rs1197062 (LINC01999): Height-Associated Variant

Key takeaways

• rs1197062, located near LINC01999 (a long intergenic non-coding RNA, meaning an RNA molecule that is not translated into protein), is one of 12,111 genetic variants significantly tied to human height, found in a study of over 5.4 million people across five ancestry groups.
• The alternate allele at this position is linked to reduced activity of the APPBP2 gene in skeletal muscle, based on GTEx tissue expression data from 953 donors.
• Together, the full set of height-linked variants (including this one) accounts for roughly 40% of height variation in people of European ancestry.
• Effect sizes were broadly similar across ancestry groups, but height prediction was less accurate in non-European populations due to allele frequency differences.

What the research says rs1197062 is one of 12,111 independent genetic variants identified as significantly associated with adult human height in a genome-wide association study (GWAS - a method that scans the genome for variants linked to a trait) of 5,380,080 individuals drawn from 281 studies spanning European, East Asian, Hispanic, African, and South Asian ancestry groups. Together, the full set of identified variants accounts for approximately 40% of the variation in height among people of European ancestry, and roughly 10-20% in other ancestry groups. Separately, GTEx v11 data from 953 donors show that the alternate allele at rs1197062 is associated with reduced expression of the APPBP2 gene in skeletal muscle tissue (slope -0.15, p=3.0e-4, FDR<0.05) GTEx Portal.

Reported associations

• Human height: rs1197062 was found to be one of 12,111 genome-wide significant variants in a meta-analysis of 5,380,080 individuals across 281 studies. Together, these variants explain nearly all of the common-variant heritability of adult height, and fall within 7,209 non-overlapping genomic segments averaging about 90 kilobases (roughly 90,000 DNA base pairs) in size, covering roughly 21% of the human genome.

Evidence quality The height association of rs1197062 is supported by a large meta-analysis (5,380,080 individuals, 281 contributing studies) across multiple ancestry groups: European (approximately 75.8% of participants), East Asian (8.8%), Hispanic (8.5%), African (5.5%), and South Asian (1.4%). No individual effect size for this specific variant is reported in the provided study text. Effect sizes and associated genomic regions were broadly similar across ancestry groups, though prediction accuracy was lower in non-European populations, likely due to differences in allele frequency and linkage disequilibrium (the tendency of nearby variants to be inherited together) within associated regions. The tissue-specific expression link with APPBP2 in skeletal muscle is based on GTEx v11 data (953 donors, FDR<0.05, a statistical threshold controlling for false discoveries) and represents a gene-regulation observation rather than a clinical outcome GTEx Portal.

Tissue-specific expression effects

• APPBP2: the alternate allele at rs1197062 is associated with reduced expression in skeletal muscle tissue GTEx Portal.

Lifestyle considerations No lifestyle considerations on file for this variant.