Table 2.

GREML-LDMS results: SNP-heritability (h²_SNP) partitioned by minor allele frequency (MAF) and linkage disequilibrium (LD) score

MAF range	1st quartile LD score	2nd quartile LD score	3rd quartile LD score	4th quartile LD score	Total
1%–9%	0.17 (0.03)*	0.01 (0.02)	0.00 (0.01)	0.00 (0.01)	0.08 (0.03)*
10%–19%	0.05 (0.03)*	0.04 (0.02)*	0.00 (0.01)	0.01 (0.01)	0.09 (0.03)*
20%–29%	0.05 (0.02)*	0.02 (0.02)	0.02 (0.01)	0.00 (0.01)	0.06 (0.03)*
30%–39%	0.02 (0.02)	0.01 (0.02)	0.02 (0.01)	0.00 (0.01)	0.05 (0.02)*
40%–49%	0.00 (0.02)	0.01 (0.02)	0.00 (0.01)	0.00 (0.01)	0.00 (0.02)
Total	0.30 (0.04)*	0.11 (0.03)*	0.03 (0.02)	0.01 (0.01)	h2SNP-SC = 0.27 (0.03) h2SNP-MS = 0.28 (0.03) h2SNP-LD = 0.45 (0.04) h2SNP-LDMS = 0.45 (0.04)

Notes: GREML = Genomic-Relatedness-Matrix Restricted Maximum Likelihood; LDMS = LD and MAF stratified. Table displays main effects for analyses with genetic variance partitioned based on MAF and LD (see “Total” column/row) and joint effects with genetic variance partitioned on both MAF and LD (see inner columns/rows). Analyses for joint effect of both MAF and LD comprised 20 genetic components, analyses for main effects of MAF were comprised of 5 genetic components, and analyses for main effects of LD were comprised of 4 genetic components. Total h²_SNP for each GREML approach are presented: SC = single component; MS = minor allele frequency stratified.

^*Indicates that the component contributes a significant portion of genetic variance to the model based on likelihood ratio test (LRT) p < .05.