Table 4.

The Top 10 Most Highly Differentiated Loci for the Amerindian Admixture Branch within the Brazil Samples Compared with the Putative Ancestral Population of the Three Admixture Components

CHR	SNP	GENPOSa	POSa	A1a	A2a	f(Eur)b	f(Amr)b	f(Afr)b	Fstc	Nearest Gened
16	rs6498115	28.170	10965511	T	C	0.000	0.908	0.000	0.908	CIITA, promoter
2	rs1834619	39.407	17901485	A	G	0.041	0.942	0.000	0.899	SMC6, intron
16	rs77979769	28.358	11343560	A	G	0.073	0.949	0.035	0.883	SOCS1, 3’ downstream
2	rs2288697	47.776	23860168	A	G	0.029	0.906	0.018	0.877	KLHL29, intron
16	rs35346036	28.164	10951098	G	A	0.065	0.957	0.088	0.872	CIITA
16	rs2021760	28.358	11343992	G	A	0.076	0.947	0.065	0.869	SOCS1, 3’ downstream
16	rs45601437	28.180	10989754	A	G	0.006	0.912	0.050	0.862	CIITA, intron
16	rs2866065	91.637	75822042	A	G	0.075	0.929	0.000	0.849	–
16	rs8054781	28.400	11384776	C	T	0.026	0.932	0.092	0.846	PRM1, promoter
15	rs16964480	35.881	37284909	G	T	0.000	0.837	0.000	0.837	MEIS2, intron

^aGENPOS is the genetic map position of the marker on a chromosome (CHR) in centiMorgans, POS is the hg19 physical map position, A1 is the reference allele, A2 the alternative.

^bf(Afr), f(Amr), f(Eur) are the estimated reference allele frequencies for SNP A1 allele in the 3 Brazil ancestral admixture components.

^cThis table shows the top ten ranked loci by Hudson Fst value, where Fst measures the genetic differentiation between the inferred second Amerindian admixture component (Amr) and a single ancestral population of all components. Fst is the Amerindian component branch-specific estimate of genetic differentiation.

^dNearest Gene is taken from the RefSeq track in the UCSC genome browser database (http://genome.ucsc.edu; last accessed October 16, 2016). Annotated SNPs are within 100 kb of the nearest gene. A promoter SNP is within 10 kb 5′ to the transcription start site; 3′ downstream SNP is within 10 kb 3′ of the nearest gene; exon and intron are within an exon or intron of the nearest gene.