Table 2.

Performance of Natural Selection Statistic in Subsampled Data

Locus	SNP	Sample Size
Full Dataset	1k	2k	5k	10k	20k	50k
LCT	rs6754311	2.15 × 10−25	4.91 × 10−17	2.97 × 10−20	1.53 × 10−23	1.17 × 10−24	2.63 × 10−25	1.02 × 10−26
	rs4988235	1.15 × 10−27	7.44 × 10−17	9.80 × 10−20	4.64 × 10−23	3.11 × 10−24	2.69 × 10−25	1.62 × 10−27
	rs17346504	8.41 × 10−7	2.86 × 10−2	1.25 × 10−2	9.49 × 10−4	6.03 × 10−5	8.12 × 10−6	9.80 × 10−7
ADH1B	rs1229984	1.26 × 10−13	3.91 × 10−9	3.51 × 10−11	1.97 × 10−12	5.54 × 10−13	1.50 × 10−13	1.31 × 10−13
IRF4	rs12203592	5.52 × 10−55	3.15 × 10−6	9.18 × 10−12	7.47 × 10−25	7.21 × 10−36	7.02 × 10−45	2.19 × 10−54
HLA	rs382259	5.38 × 10−13	8.68 × 10−9	1.23 × 10−10	7.07 × 10−12	1.85 × 10−12	7.51 × 10−13	5.77 × 10−13
	rs9268628	8.66 × 10−18	3.62 × 10−5	3.41 × 10−7	5.97 × 10−12	2.10 × 10−14	2.68 × 10−16	1.00 × 10−17
	rs4394275	9.36 × 10−12	8.40 × 10−2	1.94 × 10−3	1.44 × 10−5	4.00 × 10−8	7.86 × 10−10	1.24 × 10−11
IGFBP3	rs150353309	5.82 × 10−12	5.90 × 10−4	1.49 × 10−5	2.72 × 10−8	3.61 × 10−10	3.34 × 10−11	6.61 × 10−12
IGH	rs34614900	5.23 × 10−9	6.33 × 10−3	2.24 × 10−4	2.26 × 10−6	2.01 × 10−7	3.32 × 10−8	5.32 × 10−9
OCA2	rs12916300	2.80 × 10−13	6.29 × 10−6	1.07 × 10−7	3.67 × 10−9	1.94 × 10−11	5.29 × 10−12	3.11 × 10−13
	rs2703951	5.11 × 10−7	1.12 × 10−1	2.45 × 10−2	7.96 × 10−4	7.17 × 10−5	4.52 × 10−6	5.74 × 10−7
TLR1	rs5743611	5.42 × 10−8	8.05 × 10−3	4.27 × 10−4	9.41 × 10−6	1.19 × 10−6	2.17 × 10−7	5.60 × 10−8
	rs4833095	6.52 × 10−7	6.07 × 10−4	3.37 × 10−4	7.35 × 10−5	3.64 × 10−5	6.03 × 10−6	7.10 × 10−7
SLC45A2	rs16891982	6.89 × 10−8	8.25 × 10−4	2.17 × 10−4	1.93 × 10−5	4.55 × 10−6	2.46 × 10−7	7.31 × 10−8

The selection statistic was computed in random subsets of individuals of specified size for each SNP in Table 1 (except for the chromosome 8 inversion region) and the known selection regions TLR1⁷⁴ and SLC45A2⁷⁶ in Table S4. We report the median selection statistic p value across 100 random subsets.