Table 3.

Results and description of SNPs that were observed to be associated with HIV-VL in the START and FIRST cohorts.

dbSNP RS ID	Gene (±5 kb)	Chr	Physical position	Strand	Ref allele	Alt allele	START estimatea	START P-value	START q-value	START rank	FIRST estimatea	FIRST P-value	FIRST q-value	FIRST rank
rs77936891	TET2	4	106122657	+	A	G	−0.264	0.000025	0.0052	1	−0.1869	0.028	0.2587	37
rs75555015	TET2	4	106151781	+	A	G	−0.2839	0.000036	0.0052	2	−0.1838	0.059	0.4421	45
rs115930414	TET2	4	106173177	+	G	T	−0.3001	0.000059	0.0057	3	−0.191	0.057	0.4421	44
rs78305976	TET2	4	106095219	+	T	A	−0.2705	0.000082	0.0059	4	−0.1934	0.023	0.2386	33
rs139100435	TET2	4	106142080	+	CTT	−	0.3156	0.00012	0.0073	5	0.5107	0.00031	0.0072	15
rs80014899	TET2	4	106141445	+	A	G	−0.2453	0.00021	0.0092	6	−0.1728	0.040	0.3282	42
rs72955180	TET2	4	106133750	+	G	T	0.4022	0.00024	0.0092	7	N/A	N/A	N/A	N/A
rs72950501	TET2	4	106197936	+	C	T	0.3072	0.00028	0.0092	8	0.5511	0.000081	0.0058	4
rs76644731	TET2	4	106132312	+	A	G	−0.2451	0.00028	0.0092	9	−0.1894	0.026	0.2531	35
rs72955179	TET2	4	106133471	+	G	A	0.3022	0.00034	0.0096	10	0.5107	0.00031	0.0072	14
rs72955193	TET2	4	106145468	+	A	G	0.3781	0.00039	0.0096	11	0.5505	0.00017	0.0058	9
rs17035325	TET2	4	106110796	+	T	C	−0.2394	0.00040	0.0096	12	−0.1761	0.036	0.305	41
rs77738124	TET2	4	106173540	+	T	C	−0.2367	0.00044	0.0096	13	−0.1561	0.059	0.4421	46
rs59519484	TET2	4	106190732	+	C	A	0.2992	0.00046	0.0096	14	0.5141	0.00036	0.0077	16
rs142786189	TET2	4	106162216	+	T	−	−0.2393	0.00053	0.0104	15	−0.1902	0.027	0.2587	36
rs78763791	LOC101929491;TET2	4	106065102	+	C	A	−0.2107	0.00073	0.0133	16	−0.2485	0.0025	0.0371	23
rs72963014	TET2	4	106168623	+	C	G	0.348	0.00091	0.0155	17	0.5336	0.00022	0.0062	12
rs72963032	TET2	4	106182446	+	A	G	0.3407	0.0010	0.0164	18	0.5451	0.00011	0.0058	6
rs59479204	TET2	4	106160495	+	A	G	0.3411	0.0011	0.0164	19	0.5458	0.00018	0.0058	11
rs17035308	LOC101929491;TET2	4	106064349	+	G	C	−0.213	0.0012	0.0169	20	−0.2392	0.0038	0.0521	25
rs58322634	TET2	4	106166139	+	A	G	0.2467	0.0013	0.0176	21	0.5561	0.000040	0.0058	1
rs137883243	TET2	4	106184236	+	ATATAAA	−	−0.2338	0.0013	0.0178	22	−0.2156	0.026	0.2531	34
rs72961199	TET2	4	106159386	+	G	A	0.3389	0.0015	0.0189	23	0.554	0.00015	0.0058	7
rs60382101	TET2	4	106160161	+	A	G	0.3372	0.0016	0.0192	24	0.554	0.00015	0.0058	8
rs72963038	TET2	4	106189156	+	C	A	0.3282	0.0017	0.0203	25	0.5731	0.000053	0.0058	2
rs79305653	TET2	4	106200234	+	T	C	−0.2254	0.0022	0.0242	26	−0.1809	0.062	0.4476	48
rs72952305	TET2	4	106201653	+	T	G	0.314	0.0035	0.0377	27	0.544	0.00026	0.0069	13
rs72963036	TET2	4	106188548	+	A	T	0.3011	0.0038	0.0397	28	0.577	0.00010	0.0058	5
rs72963031	TET2	4	106182132	+	A	T	0.2422	0.014	0.1276	31	0.4754	0.00068	0.0138	17
rs60786079	TET2	4	106197750	+	G	A	0.1663	0.015	0.1402	32	0.5261	0.000061	0.0058	3
rs72963046	TET2	4	106194419	+	C	A	0.2547	0.019	0.1601	34	0.5501	0.00017	0.0058	10
rs6811468	TET2	4	106082473	+	A	G	0.1042	0.19	0.7998	69	0.3239	0.0024	0.0371	22
rs12694101	IDH1; PIKFYVE	2	209128892	+	G	A	0.0096	0.77	0.9674	231	−0.1913	0.0014	0.0233	20
rs72963007	TET2	4	106164723	+	G	A	N/A	N/A	N/A	N/A	0.5476	0.00093	0.0169	19
rs72961197	TET2	4	106158738	+	G	A	N/A	N/A	N/A	N/A	0.5476	0.00093	0.0169	18
rs72955158	TET2	4	106110032	+	A	G	N/A	N/A	N/A	N/A	0.4082	0.0018	0.0302	21

N/A indicates that a particular SNP did not pass QC or the MAF cut-off for that particular study and was therefore not included in the GLM.

MAF, minor allele frequency; QC, quality control; TET2, ten-eleven methylcytosine dioxygenase 2; VL, viral load.

^∗SNPs were ordered by P-value (low to high) with rank = 1 for the SNP with the lowest P-value.

^aEstimates are presented for the alternate allele.