Table 2. Regions identified across the genome which contains an overrepresentation of SNPs that exhibit strong correlations between allele frequencies and latitude in 22 East and South-East Asian populations in the HapMap, HGDP and SGVP.
| Chr | Start (Mb) | End (Mb) | MAF latitude correlation Pa (rsID) | FST (CHB vs CHS) | XP-EHHb (direction) | iHS (CHB) | iHS (CHS) | SNP loadings (rsID) | Genes |
|---|---|---|---|---|---|---|---|---|---|
| Top 0.1% | |||||||||
| 6 | 32.610 | 33.110 | 2.1 × 10−5 (rs6901084) | Top 0.5% | Top 0.5% (positive) | Top 0.01% | Top 0.01% | Top 0.1% (rs9268832) | HLA-DRB1, HLA-DQA1-2, HLA-DOB, PSMB9, BRD2, TAP2, PSMB8, TAP1, HLA-DMB, HLA-DMA, HLA-DOA |
| 8 | 32.155 | 32.655 | 2.0 × 10−4 (rs4489283) | No evidence | Top 0.5% (positive) | Top 0.5% | Top 0.5% | Top 0.1% (rs4489283) | NRG1 |
| Top 0.5% | |||||||||
| 3 | 39.038 | 39.538 | 6.6 × 10−5 (rs2370969) | No evidence | Top 0.1% (negative) | Top 0.5% | Top 0.1% | Top 0.1% (rs1464047) | WDR48, GORASP1, TTC21A, AXUD1, CMYA1, CX3CR1, CCR8, SLC25A38, LAMR1, MOBP |
| 3 | 136.038 | 136.538 | 9.3 × 10−4 (rs6762261) | No evidence | No evidence | Top 0.1% | Top 0.5% | Top 0.5% (rs6788931) | EPHB1 |
| 6 | 18.610 | 19.110 | 9.5 × 10−4 (rs986148) | No evidence | Top 0.1% (positive) | Top 0.1% | No evidence | No evidence | NA |
Abbreviations: CHB, Han Chinese from Beijing; CHS, Singapore Chinese with South China ancestries; HGDP, Human Genome Variation Project; iHS, integrated haplotype score; SGVP, Singapore Genome Variation Project; XP-EHH, cross-population extended haplotype homozygosity.
Bonferroni corrected P-value for the test of correlation between allele frequencies and latitude of the 22 East and South-East Asian populations from HapMap, HGDP and SGVP. The Bonferroni correction is performed by multiplying the empirical P-value by the number of SNPs found in each region.
XP-EHH between CHB and CHS, with positive indicating evidence of positive selection in CHB, whereas negative indicating evidence of positive selection in CHS.
The table highlights the genomic stretches found in the top 0.1 and 0.5% of the genome-wide distribution for regional evidence of clinical variation in allele frequencies that are supported by concordant information from the SNP loadings of the first axis of variation in a principal component analysis of the 22 populations and from other bioinformatic evidences from the comparisons between CHB and CHS (FST, XP-EHH and differential signals of iHS). For each region, the SNP with the strongest evidence of MAF latitude correlation is reported.