Skip to main content
. Author manuscript; available in PMC: 2009 May 28.
Published in final edited form as: Nature. 2007 Oct 18;449(7164):913–918. doi: 10.1038/nature06250

Table 1.

The twenty-two strongest candidates for natural selection

Region Chr:position
(MB, HG17)		 Selected population Long Haplotype Test Size (Mb) Total SNPs with
Long Haplotype
Signal		 Subset of
SNPs that
fulfil criteria
1		 Subset of
SNPs that
fulfil criteria
1 and 2		 Subset of SNPs
that fulfil
criteria 1, 2
and 3		 Genes at or near SNPs that
fulfil all three criteria
1 chr1:166 CHB+JPT LRH, iHS 0.4 92 39 30 2 BLZF1, SLC19A2
2 chr2:72.6 CHB+JPT XP-EHH 0.8 732 250 0 0
3 chr2:108.7 CHB+JPT LRH, iHS, XP-EHH 1.0 972 265 7 1 EDAR
4 chr2:136.1 CEU LRH, iHS, XP-EHH 2.4 1,213 282 24 3 RAB3GAP1, R3HDM1, LCT
5 chr2:177.9 CEU,CHB+JPT LRH, iHS, XP-EHH 1.2 1,388 399 79 9 PDE11A
6 chr4:33.9 CEU,YRI, CHB+JPT LRH, iHS 1.7 413 161 33 0
7 chr4:42 CHB+JPT LRH, iHS, XP-EHH 0.3 249 94 65 6 SLC30A9
8 chr4:159 CHB+JPT LRH, iHS, XP-EHH 0.3 233 67 34 1
9 chr10:3 CEU LRH, iHS, XP-EHH 0.3 179 63 16 1
10 chr10:22.7 CEU, CHB+JPT XP-EHH 0.3 254 93 0 0
11 chr10:55.7 CHB+JPT LRH, iHS, XP-EHH 0.4 735 221 5 2 PCDH15
12 chr12:78.3 YRI LRH, iHS 0.8 151 91 25 0
13 chr15:46.4 CEU XP-EHH 0.6 867 233 5 1 SLC24A5
14 chr15:61.8 CHB+JPT XP-EHH 0.2 252 73 40 6 HERC1
15 chr16:64.3 CHB+JPT XP-EHH 0.4 484 137 2 0
16 chr16:74.3 CHB+JPT, YRI LRH, iHS 0.6 55 35 28 3 CHST5, ADAT1, KARS
17 chr17:53.3 CHB+JPT XP-EHH 0.2 143 41 0 0
18 chr17:56.4 CEU XP-EHH 0.4 290 98 26 3 BCAS3
19 chr19:43.5 YRI LRH, iHS, XP-EHH 0.3 83 30 0 0
20 chr22:32.5 YRI LRH 0.4 318 188 35 3 LARGE
21 chr23:35.1 YRI LRH, iHS 0.6 50 35 25 0
22 chr23:63.5 YRI LRH, iHS 3.5 13 3 1 0
Total SNPs 16.74 9,166 2,898 480 41

Twenty-two regions were identified at a high threshold for significance (Methods), based on the LRH, iHS and/or XP-EHH test. Within these regions, we examined SNPs with the best evidence of being the target of selection on the basis of having a long haplotype signal, and by fulfilling three criteria: (1) being a high-frequency derived allele; (2) being differentiated between populations and common only in the selected population; and (3) being identified as functional by current annotation. Several candidate polymorphisms arise from the analysis including well-known LCT and SLC24A5 (ref. 2), as well as intriguing new candidates.