RETRACTED ARTICLE: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

Cai, Zexi; Guldbrandtsen, Bernt; Lund, Mogens Sandø; Sahana, Goutam

doi:10.1186/s12863-018-0620-0

Table 1 Lead SNPs from genome-wide associated regions for fat yield in Nordic Holstein cattle. Base positions are given as position in UMD 3.1.1 [49]

From: RETRACTED ARTICLE: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

BTA	base position	Imputation accuracy	Effect	–log₁₀(p)	Region	Gene	Annotation
2	126979882	0.9972	−1.31	11.46	126041707~ 127230070	PIGV (near)	Downstream
2	85991577^b	0.9542	1.30	8.91	85042155~ 86241732	ANKRD44	Intron
3	7226390	0.9998	−1.09	9.01	6264604~ 7476473	NOS1AP	Intron
5	93948357	0.9906	3.28	62.41	93698481~ 94198475	MGST1	Intron
5	20284735^b	0.9692	−1.30	9.79	20035379~ 20534779	5S_rRNA	intergenic
6	95497933	0.9996	−1.45	14.76	95248213~ 95747954	PAQR3	intergenic
6	32950721^b	0.4975	6.33	11.39	32367171~ 33200834	ENSBTAG00000047255	Intron
7	57287990	0.8807	−1.66	20.11	57038213~ 57538309	KCTD16	Intron
9	38715137	0.9809	−1.47	8.89	38345408~ 38965425	LAMA4	Intron
11	88771449	0.9876	1.16	10.43	88521462~ 89021477	ENSBTAG00000047976	intergenic
11	15323223^b	0.8962	−1.32	9.81	14855568~ 15573444	TTC27	Intron
11	55681193^c	0.9948	−1.60	9.91	55423855~ 55931229	CTNNA2	Intron
12	68965758	0.9957	−1.10	8.93	68502223~ 69216445	ENSBTAG00000045195	intergenic
14^a	1802265	0.9398	−6.93	240.56	1549133~ 2049435	DGAT1	missense
14^a	1802266	0.9362	−6.93	240.56	1549133~ 2049435	DGAT1	missense
15	65891100	0.9992	1.50	12.99	65363764~ 66141839	ELF5	intergenic
15	25044706^b	0.9908	−1.17	9.80	24795472~ 25295470	ZBTB16	Intron
17	62543160	0.9898	1.14	10.49	62224291~ 62793298	TBX5	Intron
18	18970551	0.9442	−1.19	10.30	18341203~ 19220732	NKD1	intergenic
19	27522927	0.8500	−1.32	10.86	26625240~ 27773016	ASGR1	intergenic
20	22609736	0.9813	1.53	14.23	21664412~ 22859809	MAP3K1	intergenic
26	20547445	0.9993	−1.76	21.46	20297497~ 20797570	COX15	Intron
26	42408595^b	0.9998	−1.21	10.30	41409014~ 42658925	TACC2	Intron
29	23609412	0.7717	2.06	10.73	22613737~ 23859451	ENSBTAG00000047094	intergenic
	Total number of significant SNPs			54,435

^a Fourteen additional SNPs on chromosome 14 located near DGAT1 gene had same highest P value (details on those not presented). ^b indicated this SNP was found on second round, ^c indicated this SNP was found on third round

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ISSN: 2730-6844

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