Table 2.
Select SNPs and Genes with Archaic Origin and Their Function Effects
| SNPs and Genes Linked to Phenotype | Reference | SNPs and Genes Linked to Phenotype | Reference | ||
|---|---|---|---|---|---|
| 1 | SELP, rs3917862, hypercoagulable state | Simonti 2016 N, E | 21 | CHORDC1, skin color | Dannemann 2017 E |
| 2 | SLC35F3, rs12049593, protein-calorie malnutrition | Simonti 2016 N, E | 22 | rs1834481, interleukin-18 levels | Sankararaman 2014 N |
| 3 | Increase in plasma prothrombin time (rs6013) | Skov 2020 N | 23 | rs11175593, Crohn's disease | Sankararaman 2014 N |
| 4 | EPAS1, hypoxia | Huerta-Sanchez 2014D, T | 24 | rs11564258, MUC19, Crohn's disease and inflammatory bowel disease | Rinker et al. 2020 N |
| 5 | rs28387074, decreased concentration of hemoglobin | Skov 2020 N | 25 | rs3118914, reduced height | Skov 2020 N |
| 6 | ASB1, morning or evening person (chronotype) | Dannemann 2017 E | 26 | rs72728264, decrease in mean corpuscular hemoglobin | Skov 2020 N |
| 7 | SLC6A11, rs901033, tobacco use disorder | Simonti 2016 N, E | 27 | SLC24A4, hair color (natural before graying) | Dannemann 2017 E |
| 8 | EXOC2, hair color (natural before graying) | Dannemann 2017 E | 28 | ADAMTSL3, impedance of leg (left and right) | Dannemann 2017 E |
| 9 | RUNX2, skin color | Dannemann 2017 E | 29 | GOLGA6L4, impedance of leg (left and right) | Dannemann 2017 E |
| 10 | GJA1, pulse rate | Dannemann 2017 E | 30 | FANCA, hair color (natural before graying) | Dannemann 2017 E |
| 11 | rs12531711, systemic lupus erthematosus, primary biliary cirrhosis | Sankararaman 2014 N | 31 | SPIRE2, hair color (natural before graying) | Dannemann 2017 E |
| 12 | BNC2, ease of skin tanning, skin color, incidence of childhood sunburn | Dannemann 2017 E | 32 | TCF25, hair color (natural before graying) | Dannemann 2017 E |
| 13 | rs3025343, smoking behavior | Sankararaman 2014 N | 33 | MC1R, hair color (natural before graying) | Dannemann 2017 E |
| 14 | rs7076156 Crohn's disease | Sankararaman 2014 N | 34 | TUBB3, hair color (natural before graying) | Dannemann 2017 E |
| 15 | rs12571093, optic disc size | Sankararaman 2014 N | 35 | rs75493593, type-2 diabetes | Sankararaman 2014 N |
| 16 | PBLD, sitting height | Dannemann 2017 E | 36 | rs75418188, type-2 diabetes | Sankararaman 2014 N |
| 17 | EXOC6, daytime dozing or sleeping (narcolepsy) | Dannemann 2017 E | 37 | rs117767867, type-2 diabetes | Sankararaman 2014 N |
| 18 | RHOG, symptoms involving urinary system | Simonti 2016 N, E | 38 | ZNF536, comparative height size at age 10 years | Dannemann 2017 E |
| 19 | rs11030043, symptoms involving urinary system | Simonti 2016 N, E | 39 | rs17632542, reduced risk of prostate cancer | Skov 2020 N |
| 20 | STIM1, symptoms involving urinary system | Simonti 2016 N, E |
Note.—All SNPs and genes have evidence for archaic introgression and functional effect. E—European, indicating that the SNP or gene was identified in a modern European population. N—Neanderthal, indicating that the source of the SNP or gene was a Neanderthal population. T—Tibetan, indicating that the SNP or gene was identified in a modern Tibetan population. D—Denisovan, indicating that the source of the SNP or gene was a Denisovan population. Citations without a modern population indicated (E or T) were detected using a broad panel of modern populations. Citations without Neanderthal or Denisovan indicated were detected using a method that generated a more general result of archaic introgression, without a specific population specified.