Genes Associated with SLE Are Targets of Recent Positive Selection

Table 2

Regions with evidence for selection on the HapMap populations.

Gene region	Chr	Mb	iHS		𝐷		𝐹ST			Empirical 𝑃 value
			Max −log(𝑄)	Pop	Max −log(𝑄)	Pop	Max −log(𝑄)	Value	Pop	Min 𝑃 value	Pop
PTPN22	1	114.158	—	—	3.6	YRI	3.2	0.75	YRI versus ASN	—	—
TNFSF4	1	171.419	2.5	ASN	2.3	ASN	2.7	0.60	YRI versus ASN	0.005	ASN
NMNAT2	1	181.484	2.5	ASN	2.4	CEU	—	—	—	0.004	ASN
NCF2	1	181.791	2.5	ASN	—	—	—	0.65	CEU versus YRI	0.004	ASN
APOBEC4	1	181.882	2.5	ASN	—	—	—	0.65	CEU versus YRI	0.004	ASN
CFH	1	194.888	—	—	—	—	3.0	0.60	YRI versus ASN	—	—
CFHR1, CFHR4	1	196.789	2.0	YRI	—	—	3.0	0.60	YRI versus ASN	—	—
TET3, DGUOK	2	74.212	2.7	CEU	2.6	ASN	3.2	0.85	YRI versus ASN	0.001	CEU
IFIH1	2	162.832	—	—	3.8	CEU	2.2	0.78	CEU versus YRI	—	—
TREX1	3	48.481	2.4	ASN	2.1	ASN	—	—	—	0.002	ASN
TNIP1	5	150.390	—	—	3.0	CEU	—	0.65	CEU versus YRI	—	—
ITPR3	6	33.697	3.4	YRI	3.3	YRI	3.3	0.60	YRI versus ASN	—	—
UHRF1BP1	6	34.868	2.5	CEU	2.4	YRI	—	0.50	—	0.004	CEU
XKR6	8	10.791	2.7	ASN	3.3	ASN	2.6	0.92	YRI versus ASN	0.003	ASN
BLK	8	11.389	2.7	ASN	3.2	ASN	2.6	0.92	YRI versus ASN	0.005	ASN
ARMC3	10	23.257	—	—	2.5	CEU	2.5	0.65	YRI versus ASN	—	—
LRRC18, WDFY4	10	49.893	—	—	2.0	ASN	2.5	0.80	YRI versus ASN	—	—
ITGAM	16	31.179	—	—	—	—	3.4	0.75	YRI versus ASN	—	—
CD226	18	65.681	—	—	3.1	CEU	3.7	0.80	CEU versus YRI	—	—

Regions were considered to show evidence for selection if the maximum −log(𝑄)>3 for either the 𝐹_ST, 𝐷, or iHS, or it had SNPs with 𝐹_ST values in the top 1% within each population comparison, or the empirical 𝑃 value estimated for the SLE-associated gene and for each population showed significant evidence for selection (𝑃 value < 0.01). Cells that did not meet these thresholds or whose −log(𝑄)>2 are marked with (—). The table shows the highest −log(𝑄) value and respective population for the iHS, 𝐷, and 𝐹_ST, the 𝐹_ST statistic (value) for SNPs in the top 1% and the population comparison, and the minimum empirical 𝑃 value in each region. 𝑄 is the rank of the observed statistic for a given SNP divided by the total number of SNPs. The statistic that is ranked is obtained independently for each of the three statistics separately for each population. For iHS, for each SNP, 25 SNPs on either side of the SNP are scanned for |iHS|>2. The proportion of SNPs in this 51 SNP window with |iHS|>2 is computed. For 𝐷, the estimated value of 𝐷 was used for ranking. For 𝐹_ST, the statistic to be ranked is obtained in a similar manner as that for iHS except for each population comparison, the thresholds for defining a significant 𝐹_ST is based on the top 5% cutoff for each population comparison. See Methods for details. Chr: chromosome, Mb: mega basepairs, Max: maximum, Min: minimum, Pop: population, ASN: East Asian, CEU: European, YRI: African.