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Table 1 Number of genetic markers mapped to different functional SNP classes

From: Predicting male fertility in dairy cattle using markers with large effect and functional annotation data

Class Definition Variant description Number of SNP
5′ Region Upstream gene variant Located within 5000 bases of the 5′ of an annotated gene 7280
5’UTR Located in the 5′ untranslated region of an annotated gene
3′ Region Downstream gene variant Located within 5000 bases of the 3′ of an annotated gene 4122
3’UTR Located in the 3′ untranslated region of an annotated gene
Non-synonymous Missense Changes one base resulting in a different amino acid sequence, but the length of the polypeptide is preserved. 1144
Nonsense Changes one base resulting in a premature stop codon, leading to a shortened polypeptide.
Synonymous Synonymous Changes one base but resulting in the same amino acid. 2090
ncRNA ncRNA Located in a non-coding RNA gene 1556