Finding SNPs by rsIDs
Chen et al in the paper ’Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.’ (Hum Mol Genet. 2013 Jun 15;22(12):2529-38) report on red blood cell traits in African Americans. The variants rs13335629 and rs9386791 are reported to be associated with multiple traits.
(a) What are the alleles and chromosome coordinates for each SNP?
(b) Is there good evidence supporting each SNP?
(c) Is there variability in the frequency of the alleles across different human populations from the 1000 Genomes Project?
(a) Search for rs13335629 and rs9386791 to find the pages describing each SNP.
rs13335629 has alleles G/A/C and is located on chromosome 16 at position 260381.
rs9386791 has alleles C/T and is located on chromosome 6 at position 109287294
(b) Both variants are supported by strong evidence as they were both discovered by a number of different labs and have frequency information from gnomAD and 1000 genomes.
(c) rs9386791 is polymorphic in all the 1000 genomes super populations. The T allele is most common in the African samples and the C allele is most common in the Asian samples.
rs13335629 is only reported to be polymorphic in the 1000 genomes African, American and South Asian super populations. These populations show a minor allele of A which is not seen in the other samples.