BMC Genomics

Table 3 Minor allele frequencies for lactose QTL tag variants

From: DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

				Discovery		Validation
Pheno	Chr	Mbp	Tag Var	All (n=12,000)	HF (n=3 704)	Je (n=1 648)	All (n=18,000)	HF (n=4 588)	Je (n=2 350)
LC	1	154.14	rs43282035	*0.226	*0.226	*0.209	*0.231	*0.211	*0.236
LC	2	127.64	rs208702482	0.203	0.277	0.094	0.204	0.281	0.092
LC	3	15.52	rs211336034	0.449	0.440	0.465	0.454	0.448	0.456
LC	3	53.84	rs109613143	0.365	*0.489	0.190	0.377	*0.483	0.189
LC	5	21.14	rs377953581	0.444	0.264	*0.291	0.464	0.291	*0.304
LC	5	31.56	rs137534989	*0.493	*0.368	0.324	*0.483	*0.341	0.326
LC	5	44.16	rs383349320	0.253	0.176	0.364	0.247	0.169	0.352
LC	6	37.76	rs43702337	0.008	0.008	0.002	0.006	0.007	0.003
LC	6	89.04	rs478177439	0.215	0.362	0.005	0.207	0.360	0.010
LC	7	8.77	rs210686953	0.450	0.458	0.452	0.448	0.460	0.446
LC	10	2.14	rs137774567	0.302	0.452	0.100	0.304	0.447	0.089
LC	15	28.36	rs211369213	0.096	0.151	0.008	0.084	0.129	0.006
LC	16	24.99	rs109379517	0.303	0.405	0.178	0.285	0.388	0.157
LC	16	67.77	rs380467601	0.406	0.411	0.364	0.403	0.420	0.352
LC	17	56.47	rs134672113	0.375	*0.462	0.161	0.366	0.484	0.173
LC	19	33.51	rs109514832	*0.351	*0.258	0.486	*0.385	*0.328	0.488
LC	19	42.99	rs517084099	0.088	0.072	0.120	0.106	0.114	0.122
LC	19	61.13	rs41923843	*0.338	*0.326	*0.351	*0.327	*0.321	*0.349
LC	20	58.45	rs135934727	0.242	0.193	0.313	0.238	0.180	0.317
LC	27	36.21	rs209987511	0.367	0.291	*0.496	0.387	0.271	*0.450
LC	28	6.56	rs110674951	*0.447	0.342	*0.092	*0.438	0.387	*0.116
LC	29	9.61	rs378183369	0.250	0.310	0.198	0.268	0.326	0.222
LY	5	93.94	rs211210569	0.320	*0.465	0.023	0.324	*0.468	0.029
LY	11	63.45	rs210726760	0.229	0.330	0.056	0.229	0.367	0.054
LY	14	1.77	rs109234250	*0.408	0.466	*0.225	*0.407	0.462	*0.207
LY	20	31.69	rs208881195	*0.458	0.401	*0.248	*0.499	0.329	*0.259
LY	26	22.96	rs208730573	0.292	0.495	0.012	0.275	0.472	0.013

Minor allele frequencies for tag variants from WGS, for discovery and validation set cows. Frequencies for each animal set are shown in total and for pure-bred subsets. Cows are defined as belonging to the Holstein-Friesian (HF) or Jersey (Je) breed if 15/16 of their ancestry is recorded to that breed. Cases where the minor allele is the reference allele are marked with an asterisk (*), in the remaining cases, the minor allele is the alternative allele

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