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

Chr: chromosome; aRanking for a region based on the best score for the SNP ± 25 kb (XP-CLR) or ± 100 kb (XP-EHH), ranked empirically by percent of the distribution (e.g. the top 10%, 1%, 0.1%, …), comparisons to CHB/JPT; bSNP score / Best score for region (SNP location ± 25 kb); positions based on hg18.

Watkins et al.

Watkins et al. BMC Genetics 2012 13:39   doi:10.1186/1471-2156-13-39

Open Data