Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation in recently admixed populations

Table 2 Top genome-wide significant SNPs in conditional meta-analysis and on each independent study

SNP	Chr	Position (GRCg37/hg19)	EA/ NEA	Genes^a	Fixed Effects Model^b			Random Effects Model^c P-value	Cochran’s Q		I²
SNP	Chr	Position (GRCg37/hg19)	EA/ NEA	Genes^a	P-value	Beta	SD	Random Effects Model^c P-value	Q	P-value	I²
rs10160510	11	88614324	T/A	GRM5	3.36E-10	−0.248	0.039	7.54E-11	11.078	0.011	72.920
rs3098576	15	27858408	T/C	(GABRG3/OCA2)	8.90E-09	0.182	0.032	1.30E-08	2.883	0.410	0.000
rs1448484	15	28283441	G/A	OCA2	3.73E-10	0.213	0.034	5.83E-10	2.237	0.525	0.000
rs1667392	15	28533565	C/G	HERC2	4.64E-09	−0.268	0.046	6.65E-09	1.048	0.306	4.580
rs36194177	15	29118784	A/G	(APBA2)	4.95E-10	0.229	0.037	2.58E-10	9.281	0.026	67.676
rs2636060	15	29425936	A/G	FAM189A1	5.71E-10	−0.231	0.037	8.79E-10	3.433	0.330	12.611
rs10416746	19	3563982	A/G	(MFSD12)	1.01E-09	0.309	0.051	1.55E-09	3.947	0.267	24.002

The table presents the results of the meta-analysis after conditioning for SLC24A5 rs1426654 and SLC45A2 rs35397, which had very strong effects in the original meta-analysis (p = 6.32 × 10^− 39, and rs35397, p = 1.98 × 10^− 24, respectively)
Chr Chromosome, EA Effect allele, NEA Non-effect allele, SD Standard deviation, M Posterior probability of an existent effect on each study, I² Heterogeneity statistic, NA Marker not genotyped
^aFor variants located in intergenic regions, nearby genes are indicated in parenthesis
^bFixed effects model, as computed in Metasoft
^cHan and Eskin’s Random Effects Model

ISSN: 2730-6844