Table 1. Candidate regulatory variants.
| Gene | Pop a | VariantType | Position b | SNP ID | Variant Alleles c | DAF (%) d | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ref | Alt | Anc c | Den | Nea | AFR | ASN | EUR | |||||
| CXXC1 | CHB | 5’UTR | 18:47814249 | rs59393148 | T | C e | A | T | C | 75 | 89 | 91 |
| LRP5 | CHB | Intronic | 11:68209477 | rs671494 | A | C e | A | A | A | 22 | 75 | 65 |
| LRP5 | CHB | Intronic | 11:68209478 | rs649772 | C | A e | C | C | C | 22 | 72 | 63 |
| RUNX2 | CHB/YRI | Intronic | 6:45420847 | rs2677100 | C | T e | C | C | C | 87 | 96 | 65 |
| RUNX2 | CHB/YRI | Intronic | 6:45511541 | rs10948238 | C e | T | T | T | T | 28 | 96 | 59 |
| RUNX2 | YRI | Intronic | 6:45511945 | rs13201287 | G | A e | G | G | G | 45 | 4 | 28 |
Gene name and the population in which the selection signal was observed are given along with the variant type, SNP ID, position, alleles and frequencies.
a Populations YRI = Yoruba in Ibadan, Nigeria; CHB = Han Chinese in Beijing, China.
b Variant position chromosome: genomic co-ordinates in human reference GRCh37.
c Variant alleles Ref = reference; Alt = alternate; Anc = ancestral; Den = archaic Denisovan; Nea = Neanderthal. The ancestral and derived states of each variant were based on a 6 way primate alignment as determined by the Ensembl compara pipeline [50, 51].
d Derived allele frequencies (DAF) AFR = Africans; ASN = East Asians; EUR = Europeans.
e Derived alleles. For rs59393148 we consider the C allele to be derived in modern humans and Neanderthals, as the archaic Denisovan hominin is homozygous for the T allele which is also more prevalent in Africa.