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. 2014 Feb 18;31(5):1275–1291. doi: 10.1093/molbev/msu077

Table 2.

The Top Ten Genes with the Most Extreme nSL Scores in the Masaai (MKK) and Yoruban (YRI) Populations.

Population SNPid Chr Position Derived Allele DAF nSL P Value Function Rec Rate Gene
MKK rs16831455 2 135690238 G 16 6.63 1e–5 Intron — ZRANB3
MKK rs309154 2 136443037 C 25 6.24 1e–5 Intron — DARS
MKK rs16838134 2 137595057 C 22 −6.12 1e–5 Intron 0.024 THSD7B
MKK rs13390171 2 135493974 A 25 5.97 1e–5 Intron — YSK4
MKK rs6430516 2 134935075 G 29 5.89 1e–5 Intron 1.449 TMEM163
MKK rs2289959 2 136140374 C 19 5.49 1e–5 Intron 0.004 R3 HDM1
MKK rs11887041 2 134773894 G 52 5.43 1e–5 Intron — MGAT5
MKK rs3769012 2 136272950 A 73 −5.31 1e–5 Intron 0.003 LCT
MKK rs4954221 2 135625932 G 70 −5.30 1e–5 Intron — RAB3 GAP1
MKK rs1050115 2 136228287 G 70 −5.25 1e–5 Coding-synon 0.003 UBXN4
YRI rs7193968 16 69230453 G 2 4.94 5e–5 Unknown — IL34*
YRI rs4312417 19 43489029 A 78 −4.85 1e–5 Intron 0.729 YIF1B*
YRI rs11880532 19 43550883 T 80 −4.83 1e–5 Intron — CATSPERG
YRI rs2866908 4 108124957 A 14 4.83 1e–5 Intron — DKK2*
YRI rs10231365 7 20398110 C 25 4.82 1e–5 Intron 1.526 ITGB8
YRI rs2413395 22 34984662 A 7 4.82 1e–5 Intron 2.325 APOL1 (lipid binding)
YRI rs8136512 22 32461239 C 28 −4.81 1e–5 Intron 1.071 LARGE*
YRI rs6687226 1 160158180 A 1 4.76 1e–5 Intron 0.057 ATF6*
YRI rs11292 10 102303597 G 20 4.73 1e–5 Untranslated-3 0.087 HIF1 AN
YRI rs10234980 7 79958990 T 25 −4.64 1e–5 Intron — CD36 (lipid binding)

Note.—The table shows the top ten |nSL| scores falling within genes in the MKK and YRI populations from HapMap3. The first column indicates the population, next columns show the SNP identification number, the location (chromosome and position) of each SNP based on HG18, the derived allele and derived allele frequency (DAF), the nSL score and P value (calculated under the demographic model for Yoruba proposed in Gutenkunst et al. [2009]; the function of the SNP, the recombination rate (Rec Rate) in cM/Mb at the site (from the DeCode recombination rate map) and the gene the SNP is located in. In the YRI population, SNPs that are not among the strongest signatures of selection according to Voight et al. (2006) are marked with an asterisk. Genes involved in lipid binding and in the metabolism of cholesterol are indicated in the table with the notation: lipid binding.