Mannose-binding lectin 2 gene polymorphisms and their association with tuberculosis in a Chinese population

Zhang, Jun-Xian; Gong, Wen-Ping; Zhu, Dong-Lin; An, Hui-Ru; Yang, You-Rong; Liang, Yan; Wang, Jie; Tang, Jing; Zhao, Wei-guo; Wu, Xue-Qiong

doi:10.1186/s40249-020-00664-9

Table 1 Information about 64 genotyped SNPs in the IL-10, IL18R1, IL1A, IL1B, STAT1, SLC11A1, SP110, IL12B, LTA, TNF, IFNGR1, MBL2, VDR, IL27, CCL2, IL12RB1, IFNGR2, and TLR8

From: Mannose-binding lectin 2 gene polymorphisms and their association with tuberculosis in a Chinese population

Gene: locus and OMIM No.^a	No.	SNP_ID	Chromosome No.	Chromosome position ^b	Intermarker distances ^c (bp)	Genic location	Base Change	MAF ^d			P^f	P value for HWE ^g test	Genotyping rate ^h(%)
Gene: locus and OMIM No.^a	No.	SNP_ID	Chromosome No.	Chromosome position ^b	Intermarker distances ^c (bp)	Genic location	Base Change	NCBI ^e	Control	Tuberculosis	P^f	P value for HWE ^g test	Genotyping rate ^h(%)
IL10: 1q31-q32 OMIN: 124092	1	rs3024496	1	206 768 519	–	3’UTR	T → C	0.0097	0.051	0.049	0.730	0.5467	99.7
	2	rs1800871	1	206 773 289	4770	Intron	T → C	0.2573	0.364	0.341	0.226	0.5098	98.7
	3	rs1800896	1	206 773 552	263	Intron	A → G	0.0340	0.092	0.092	0.964	0.8843	100
IL18R1: 2q12 OMIN: 604494	1	rs3771167	2	102 369 728	–	Intron	T → C	0.0485	0.035	0.035	0.902	0.4203	100
	2	rs1974675	2	102 369 915	187	Intron	C → T	0.1456	0.136	0.126	0.435	0.8773	99.8
	3	rs6758936	2	102 374 909	4994	Intron	G → A	0.1699	0.142	0.141	0.944	0.6809	99.8
	4	rs6750020	2	102 378 254	3345	Intron	G → A	0.4806	0.459	0.442	0.376	0.1350	99.6
	5	rs1035130	2	102 384 942	6688	Exon 6 F251F	G → A	0.3495	0.317	0.299	0.301	0.1045	99.5
	6	rs3771158	2	102 393 434	8492	Intron	T → C	0.0971	0.097	0.088	0.439	0.7258	99.7
IL1A: 2q14 OMIN: 147760	1	rs17561	2	112 779 646	–	Exon 4 A114S	G → T	0.0631	0.121	0.098	0.063	0.8821	99.6
IL1A: 2q14 OMIN: 147760	2	rs3783526	2	112 784 230	4584	Intron	A → G	0.3689	0.351	0.367	0.374	0.0129	99.3
IL1B: 2q14 OMIN: 147720	1	rs2853550	2	112 829 544	45 314	Intron	C → T	0.0825	0.111	0.112	0.913	0.1487	99.9
	2	rs1143633	2	112 832 890	3346	Intron	A → G	0.4126	0.435	0.426	0.658	0.5667	98.9
	3	rs1143627	2	112 836 810	3920	UTR-5	T → C	0.4563	0.497	0.489	0.685	0.7878	97.0
STAT1: 2q32.2 OMIN: 600555	1	rs2280235	2	190 979 104	–	Intron	C → T	0.4660	0.484	0.465	0.335	0.2941	98.7
	2	rs16833155	2	190 996 651	17 547	Intron	C → T	0.0291	0.053	0.054	0.982	0.6981	99.9
	3	rs13029247	2	191 001 932	5281	Intron	C → T	0.5000	0.476	0.462	0.463	0.0728	98.8
	4	rs7576984	2	191 003 857	1925	Intron	C → A	0.1650	0.167	0.160	0.647	0.2140	99.7
	5	rs2066802	2	191 009 941	6084	Exon 1 L21L	T → C	0.2427	0.218	0.210	0.620	0.2973	99.2
SLC11A1: 2q35 OMIN: 600266	1	rs2276631	2	218 384 290	–	Exon 2 F66F	G → A	0.1408	0.144	0.149	0.665	0.3834	99.2
	2	rs17221959	2	218 387 907	3617	Exon 7 G249G	C → T	0.1068	0.099	0.112	0.295	0.9842	95.4
	3	rs17235409	2	218 395 009	7102	Exon 14 D543N	G → A	0.1408	0.138	0.125	0.311	0.5529	99.1
SP110: 2q37.1 OMIN: 604457	1	rs9783992	2	230 170 873	–	Intron	T → C	0.0049	0.002	0.002	0.989	0.9645	99.9
	2	rs10165685	2	230 174 882	4009	Intron	G → A	0.1262	0.159	0.157	0.845	0.6981	99.8
	3	rs957683	2	230 178 660	3778	Intron	T → C	0.3738	0.456	0.445	0.566	0.1516	98.7
	4	rs41345344	2	230 200 212	21 552	Intron	C → G	0.2718	0.170	0.185	0.322	0.4374	98.5
	5	rs1365776	2	230 207 994	7781	Exon 7 G305R	A → G	0.1068	0.126	0.114	0.351	0.4184	99.6
IL12B: 5q31.1-q33.1 OMIN: 161561	1	rs1368439	5	159 315 006	–	3’URT	T → G	0.0097	0.004	0.003	0.496	0.9289	99.8
	2	rs919766	5	159 320 556	5550	Intron	A → C	0.0437	0.052	0.053	0.901	0.7283	100
	3	rs3212217	5	159 328 122	7566	Intron	G → C	0.4417	0.455	0.427	0.145	0.1761	99.6
	4	rs2546892	5	159 328 467	345	Intron	G → A	0.1845	0.186	0.212	0.101	0.8839	96.5
LTA: 6p21.3 OMIN: 153440	1	rs2009658	6	31 570 467	–	Intron	C → G	0.1845	0.144	0.171	0.057	0.3741	99.4
	2	rs1800683	6	31 572 294	1827	5’UTR	G → A	0.4175	0.438	0.420	0.342	0.5831	98.7
	3	rs2229094	6	31 572 779	485	Exon 1 C13R	T → C	0.2282	0.190	0.229	0.015	0.1732	99.3
	4	rs2229092	6	31 572 980	201	Exon 2 H51P	A → C	0.0243	0.021	0.024	0.631	0.0871	99.9
	5	rs1041981	6	31 573 007	27	Exon 2 T60N	C → A	0.4175	0.437	0.419	0.349	0.6545	99.0
TNF: 6p21.3 OMIN: 191160	1	rs1800629	6	31 575 254	2247	Intron	G → A	0.0922	0.054	0.069	0.100	0.1735	99.5
TNF: 6p21.3 OMIN: 191160	2	rs3093662	6	31 576 412	1158	Intron	A → G	0.0340	0.038	0.048	0.183	0.7276	99.3
IFNGR1: 6q23.3 OMIN: 107470	1	rs1887415	6	137 198 101	–	Exon 7 L467P	T → C	0.0194	0.029	0.031	0.743	0.5056	99.7
	2	rs2234711	6	137 219 383	21 282	5’UTR	C → T	0.4757	0.453	0.448	0.811	0.2336	99.3
MBL2: 10q11.2 OMIN: 154545	1	rs2099902	10	52 766 089	–	3’UTR	T → C	0.2670	0.198	0.255	0.001	0.4386	99.3
	2	rs930507	10	52 768 506	2417	Exon 4 L126L	C → G	0.2427	0.191	0.237	0.004	0.8992	97.1
	3	rs10824793	10	52 769 720	1214	Intron	A → G	0.3398	0.285	0.336	0.004	0.9966	99.9
	4	rs7916582	10	52 773 235	3515	Intron	T → C	0.1456	0.111	0.126	0.232	0.6949	99.6
VDR: 12q13.11 OMIN: 601769	1	rs2239184	12	47 850 800	–	Intron	C → T	0.2913	0.279	0.271	0.637	0.8753	99.8
	2	rs2248098	12	47 859 573	8773	Intron	T → C	0.2621	0.292	0.281	0.519	0.2028	99.7
	3	rs1540339	12	47 863 543	3970	Intron	A → G	0.2670	0.289	0.316	0.124	0.3715	99.7
	4	rs10783219	12	47 901 705	38 162	Intron	A → T	0.4175	0.433	0.465	0.110	0.4119	94.3
	5	rs7139166	12	47 906 551	4846	Intron	C → G	0.0243	0.028	0.027	0.852	0.5221	99.9
IL27: 16p11 OMIN: 608273	1	rs181206	16	28 502 082	–	Exon 4 L119R	T → C	0.1456	0.136	0.129	0.621	0.3844	99.0
CCL2: 17q11.2-q12 OMIN: 158105	1	rs4586	16	34 256 250	–	Exon 2 C35C	C → T	0.3641	0.412	0.380	0.092	0.9518	99.1
IL12RB1: 19p13.1 OMIN: 601604	1	rs2305740	19	18 069 426	–	Intron	A → G	0.0922	0.136	0.110	0.040	0.7880	99.9
	2	rs401502	19	18 069 603	177	Exon 11 G378R	C → G	0.3350	0.369	0.344	0.186	0.5334	99.8
	3	rs375947	19	18 069 641	38	Exon 11 M365T	A → G	0.3350	0.368	0.342	0.164	0.4755	99.5
	4	rs17852635	19	18 075 765	6124	Exon 7 P228P	G → A	0.3350	0.368	0.332	0.055	0.6152	99.1
	5	rs11575934	19	18 075 808	43	Exon 7 Q214R	A → G	0.3350	0.375	0.339	0.051	0.9668	98.8
IFNGR2: 21q22.11 OMIN: 147569	1	rs1059293	21	33 437 386	–	3’URT	T → C	0.1553	0.121	0.114	0.578	0.0179	99.5
TLR8: Xp22 OMIN: 300366	1	rs3764880	X	12 906 707	–	Exon 1 M1V	G → A	0.1778	0.153	0.155	0.917	–	99.5
	2	rs5744068	X	12 916 939	10 232	Intron	C → T	0.2250	0.017	0.019	0.667	–	99.9
	3	rs2159377	X	12 919 394	2455	Exon 2 D136D	T → C	0.2813	0.210	0.205	0.771	–	99.3
	4	rs5744080	X	12 919 685	291	Exon 2 H233Q	T → C	0.2313	0.194	0.184	0.504	–	99.7
	5	rs2407992	X	12 920 993	1308	Exon 2 L669L	C → G	0.2250	0.190	0.177	0.379	–	99.1
	6	rs3747414	X	12 921 293	300	Exon 2 I769I	A → C	0.3221	0.196	0.177	0.225	–	99.0
	7	rs5744088	X	12 922 445	1152	3’URT	G → C	0.0500	0.025	0.024	0.958	–	98.9

^aOMIM, Online Mendelian Inheritance in Man (http://www.ncbi.nlm.nih.gov/Omim)
^bSNP position in the NCBI dbSNP database (http://www.ncbi.nlm.nih.gov/SNP)
^cIntermarker distances, the distance between two adjacent SNP sites on the same gene sequence. The intermarker distance of first SNP was showed as “——”
^dMAF, minor allele frequency
^eMAF for Chinese in the NCBI dbSNPs database
^fP value for difference in allele distributions between tuberculosis and control group
^gHWE Hardy-Weinberg equilibrium in the control group
^hGenotyping Rate, rate of actual genotyping samples to total samples
-: Not applicable

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