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/s12863-019-0717-0

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: 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
1	71,227,484	0.9745	−1.77	9.66	70,442,929~71,477,578	TNK2	intron
2	126,979,882	0.9972	−1.31	11.46	126,041,707~127,230,335	PIGV (near)	downstream
2	85991577^b	0.9542	1.30	8.91	85,042,155~86,241,732	ANKRD44	intron
3	7,226,390	0.9998	−1.09	9.01	6,264,604~7,476,497	NOS1AP	intron
5	93,948,357	0.9906	3.28	62.41	93,698,481~94,198,670	MGST1	intron
5	20284735^b	0.9692	−1.30	9.79	20,035,379~20,534,779	5S_rRNA (near)	intergenic
6	95,497,933	0.9996	−1.45	14.76	95,248,213~95,747,954	PAQR3 (near)	intergenic
6	32950721^b	0.4975	6.33	11.39	32,367,171~33,200,834	ENSBTAG00000047255	intron
7	57,287,990	0.8807	−1.66	20.11	57,038,215~57,538,309	KCTD16	intron
9	38,715,137	0.9809	−1.47	8.89	38,345,408~38,965,425	LAMA4	intron
11	88,771,449	0.9876	1.16	10.43	88,521,462~89,021,477	ENSBTAG00000047976 (near)	intergenic
11	15323223^b	0.8962	−1.32	9.81	14,855,568~15,573,444	TTC27	intron
12	68,965,758	0.9957	−1.10	8.93	68,502,223~69,216,445	ENSBTAG00000045195 (near)	intergenic
14^a	1,802,265	0.9398	−6.93	240.56	1,549,133~2,049,435	DGAT1	missense
14^a	1,802,266	0.9362	−6.93	240.56	1,549,133~2,049,435	DGAT1	missense
14	67981742^b	0.7652	1.65	8.71	67,117,232~68,231,920	STK3	intron
14	1321721^c	0.4442	1.46	8.82	1,087,168~1,583,427	ENSBTAG00000046435	missense
15	65,891,100	0.9992	1.50	12.99	65,641,131~66,141,839	ELF5 (near)	intergenic
15	25044706^b	0.9908	−1.17	9.80	24,795,472~25,295,470	ZBTB16	intron
16	31,496,700	0.9501	−1.37	9.32	30,519,873~31,746,789	CNST	intron
17	62,543,160	0.9898	1.14	10.49	62,224,291~62,793,298	TBX5	intron
18	18,970,551	0.9442	−1.19	10.30	18,341,203~19,220,732	NKD1 (near)	intergenic
19	27,522,927	0.8500	−1.32	10.86	26,625,240~27,773,922	ASGR1 (near)	intergenic
20	22,609,736	0.9813	1.53	14.23	21,664,412~22,859,809	MAP3K1 (near)	intergenic
20	44186112^b	0.9997	1.53	10.20	43,936,468~44,436,133	ENSBTAG00000040572 (near)	intergenic
26	20,547,445	0.9993	−1.76	21.46	20,299,309~20,797,570	COX15	intron
26	42408595^b	0.9998	−1.21	10.30	41,409,014~42,658,925	TACC2	intron
29	23,609,412	0.7717	2.06	10.73	22,613,737~23,859,451	ENSBTAG00000047094 (near)	intergenic
Total number of significant SNPs					52,334

^aFourteen additional SNPs on chromosome 14 located near DGAT1 gene had same highest P value (details on those not presented). Note, ^bindicated this SNP was found on second round, ^cindicated this SNP was found on third round

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ISSN: 2730-6844

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