Table 1 Summary information of highly differentiated functional SNPs at ZTGS. It is noted that in the column “allele”, the first allele is the ancestral state, while the second one with highlight is the derived state. PRD, probably disease-causing; BNG, benign; iTMD, in transmembrane domain; NT, N-terminus; nTMD, near transmembrane domain; IV, intro variant; UGV, upstream gene variant; RRV, regulatory region variant; LS- FST, Locus-specific FST
rsID | Gene | Position | Allele | FEUR | FASN | FAFR | FAMR | LS-FST | Type | Database | Effect or Related | PolyPhen-2 | Topology and location | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
rs1871534 | SLC39A4 | 8:145639681 | G/C | 0.002 | 0.000 | 0.873 | 0.081 | 0.763 | Missense | RegulomeDB | Leu/Val | PRD: 0.991 | iTMD (Fig. S4A) | |
rs1047626 | SLC30A9 | 4:42003671 | A/G | 0.750 | 0.953 | 0.126 | 0.737 | 0.387 | Missense | - | Met/Val | BNG: 0.000 | NT ()  Analysis of putative selected haplotypes carrying 7 14nSNPs in SLC30A9. (A) Haplotypes shared among different continental groups. African populations are more likely to harbor haplotype CAGAGAC, while in non-African populations, haplotype CGGAGAC is much more pervasive, especially in East Asians in whom the haplotype frequency is nearly fixed. (B) Graphical depictions of SLC30A9 haplotypes constructed from 7 14nSNPs with haplotype frequencies derived from the 1000 Genomes Project. Hap1 (CAGAGAC) is the same as the haplotype in a chimpanzee (Chimp) and a Neanderthal (Nean). Hap2 (CGGAGAC) is different from Hap1 at rs1047626 of which the derived allele can alter an amino acid change from methionine acid to valine (M50V). (C) Predicted membrane topology of human SLC30A9 generated using HMMTOP and visualized with TeXtopo. Location of rs1047626 carried by the possible selected haplotype is indicated. | |
rs2466517 | SLC39A11 | 17:70943990 | T/C | 0.001 | 0.002 | 0.343 | 0.055 | 0.212 | Missense | RegulomeDB | Thr/Ala | BNG: 0.000 | nTMD (Fig. S4B) | |
rs11011935 | SLC39A12 | 10:18280113 | T/C | 0.000 | 0.000 | 0.238 | 0.022 | 0.158 | Missense | RegulomeDB | Phe/Leu | BNG: 0.000 | nTMD (Fig. S4C) | |
rs2010519 | SLC39A13 | 11:47431728 | G/A | 0.001 | 0.012 | 0.221 | 0.000 | 0.135 | Missense | - | Glu/Gly | BNG: 0.000 | NT (Fig. S4D) | |
rs2272662 | SLC39A4 | 8:145639726 | T/C | 0.541 | 0.496 | 0.087 | 0.416 | 0.130 | Missense | RegulomeDB | Thr/Ala | BNG: 0.012 | iTMD (Fig. S4A) | |
rs75920625 | SLC39A4 | 8:145639654 | T/C | 0.001 | 0.000 | 0.135 | 0.018 | 0.092 | Missense | RegulomeDB | Thr/Ala | BNG: 0.012 | nTMD (Fig. S4A) | |
rs61756712 | SLC30A4 | 15:45814306 | A/G | 0.001 | 0.008 | 0.342 | 0.045 | 0.224 | Splice | RegulomeDB | - | - | ||
rs759071 | SLC39A3 | 19:2728577 | G/A | 0.327 | 0.632 | 0.817 | 0.283 | 0.168 | eQTL | RegulomeDB | - | - | ||
rs6832846 | SLC39A8 | 4:103181749 | A/G | 0.787 | 0.526 | 0.986 | 0.705 | 0.112 | eQTL | RegulomeDB | - | - | ||
rs151368 | SLC39A8 | 4:103181113 | A/T | 0.787 | 0.526 | 0.986 | 0.705 | 0.112 | eQTL | RegulomeDB | - | - | ||
rs11889699 | SLC39A10 | 2:196528101 | A/G | 0.588 | 0.366 | 0.127 | 0.377 | 0.108 | eQTL | RegulomeDB | - | - | ||
rs17278473 | SLC39A8 | 4:103243101 | C/T | 0.400 | 0.024 | 0.179 | 0.324 | 0.097 | eQTL | RegulomeDB | - | - | ||
rs151372 | SLC39A8 | 4:103174196 | C/T | 0.787 | 0.528 | 0.951 | 0.700 | 0.093 | eQTL | RegulomeDB | - | - | ||
rs950027 | SLC30A4 | 15:45801035 | T/C | 0.452 | 0.947 | 0.953 | 0.652 | 0.210 | IV | GWAS | Response to fenofibrate | - | ||
rs11264736 | SLC39A1 | 1:153939130 | T/C | 0.494 | 0.949 | 0.730 | 0.666 | 0.123 | UGV | GWAS | Lentiform nucleus volume | - | ||
rs17060812 | SLC39A14 | 8:22228828 | C/T | 0.039 | 0.066 | 0.341 | 0.070 | 0.111 | RRV | PharmGKB | Nortriptyline | - | ||
