Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria

Naka, Izumi; Nishida, Nao; Patarapotikul, Jintana; Nuchnoi, Pornlada; Tokunaga, Katsushi; Hananantachai, Hathairad; Tsuchiya, Naoyuki; Ohashi, Jun

doi:10.1186/1475-2875-8-232

Table 1 Allele frequencies and association tests for SNPs in 5q31 cytokine cluster

From: Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria

SNP rs#	Gene	Allelic state		Frequency of derived allele		Association P value
SNP rs#	Gene	Ancestral	Derived	Severe malaria	Mild malaria	Raw	Permutation
rs162887	SLC22A4	C	T	0.369	0.402	0.381	1.000
rs3792876	SLC22A4	C	T	0.234	0.236	0.944	1.000
rs3792878	SLC22A4	G	A	0.954	0.932	0.235	0.996
rs3805665	SLC22A4	G	A	0.23	0.237	0.823	1.000
rs3805668	SLC22A4	G	A	0.229	0.236	0.818	1.000
rs270608	SLC22A4	A	G	0.338	0.379	0.328	1.000
rs270607	SLC22A4	C	T	0.372	0.397	0.515	1.000
rs2073839	SLC22A4	C	T	0.234	0.236	0.950	1.000
rs3828673	SLC22A4	G	A	0.234	0.236	0.950	1.000
rs3792885	SLC22A4	A	T	0.229	0.236	0.818	1.000
rs272842	SLC22A4	T	C	0.348	0.299	0.181	0.985
rs3761659	SLC22A4	C	G	0.234	0.236	0.950	1.000
rs3805673	SLC22A4	G	A	0.228	0.237	0.771	1.000
rs273915	SLC22A4	G	C	0.375	0.397	0.563	1.000
rs272887	SLC22A4	C	T	0.372	0.397	0.515	1.000
rs273909	SLC22A4	T	C	0.071	0.093	0.307	1.000
rs272879	SLC22A4	G	C	0.344	0.297	0.201	0.992
rs272873	SLC22A4	C	T	0.167	0.175	0.773	1.000
rs2306772	SLC22A4	G	A	0.234	0.236	0.950	1.000
rs272867		C	T	0.344	0.298	0.205	0.992
rs3788987	SLC22A5	G	A	0.232	0.238	0.843	1.000
rs2631362	SLC22A5	T	C	0.365	0.376	0.769	1.000
rs2631359	SLC22A5	G	A	0.363	0.379	0.671	1.000
rs4646301	SLC22A5	G	A	0.236	0.253	0.614	1.000
rs274571	SLC22A5	T	C	0.365	0.379	0.719	1.000
rs2073642	SLC22A5	C	T	0.241	0.254	0.707	1.000
rs183898	SLC22A5	G	C	0.361	0.381	0.597	1.000
rs4646305	SLC22A5	G	A	0.237	0.251	0.678	1.000
rs274559	SLC22A5	C	T	0.348	0.299	0.181	0.985
rs274558	SLC22A5	C	T	0.353	0.299	0.144	0.965
rs274554	SLC22A5	A	G	0.837	0.887	0.059	0.748
rs274553	SLC22A5	G	C	0.163	0.113	0.059	0.748
rs274551	SLC22A5	C	T	0.161	0.113	0.072	0.804
rs274549	SLC22A5	G	T	0.163	0.113	0.059	0.748
rs274547	SLC22A5	T	A	0.839	0.887	0.072	0.804
rs2285673	LOC441108	C	T	0.227	0.199	0.388	1.000
rs2269822	LOC441108	C^b	T	0.282	0.281	1.000	1.000
rs3749834		C	T	0.236	0.238	0.929	1.000
rs2070730	IRF1	C	T	0.418	0.407	0.765	1.000
rs2070727	IRF1	G	T	0.42	0.406	0.725	1.000
rs2070723	IRF1	C	T	0.582	0.593	0.765	1.000
rs2070722	IRF1	G	T	0.596	0.587	0.823	1.000
rs739718^a		A	G	0.257	0.261	0.903	1.000
rs2069812^a	IL5	T	C	0.241	0.302	0.083	0.848
rs2299015	RAD50	A	C	0.111	0.186	0.008	0.193
rs2299014	RAD50	T	G	0.074	0.07	0.838	1.000
rs2243677	RAD50	G	A	0.887	0.804	0.004	0.107
rs2522414	RAD50	G	C	0.887	0.804	0.004	0.107
rs2299013	RAD50	C^c	G	0.104	0.186	0.004	0.101
rs2252775	RAD50	A	C	0.11	0.186	0.007	0.174
rs2522394	RAD50	A	G	0.887	0.804	0.004	0.107
rs2245460	RAD50	A	T	0.112	0.189	0.006	0.160
rs2301713	RAD50	T	C	0.113	0.186	0.010	0.242
rs3798135	RAD50	G	A	0.113	0.186	0.010	0.242
rs2237060	RAD50	A	C	0.04	0.055	0.351	1.000
rs2074369	RAD50	C	T	0.883	0.804	0.006	0.158
rs2240032	RAD50	C	T	0.106	0.183	0.006	0.152
rs1881457	IL13	A	C	0.124	0.219	0.002	0.046^d
rs1800925	IL13	T	C	0.894	0.826	0.014	0.296
rs2066960	IL13	A	C	0.628	0.636	0.830	1.000
rs20541^a	IL13	C	T	0.33	0.389	0.115	0.924
rs2070874	IL4	T	C	0.273	0.274	0.975	1.000
rs2243270	IL4	G	A	0.263	0.266	0.913	1.000
rs2243289	IL4	A	G	0.729	0.736	0.825	1.000
rs1468215	KIF3A	T	A	0.26	0.247	0.725	1.000
rs3798132	KIF3A	A	G	0.352	0.336	0.685	1.000
rs3798130	KIF3A	G	A	0.671	0.677	0.882	1.000
rs2299007	KIF3A	T	C	0.383	0.431	0.219	0.994
rs2237057	KIF3A	T	C	0.742	0.75	0.818	1.000
rs2299006	KIF3A	G	C	0.654	0.667	0.738	1.000
rs2299005	KIF3A	T	C	0.661	0.668	0.836	1.000
rs3798129	KIF3A	A	T	0.336	0.337	0.975	1.000
rs3756754	KIF3A	C	T	0.022	0.013	0.366	1.000
rs256871	SEPT8	C	T	0.609	0.635	0.490	1.000
rs30534	SEPT8	G	A	0.391	0.365	0.490	1.000
rs30533	SEPT8	T	C	0.386	0.371	0.686	1.000
rs39588	SEPT8	C	G	0.383	0.369	0.717	1.000
rs256875	SEPT8	T	C	0.385	0.379	0.888	1.000
rs392916	SEPT8	T	A	0.532	0.561	0.459	1.000
rs30527	SEPT8	C	T	0.62	0.639	0.620	1.000
rs30524	SEPT8	G	T	0.383	0.362	0.573	1.000
rs757537	ANKRD43	T	C	0.131	0.157	0.357	1.000

^a SNP genotyped by TaqMan assay.
^b Allelic state could not be inferred.
^c Allelic state inferred based on the sequence of rhesus macaque.
^d Permutation P value < 0.05.

Back to article page

ISSN: 1475-2875

Contact us

Submission enquiries: journalsubmissions@springernature.com

Malaria Journal

Contact us