A genome-wide association study of mitochondrial DNA copy number in two population-based cohorts

Table 2 Summary statistics for top SNPs associated with mtDNA CN in two random-effects meta-analyses

Meta-analysis 1: ALSPAC mothers (N = 5461) and UKBS females (N = 1338)
rsID	Cluster	chr:pos_nonEA_EA	β (SE) P	Q P (het)	I ²	β (SE) P (ALSP)	β (SE) P (UKBSF)	Location	Lead SNP locus (or distance to genes within 200 kb, in bp)	Genes in this cluster	β (SE) P (CC)^a
rs12873707	13:104777684-104810437	13:104810437_T_C	0.159 (0.030) p = 9.27E−08	0.169 p = 0.681	0	0.165 (0.033) p = 4.34E−07	0.131 (0.076) p = 0.084	Intergenic	.	.	0.081 (0.060) p = 0.176
rs709591	17:38140926-38179290	17:38175561_T_A	− 0.084 (0.016) p = 1.54E−07	0.092 p = 0.762	0	− 0.086 (0.018) p = 1.05E−06	− 0.073 (0.038) p = 0.056	UTR3	MED24	CSF3, MED24, PSMD3	− 0.025 (0.033) p = 0.453
Meta-analysis 2: ALSPAC mothers (white cell samples only, N = 3405) and UKBS females (N = 1338)
rsID	Cluster	chr:pos_nonEA_EA	β (SE) P	Q P (het)	I ²	β (SE) P (ALSP)	β (SE) P (UKBSF)	Location	Lead SNP locus (or distance to genes within 200 kb, in bp)	Genes in this cluster	β (SE) P (CC)^a
rs150387260	8:53704895-53704896	8:53704896_G_A	0.405 (0.084) p = 1.65e−06	0.025 p = 0.875	0	0.397 (0.098) p = 4.98e−05	0.428 (0.169) p = 0.011	intergenic	RB1CC1 (dist = 77,870), NPBWR1 (dist = 147,572)	.	0.720 (0.336) p = 0.032

The top panel shows hits p < 1e−06 from the meta-analysis of all ALSPAC mothers (N = 5461) and UKBS females (N = 1338): ‘Meta-analysis 1’. The lower panel shows a meta-analysis restricted to females with DNA extracted from white cells (3405 ALSPAC mothers, 1338 UKBS females). In Meta-analysis 2, there were no associations at p < 1e−06, so instead the next strongest association is shown
Abbreviations: rsID SNP identifier; chr:pos_nonEA_EA chromosome, position, non-effect allele, effect allele; β regression coefficient (additive model); SE standard error; P p value; Q Cochran’s Q statistic; bp base pairs; P (het) p value for heterogeneity; I² statistic for heterogeneity; P (ALSP) p value in ALSPAC analysis contributing to meta-analysis (N = 5461 or N = 3405); P (UKBSF) p value in UKBS females analysis; P (CC) P (cell-proportion adjusted version of meta-analysis)
^aNB large drop in number of ALSPAC mothers after cell-proportion adjustment (see Table 1)

ISSN: 1479-7364