Location: chr6:98102413 - 98102413(1)
Variant Alleles: C/A Ancestral Allele: C Minor Allele: A Minor Allele Frequency: 0.393021
rs1906252, located at chromosome 6q16.1 has been associated with cognitive function and education in two independent studies ([PMID 23722424]; [PMID 25951819]). rs1906252 is intergenic between MIR2113 and LOC100190924 (alfred.med.yale.edu). rs1906252 is about 700 kilobases from the nearest annotated gene and is located in an intron of a long intergenic non-coding RNA that is expressed in human brain tissue (Halbritter et al., 2012).
In the Trampush et al. study they used cohorts in the Cognitive Genomics Consortium (COGENT) with up to 20,495 healthy individuals. COGENT is an international GWAS collaboration created to analyze g as well as other neurocognitive processes in healthy individuals (Donohoe et al., 2013). They looked at the relationship between general cognitive ability (“g”) and variants associated with educational attainment. The general cognitive ability factor (“g”) explains 40-50% of the overall variance in performance on diverse laboratory measures of neurocognitive functioning (Johnson et al., 2008). Low g is associated with lower educational attainment and income as well as a variety of other health measures (Johnson et al., 2009). They found that rs1906252 was significantly associated with g in the COGENT population (p=1.47x10-4). They found that the minor (A) allele was associated with higher g scores.
Another paper (Rietveld et al., 2013) found a significant association between a close proxy SNP (rs9320913) and years of schooling. rs9320913 is located on chromosome 6 with A as the effective allele. They conducted a GWAS of educational attainment in a discovery sample of 101,069 individuals and then in a replication sample of 25,490 individuals. In the combined discovery and replication samples of 126,559 individuals, they found a p-value of 3.50x10-10. To analyze educational attainment, they used the quantitative variable of an individual’s years of schooling. They found that rs9320913 explains 0.022% of phenotypic variance in the replication sample. This R2 accounts for a difference of around 1 month of schooling per allele.
Cornelius, R.A. (2013) GWAS of 126,559 Individuals Identifies Genetic Variants Associated with Educational Attainment. Science 340(6139):1467-1471
Donohoe G. (2013) Neurocognitive phenomics: Examining the genetic basis of cognitive abilities. Psychol Med 43(10):2027–2036.
Halbritter F. (2012) GeneProf: Analysis of high- throughput sequencing experiments. Nature Methods 9:7–8.
Johnson W. (2008) Still just 1g: Consistent results from five test batteries. Intelligence 36:81–95.
Trampush, J.W. (2015) Independent Evidence for an Association between General Cognitive Ability and a Genetic Locus for Educational Attainment. Am J Med Genet Part B 9999:1–11.