Table 1.
Merged regions under selection and SNPs most likely to be selected in PNG highlanders
| Merged top regions | Score | Protein coding genes in the region | Candidate SNP for the region | DAF | Significant association (UK Biobank) | Introgressed haplotype in PNG highlanders | Archaic origin |
|---|---|---|---|---|---|---|---|
| chr1 :95529290-95736826 | XPEHH | – | rs887476833-G>A | 0.55 | –b | – | – |
| chr2 :151012094-151201575 | PBS | – | rs74621527-G>A | 0.92 | – | chr2 :151077551-151194524 | Neanderthal |
| chr3 :13010340-13217789 | XPEHH | IQSEC1 | rs374181005-C>T | 0.41 | –b | chr3 :13132090-13174330 | Denisovan |
| chr3 :61779523-62009858 | PBS, Fisher | PTPRG | rs79600167-G>A | 0.77 | – | chr3 :61798966-61853037 | Neanderthal |
| chr4 :110182324-110384099 | XPEHH | ELOVL6 | rs943845085-A>G | 0.42 | –b | chr4 :110232325-110334098 | Neanderthal |
| chr4 :152704503-152970509 | XPEHH | TIGD4, ARFIP1, FHDC1 | rs369030953-A>G | 0.59 | – | – | – |
| chr6 :30916070-31153184a | XPEHH |
VARS2, SFTA2, MUCL3, MUC21, MUC22, HCG22, C6orf5, PSORS1C1, CDSN, PSORS1C2, PSORS1C1, CCHCR1 |
rs940110341-A>C | 0.61 | – | chr6 :31077777-31112941 | ambiguous |
| chr6 :33006055-33132312a | PBS, Fisher | HLA-DAO, HLA-DPA1, HLA-DPB2 | rs9277772-T>C | 0.21 |
Body proportion, blood composition, other phenotypes (Supplementary Table S13) |
– | – |
| chr7:147590904-147718219 | PBS | CNTNAP2 | rs17170618-T>C | 0.52 | – | chr7:147665094-147696027 | Denisovan |
| chr9:85458922-85745092 | XPEHH | AGTPBP1 | rs28728004-C>A | 0.69 | – | – | – |
| chr10:131112245-131235951 | PBS | TCERG1L | rs10829909-T>G | 0.43 | – | chr10:131130857-131157433 | Denisovan |
| chr12:6452552-6662260 | XPEHH |
LINC02388c, TAPBPL, VAMP1, MRPL51, GAPDH, NOP2, LPAR5, ING4, ACRBP, CHD4,IFFO1, NCAPD2 |
rs74576183-A>G | 0.71 | Blood composition (Table S13) | – | – |
| chr12:9886812-10055333 | Fisher | KLRF2, CLEC2A, CLEC12A, CLEC1B, CLEC12B, CLEC9A | rs536947-C>T | 0.91 | – | chr12:9904201-10023903 | Denisovan |
| chr12:58391529-58634980 | XPEHH, PBS, Fisher | – | rs376870800-C>T | 0.70 | – | chr12:58451248-58568114 | ambiguous |
| chr12:103783315-104121479 | Fisher | NT5DC3, HSP90B1, GLT8D2, HCFC2, NFYB, TDG | rs1032698711-G>A | 0.47 | –b | chr12:103839272-104061448 | Denisovan |
| chr13:47639988-47825193 | PBS | – | rs1033760372-C>A | 0.19 | –b | – | – |
| chr13:104734734-104875020 | PBS, Fisher | – | rs16965509-G>A | 0.50 | - | chr13:104787393-104824094 | Denisovan |
| chr14:60157772-60377317 | Fisher | PCNX4, DHRS7, PPM1A | rs1033848215-A>G | 0.32 | – | – | – |
| chr14:92230479-92401520 | Fisher | SLC24A4 | rs8003454-C>T | 0.52 | – | chr14:92370144-92392663 | ambiguous |
| chr18:4072997-4251153 | XPEHH, Fisher | DLGAP1 | rs371858795-T>C | 0.77 | – | chr18:4136427-4203633 | Denisovan |
| chr22:45519818-45644906 | PBS, Fisher | FBLN1 | rs1601558750-C>T | 0.10 | – | – | – |
Genomic coordinates are given for GRCh38.
Genes in bold are the closest to the candidate SNP defined with CLUES for the region.
The introgressed archaic haplotypes with the highest frequency in each candidate region for selection in PNG highlanders are reported. Introgressed haplotype with which the candidate SNP in high LD (r² > 0.5) with at least one archaic SNP are in bold. The putative source of introgression is based on hmmix results.
DAF is given for PNG highlanders.
aReference Assembly Alternate Haplotype Sequence Alignments.
bCandidate SNP was not present in the UK Biobank, association is shown for the closest SNP within 50 bp upstream and downstream region.
clong intergenic non-protein coding RNA.