Table 1 Summary of the markers on the XT-50K genotyping array.

From: Genome-wide fine-mapping identifies pleiotropic and functional variants that predict many traits across global cattle populations

Variant type

Count

SNP

45,226

INDEL

1285

Gene body

18,569

Regulatory

13,627

Evolutionary

2157

Multi-trait p < 0.05 in either sex

39,756

Multi-trait π > 0.9 in either sex

37,503

Low MAF

3373

  1. Gene body: not annotated as ‘intergenic’ from Ensembl VEP31 and NGS-variant32. Regulatory: milk fat mQTLs, sQTLs, aseQTLs, eeQTLs, geQTLs and variants under ChIP-Seq peaks. Evolutionary: variants at sites conserved across 100 vertebrate species and/or under selection. Multi-trait p: p-value of the multi-trait meta-analysis (chi-square test11) of 34 single-trait GWAS in each sex. Multi-trait π: multi-trait posterior probability of non-zero effects across 34 traits as summed across single-trait BayesRC runs. Low MAF: variants with minor allele frequency <5% in both sexes.
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