Table 2 Location and regional genomic features of highly-differentiated New World SNPs
SNP rs number | Chr | Position | Derived allele | XP-CLR Ranka (percent) | XP-CLR scoreb | XP-EHH region | XP-EHH Ranka (percent) | Gene | Gene function |
|---|---|---|---|---|---|---|---|---|---|
rs2320170 | 2 | 95,603,500 | A | 10 | 7 / 7 | − | − | 5′ of TRIM43 | Zn-finger protein |
rs3774089 | 3 | 10,931,071 | T | 0.1 | 13 / 109 | 10,807,575 – 11,007,575 | 0.02 | SLC6A11 (intronic) | GABA transporter |
rs1344869 | 3 | 21,282,605 | G | 0.1 | 93/ 152 | 21,152,068 – 21,352,068 | 1 | − | − |
rs9847307 | 3 | 64,500,753 | A | 10 | 2 / 23 | − | − | ADAMTS9 (intronic) | Protease |
rs17617120 | 5 | 155,231,791 | T | 0.1 | 22 / 127 | 155,086,458 – 155,286,458 | 2 | SGCD (intronic) | Cardiac, skeletal |
rs17617422 | 5 | 155,249,830 | G | 0.1 | 80 / 130 | 155,086,458 – 155,286,458 | 2 | SGCD (intronic) | Cardiac, skeletal |
rs11960137 | 5 | 155,270,659 | G | 0.1 | 130 / 150 | 155,086,458 – 155,286,458 | 2 | SGCD (intronic) | Cardiac, skeletal |
rs2642515 | 7 | 145,998,474 | T | 1 | 103 / 103 | 145,884,552 – 146,084,552 | 2 | CNTNAP2 (intronic) | Neurexin, regulated by FOXP2 |
rs174547 | 11 | 61,327,359 | T | 10 | 21 / 23 | − | − | FADS1 (intronic) | Fatty acid desaturase |
rs174548 | 11 | 61,327,924 | C | 10 | 20 / 25 | − | − | FADS1 (intronic) | Fatty acid desaturase |
rs174549 | 11 | 61,327,958 | G | 10 | 20 / 25 | − | − | FADS1 (intronic) | Fatty acid desaturase |
rs11610143 | 12 | 50,635,338 | G | 1 | 26 / 82 | 50,502,870 – 50,702,870 | 0.04 | ACVR1B (intronic) | Signaling, growth factor receptor |
rs7955663 | 12 | 127,800,083 | A | 10 | 1 / 11 | − | − | − | − |
rs1538142 | 13 | 37,344,432 | C | 0.1 | 123 / 177 | 37,244,768 – 37,444,768 | 2.5 | 5′ of TRPC4 | Ca2+ channel |
rs693092 | 13 | 87,858,156 | G | 1 | 24 / 68 | 87,851,770 – 88,051,770 | 2 | − | − |
rs9515075 | 13 | 88,033,482 | C | 0.1 | 105 / 189 | 87,851,770 – 88,051,770 | 2 | − | − |
rs566514 | 13 | 32,551,339 | T | 10 | 19 / 32 | − | − | 5′ of STARD13 | GTP-binding, Lipid transfer |
rs7170342 | 15 | 32,755,246 | C | 10 | 6 / 21 | 32,602,304 – 32,802,304 | 1 | 5′of AA496137 | Expressed in testes |
rs4924116 | 15 | 35,086,443 | C | 1 | 10 / 56 | 34,986,366 – 35,186,366 | 1 | MEIS2 (intronic) | Homeobox, development |
rs12439270 | 15 | 58,029,372 | C | 1 | 57 / 87 | 57,850,426 – 58,050,426 | 1 | 5′of FOXB1 | Transcription factor |
rs1452501 | 16 | 79,180,763 | T | 10 | 8 / 21 | − | − | − |  |
rs470113 | 22 | 39,059,560 | A | 1 | 38 / 101 | − | − | TNRC6B (3′UTR) | Nucleotide binding |