Multiple QTL underlie milk phenotypes at the CSF2RB locus

Table 3 Median gene expression levels and top variants identified in eQTL analyses

Gene	Ensembl	FPKM	TPM	Top variant	MAF	Beta	SE	P
APOL3	ENSBTAG00000040244	0.934	1.166	rs433710540	0.101	0.128	0.0315	4.84 × 10⁻⁵
CSF2RB	ENSBTAG00000009064	61.888	80.081	rs384734208	0.439	0.428	0.0401	1.33 × 10⁻²⁶
EIF3D	ENSBTAG00000001988	9.139	11.461	rs110614216	0.353	− 0.072	0.0138	1.66 × 10⁻⁷
FOXRED2	ENSBTAG00000000015	0.142	0.179	rs385243246	0.176	0.036	0.0133	6.52 × 10⁻³
IFT27	ENSBTAG00000026657	0.904	1.107	rs110654851	0.440	0.046	0.0103	8.01 × 10⁻⁶
IL2RB	ENSBTAG00000016345	0.285	0.359	rs43436480	0.364	0.058	0.0184	1.61 × 10⁻³
MPST	ENSBTAG00000030648	1.564	1.957	rs109488885	0.314	− 0.053	0.0144	2.40 × 10⁻⁴
MYH9	ENSBTAG00000010402	14.448	17.497	rs377857213	0.034	0.280	0.0715	9.07 × 10⁻⁵
NCF4	ENSBTAG00000007531	0.406	0.513	rs209273109	0.443	0.137	0.0168	4.30 × 10⁻¹⁶
TST	ENSBTAG00000030650	2.131	2.662	rs109922126	0.073	− 0.152	0.0313	1.19 × 10⁻⁶
TXN2	ENSBTAG00000000014	4.345	5.653	rs109450151	0.454	− 0.080	0.0116	5.85 × 10⁻¹²

Genes with FPKM values less than 0.1 are not shown. Gene symbols are from VGNC and Ensembl. Beta is the effect size of the minor allele on gene expression, measured in VST-transformed units. Three genes have eQTL which exceed the genome-wide significance threshold 5 ×10⁻⁸ [60]

ISSN: 1297-9686