue-specific expression effects
- SYNGR2: the alternate allele is associated with reduced expression in the pituitary gland (strongest effect), minor salivary gland, pancreas, and thyroid; all four tissues show the same direction of change GTEx Portal.
- AFMID: the alternate allele shows opposing tissue-specific directions - reduced expression in thyroid and sun-exposed lower-leg skin, but increased expression in whole blood GTEx Portal.
- TK1: the alternate allele is associated with increased expression in tibial artery tissue GTEx Portal.
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is the TK1 gene and what does rs1071664 have to do with it?
TK1 (thymidine kinase 1) is a gene in whose region rs1071664 is located. Tissue-specific gene expression data show that the alternate allele at this variant is associated with increased TK1 expression in tibial artery tissue, suggesting a potential regulatory role at this locus, though the functional significance is not established.
What blood traits is rs1071664 associated with?
rs1071664 was identified through a large genome-wide association study covering 29 blood cell phenotypes in more than 563,000 participants. The available study data do not specify which individual blood cell phenotype this variant is primarily associated with.
Why does rs1071664 have opposite effects on AFMID expression in different tissues?
Gene expression data from GTEx show that the alternate allele increases AFMID expression in whole blood while decreasing it in thyroid and sun-exposed skin. This directional conflict likely reflects different regulatory contexts in each tissue type, though the functional consequences are not established.
What is SYNGR2 and why is its expression affected by rs1071664?
SYNGR2 (synaptogyrin-2) is a gene near this locus. Expression data show that the alternate allele at rs1071664 is consistently linked to reduced SYNGR2 expression across four tissues - pituitary, minor salivary gland, pancreas, and thyroid - making this variant an expression quantitative trait locus (eQTL) for SYNGR2 across multiple secretory tissues.
Is rs1071664 linked to any disease or health condition?
The available evidence places rs1071664 in the context of blood cell trait genetics and gene expression variation. No direct disease associations are described in the provided studies for this variant specifically.