IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis

Table 2 Identified genetic variants associated with HIV-1 reservoir features

SNP	Chr	Pos.	Allele	Candidate genes	Variant type	Replication	Index SNP	Trait	P value	Beta
rs2613996^A	11	470331	A	PTDSS2^{B, C}	Regulatory region variant, intronic variant	McLaren et al, 2013	rs2613996	CA HIV-1 DNA	9.72 × 10^-10	0.18
rs2613996^A	11	470331	A	PTDSS2^{B, C}	Regulatory region variant, intronic variant	McLaren et al, 2013	rs7113204	RNA:DNA ratio	2.19 × 10^-7	− 0.284
rs7113204	11	500248	G	RNH1^B, PTDSS2^C, IRF7^C	Intronic variant	–	rs7113204	RNA:DNA ratio	1.72 × 10–⁷	− 0.199
rs12366210	11	650994	G	DEAF1^B	Intronic variant	–	rs7113204	RNA:DNA ratio	3.26 × 10⁻⁷	− 0.165
rs7817589	8	82154232	C	RP11-1149 M10.2, PAG1^D	Upstream gene variant	–	rs7817589	RNA:DNA ratio	2.17 × 10⁻⁷	0.252

^A rs2613996 is the top QTL SNP to CA HIV-1 DNA and also an independent QTL SNP to the RNA:DNA ratio. Also, the SNP is located on the second intron of PTDSS2
^B The gene where the SNP is located
^C Genes that are identified as AIDS-related by hands (e.g., from literature)
^D Co-regulated with lncRNA gene RP11-1149 M10.2

ISSN: 1741-7015