Table 2.
Merged regions under selection and SNPs most likely to be selected in PNG lowlanders
| Merged top regions | Score | Protein coding genes in the region | Candidate SNP for the region | DAF | Significant association (UK Biobank) | Introgressed haplotype | Archaic origin |
|---|---|---|---|---|---|---|---|
| chr1:88800562-89326878 | XPEHH, PBS, Fisher |
PKN2, GTF2B, KYAT3, RBMXL1, GBP3, GBP1, GBP2, GBP7, GBP4, GBP5 |
rs368120563-T>C | 0.87 | – | chr1:89054418-89202534 | ambiguous |
| chr1:237827847-237992467 | PBS | RYR2, ZP4 | rs1574154373-T>C | 0.14 | –b | – | – |
| chr2:124085628-124249405 | PBS | CNTNAP5 | rs7583123-G>T | 0.49 | – | – | – |
| chr2:200238798-200432145 | PBS | SPATS2L | chr2:200269472-A>G | 0.05 | –b | – | – |
| chr2:241759136-242088831a | XPEHH, PBS, Fisher | GAL3ST2, NEU4, PDCD1, RTP5, FAM240C | rs376150658-C>G | 0.23 | –b | chr2:241811883-241869518 | Neanderthal |
| chr4:82750503-83146792 | Fisher | SCD5, SEC31A, LIN54, COPS4, PLAC8 | rs4693058-C>T | 0.76 | Blood composition | chr4:82755644-83083169 | Denisovan |
| chr4:171791098-171986729 | Fisher | GALNTL6 | rs926184421-G>T | 0.08 | Other phenotypesb | – | – |
| chr5:65504470-65708617 | XPEHH |
CENPK, TRIM23, SGTB, PPWD1, SHLD3, TRAPPC13 |
rs36003688-T>C | 0.31 | – | – | – |
| chr6:85266477-85483888 | PBS | NT5E | rs989789809-T>C | 0.14 | –b | chr6:85340299-85364688 | Denisovan |
| chr7:129548370-129836070 | XPEHH, Fisher | NRF1, UBE2H | rs6950082-T>A | 0.49 | Blood composition, other phenotypesb | chr7:129553314-129774681 | Denisovan |
| chr8:133791891-133962825 | PBS | – | rs187915256-A>G | 0.99 | –b | – | – |
| chr9:93717217-93877803 | XPEHH | – | rs372277219-G>A | 0.22 | – | chr9:93752325-93867864 | Neanderthal |
| chr12:120353731-120666335 | Fisher | MSI1, COX6A1, GATC, TRIAP1, SRSF9, DYNLL1,COQ5, RNF10,POP5, CABP1 | rs75047318-T>C | 0.07 | Blood composition, body proportion, respiratory capacities, other phenotypes | chr12:120368947-120395906 | ambiguous |
| chr13:61590770-61993327 | XPEHH | – | rs537391125-A>G | 0.94 | –b | – | – |
| chr13:89660867-89920623a | Fisher | – | rs72634302-G>A | 0.48 | – | – | – |
| chr14:37137933-37382802 | XPEHH | SLC25A21, MIPOL1 | rs1594377001-G>A | 0.05 | –b | – | – |
| chr14:77312867-77558267 | PBS, Fisher | POMT2, GSTZ1, SAMD15, NOXRED1, VIPAS39, ISM2,SPTLC2, TMED8, AHSA1 | rs12885954-C>T | 0.57 | – | – | – |
| chr16:87806834-87928392 | XPEHH | SLC7A5, CA5A | rs2287123-G>A | 0.32 | Other phenotypes | – | – |
| chr17:54003406-54222843 | XPEHH | – | rs575590765-G>A | 0.11 | –b | chr17:54036011-54160414 | Denisovan |
| chr18:41133289-41618597 | Fisher | – | rs2848745-G>C | 0.95 | – | – | – |
| chr19:11708670-12108034 | PBS | ZNF823, ZNF441, ZNF491, ZNF440, ZNF439, ZNF69,ZNF700, ZNF763, ZNF433, ZNF20, ZNF878, ZNF844 | rs900717974-C>T | 0.11 | –b | chr19:11708670-12108034 | Neanderthal |
| chr19:16344294-16576199 | XPEHH | EPS15L1, CALR3, CHERP, C19orf44, SLC35E1, MED26 | rs1870071-C>T | 0.76 | Blood composition | – | – |
| chr19:54176104-54330609a | PBS, Fisher | MBOAT7, TSEN34, RPS9, LILRB3, LILRA6, LILRB5, LILRB2, LILRA5 | rs1600734199-T>C | 0.13 | –b | – | – |
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 lowlanders 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 lowlanders.
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.