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

BMC Genomics

Table 6 Correlations between lactose QTL and co-localised eQTL

Phenotype	Locus	Gene	eQTL PVal	Tag PVal	Pearson	Spearman	LD (R ²)
LC	chr1:154.14Mbp	SH3BP5	2.58×10⁻³²	6.18×10⁻³²	0.173	0.071	0.993
LC	chr3:15.52Mbp	SLC50A1	8.70×10⁻¹⁶	8.70×10⁻¹⁶	0.705	0.272	1.000
LC	chr3:53.84Mbp	LRRC8C	3.46×10⁻³⁹	1.53×10⁻³⁶	0.900	0.868	0.816
LC	chr5:44.16Mbp	RAB3IP	9.10×10⁻²³	2.22×10⁻²²	0.835	0.489	0.979
LC	chr10:2.14Mbp	NREP	6.12×10⁻¹⁰	1.55×10⁻⁹	0.822	0.774	0.676
LC	chr16:67.77Mbp	IVNS1ABP	4.54×10⁻²⁷	6.54×10⁻²⁴	0.812	0.339	0.887
LC	chr17:56.47Mbp	P2RX4	2.46×10⁻³⁹	3.26×10⁻¹³	0.743	0.692	0.280
LC	chr19:42.99Mbp	GHDC	1.80×10⁻²²	5.77×10⁻¹⁶	0.951	0.849	0.981
LC	chr19:42.99Mbp	DHX58	1.77×10⁻⁸	1.31×10⁻⁵	0.918	0.802	1.000
LC	chr19:42.99Mbp	STAT5B	5.72×10⁻⁹	1.51×10⁻⁶	0.915	0.773	0.524
LC	chr19:61.13Mbp	KCNJ2	1.72×10⁻²⁶	1.72×10⁻²⁶	0.870	0.645	1.000
LC	chr20:58.45Mbp	ANKH	2.40×10⁻¹⁶	2.40×10⁻¹⁶	0.783	0.404	1.000
LC	chr27:36.21Mbp	GPAT4	3.67×10⁻²¹	3.49×10⁻¹⁹	0.812	0.607	0.909
LC	chr29:9.61Mbp	PICALM	2.40×10⁻⁵⁴	2.40×10⁻⁵⁴	0.752	0.600	1.000
LC	chr29:9.61Mbp	EED	2.31×10⁻⁹	2.43×10⁻⁹	0.319	0.356	0.994
LY	chr5:93.94Mbp	MGST1	3.18×10⁻⁴³	9.37×10⁻⁴³	0.769	0.486	0.934
LY	chr14:1.77Mbp	DGAT1	8.87×10⁻⁴²	3.68×10⁻³⁹	0.946	0.829	0.923
LY	chr14:1.77Mbp	CCDC166	2.93×10⁻⁸	8.53×10⁻³	0.216	0.703	0.066

Co-localised genes for each lactose locus, where: the Pearson or Spearman correlation between the lactose QTL and eQTL is greater than 0.7, or, the LD between the top variants in the lactose QTL and eQTL is greater than 0.9. The p-value shown for the eQTL is that of the most significant SNP. The tag p-value is the significance of the lactose phenotype tag variant for the eQTL. Within each locus, genes are shown in descending order by Pearson correlation. Only eQTL which pass Bonferroni correction (threshold p=2.59×10⁻⁸) are shown

ISSN: 1471-2164