Table 2 Summary of genotyped and imputed... | American Society of Hematology

Table 2

Summary of genotyped and imputed SNP data generated from the GWAS-HCT dataset using the Affymetrix 5.0 Array and the HapMap release 22 SNPs

Gene	Type	rs number	Chr	Alleles*	MAF	Call rate	p_HWE	Average posterior probability	Status
CD31	Genotyped	rs1131012	17	C/T	0.472	0.98	0.08	0.98	Pass
CD31	Imputed	rs668	17	G/C	0.494	0.966	0.7	0.978	Pass
CTLA4	Genotyped	rs3087243	2	A/G	0.446	1	0.814	1	Pass
ESR1	Imputed	rs2234693	6	C/T	0.35	0.642	0.121	0.831	Fail
FAS	Imputed	rs1800682	10	G/A	0.464	0.899	0.218	0.948	Fail
HPSE	Genotyped	rs4364254	4	C/T	0.296	0.999	0.349	0.999	Pass
HPSE	Imputed	rs4693608	4	G/A	0.328	0.62	0.668	0.817	Fail
IL10	Imputed	rs1800871	1	A/G	0.238	0.951	0.352	0.972	Pass
IL10	Imputed	rs1800872	1	T/G	0.238	0.951	0.359	0.972	Pass
IL10	Imputed	rs1800896	1	C/T	0.472	0.799	0.245	0.898	Fail
IL10RB	Imputed	rs2834167	21	G/A	0.162	0.353	0.027	0.722	Fail
IL1B	Imputed	rs16944	2	A/G	0.359	0.944	0.44	0.962	Pass
IL2	Imputed	rs2069762	4	C/A	0.317	0.998	0.115	0.998	Pass
IL23R	Genotyped	rs11209026	1	A/G	0.064	0.998	0.598	0.998	Pass
IL6	Genotyped	rs1800795	7	C/G	0.375	0.998	0.006	0.998	Pass
MTHFR	Imputed	rs1801131	1	G/T	0.304	0.946	0.238	0.967	Pass
MTHFR	Imputed	rs1801133	1	A/G	0.182	0.449	0.221	0.77	Fail
RFC1	Imputed	rs1057807	4	G/A	0.425	0.999	0.166	0.999	Pass
RFC1	Imputed	rs4975003	4	C/G	0.441	0.893	0.274	0.932	Fail
RFC1	Imputed	rs6844176	4	C/T	0.494	0.748	0.047	0.878	Fail
TNF	Genotyped	rs1799964	6	C/T	0.205	1	0.063	1	Pass
TNF	Imputed	rs1800629	6	A/G	0.135	0.926	0.726	0.965	Pass
TNF	Imputed	rs1800630	6	A/C	0.152	0.996	0.153	0.997	Pass
TNFRII	Imputed	rs1061622	1	G/T	0.227	0.964	0.12	0.971	Pass
VEGFA	Imputed	rs699947	6	A/C	0.114	0.141	0.244	0.633	Fail
VEGFA	Imputed	rs833061	6	C/T	0.183	0.094	0.283	0.607	Fail

Gene	Type	rs number	Chr	Alleles*	MAF	Call rate	p_HWE	Average posterior probability	Status
CD31	Genotyped	rs1131012	17	C/T	0.472	0.98	0.08	0.98	Pass
CD31	Imputed	rs668	17	G/C	0.494	0.966	0.7	0.978	Pass
CTLA4	Genotyped	rs3087243	2	A/G	0.446	1	0.814	1	Pass
ESR1	Imputed	rs2234693	6	C/T	0.35	0.642	0.121	0.831	Fail
FAS	Imputed	rs1800682	10	G/A	0.464	0.899	0.218	0.948	Fail
HPSE	Genotyped	rs4364254	4	C/T	0.296	0.999	0.349	0.999	Pass
HPSE	Imputed	rs4693608	4	G/A	0.328	0.62	0.668	0.817	Fail
IL10	Imputed	rs1800871	1	A/G	0.238	0.951	0.352	0.972	Pass
IL10	Imputed	rs1800872	1	T/G	0.238	0.951	0.359	0.972	Pass
IL10	Imputed	rs1800896	1	C/T	0.472	0.799	0.245	0.898	Fail
IL10RB	Imputed	rs2834167	21	G/A	0.162	0.353	0.027	0.722	Fail
IL1B	Imputed	rs16944	2	A/G	0.359	0.944	0.44	0.962	Pass
IL2	Imputed	rs2069762	4	C/A	0.317	0.998	0.115	0.998	Pass
IL23R	Genotyped	rs11209026	1	A/G	0.064	0.998	0.598	0.998	Pass
IL6	Genotyped	rs1800795	7	C/G	0.375	0.998	0.006	0.998	Pass
MTHFR	Imputed	rs1801131	1	G/T	0.304	0.946	0.238	0.967	Pass
MTHFR	Imputed	rs1801133	1	A/G	0.182	0.449	0.221	0.77	Fail
RFC1	Imputed	rs1057807	4	G/A	0.425	0.999	0.166	0.999	Pass
RFC1	Imputed	rs4975003	4	C/G	0.441	0.893	0.274	0.932	Fail
RFC1	Imputed	rs6844176	4	C/T	0.494	0.748	0.047	0.878	Fail
TNF	Genotyped	rs1799964	6	C/T	0.205	1	0.063	1	Pass
TNF	Imputed	rs1800629	6	A/G	0.135	0.926	0.726	0.965	Pass
TNF	Imputed	rs1800630	6	A/C	0.152	0.996	0.153	0.997	Pass
TNFRII	Imputed	rs1061622	1	G/T	0.227	0.964	0.12	0.971	Pass
VEGFA	Imputed	rs699947	6	A/C	0.114	0.141	0.244	0.633	Fail
VEGFA	Imputed	rs833061	6	C/T	0.183	0.094	0.283	0.607	Fail

Chr indicates chromosome; HWE, Hardy-Weinberg equilibrium MAF, minor allele frequency; and SNP, single-nucleotide polymorphism.

The first allele is designated as the minor allele, and the second allele is designated as the major allele.