. 2015 Nov 16;10(11):e0142130. doi: 10.1371/journal.pone.0142130

Table 2. SNPs reaching suggestive significance in single variant logistic regression for persistent S. aureus carrier vs. non-carrier (top) and intermittent S. aureus carrier vs. non-carrier (bottom), including PC1 and PC2 as covariates.

					Persistent Carrier (PC) vs. Non Carrier Eigenscore 1,2	Intermittent Carrier (INT) vs. Non Carrier Eigenscore 1,2
SNP	Chr	Position	Risk allele	Non-risk allele	OR (95% CI) [p value]	OR (95% CI) [p value]	IMPUTE2 info score	Freq (all)	Freq (PC)	Freq (INT)	Freq (controls)	Genes within 50 kb of locus	Location of sentinel SNP
rs118047622	7	130819082	C	G	2.57 (1.74–3.80) [2.22E-06]	1.72 (1.08–2.75) [2.25E-02]	0.89	0.16	0.24	0.19	0.13	LINC-PINT, MKLN1	Intronic MKLN1 ^A
rs138799235	9	112129775	C	T	3.00 (1.94–4.63) [7.57E-07]	1.04 (0.60–1.79) [8.91E-01]	0.98	0.11	0.19	0.09	0.09	EPB41L4B ^B , PTPN3 ^C	Intergenic EPB41L4B and PTPN3
rs4918947	10	97293912	A	G	3.91 (2.24–6.83) [1.61E-06]	0.69 (0.32–1.48) [3.37E-01]	0.99	0.06	0.12	0.03	0.05	SORBS1 ^D , ALDH18A1 ^E	Intronic SORBS1
rs2421770	11	35320880	C	G	1.83 (1.40–2.38) [7.81E-06]	1.25 (0.92–1.72) [1.57E-01]	0.98	0.65	0.76	0.67	0.62	SLC1A2 ^F	Intronic SLC1A2
rs734102	11	69624482	C	T	3.68 (2.13–6.35) [2.79E-06]	1.51 (0.83–2.75) [1.80E-01]	0.99	0.94	1.00	0.95	0.92	FGF3 ^G , FGF4 ^G	Downstream FGF3
rs61440199	3	20111546	A	G	2.63 (1.36–5.11) [4.20E-03]	8.68 (4.16–18.13) [8.68E-09]	0.99	0.05	0.07	0.12	0.03	KAT2B ^H , SGOL1 ^I , PP2D1 ^J , SGOL1-AS1 ^K , MIR3135A ^L	Intronic KAT2B
rs7611684	3	23482812	A	G	1.31 (0.84–2.06) [2.32E-01]	3.26 (1.98–5.35) [3.12E-06]	0.96	0.11	0.12	0.21	0.10	UBE2E2 ^M	Intronic UBE2E2
rs11127662	3	79771987	G	C	1.27 (0.73–2.20) [3.99E-01]	4.32 (2.37–7.87) [1.84E-06]	0.99	0.07	0.07	0.15	0.06	ROBO1 ^N	Intronic ROBO1
rs16993852	4	37737989	T	C	3.48 (1.85–6.52) [1.03E-04]	6.93 (3.31–14.52) [2.84E-07]	0.98	0.06	0.09	0.12	0.04	RELL1 ^O	Intergenic RELL1 and PGM2 ^P
rs222458	6	52890625	A	G	1.02 (0.53–1.94) [9.53E-01]	4.77 (2.39–9.49) [8.71E-06]	1.00	0.05	0.04	0.11	0.04	GSTA4 ^Q , RN7SK ^R , ICK ^S , RN7SL244P ^T , FBXO9 ^U	Intronic ICK
rs1682522	14	87641837	T	A	1.05 (0.70–1.59) [7.99E-01]	3.16 (1.99–4.99) [9.21E-07]	0.91	0.14	0.13	0.25	0.12	LOC283585 ^V , GALC ^W	Intergenic LOC283585 and GALC
rs8088420	18	56511908	C	T	1.17 (0.85–1.60) [3.45E-01]	2.48 (1.73–3.55 [6.98E-07])	0.94	0.27	0.28	0.41	0.25	RNU6-219P ^X , ZNF532 ^Y , RN7SL112P ^Z	Intergenic MALT1 ^AA and ZNF532

^AMuskelin 1; encodes an intracellular mediator of cell morphology and cytoskeletal responses [52, 53].

^BErythrocyte membrane protein band 4.1 like 4B (also known as Ehm2); involved in membrane and cytoskeletal interactions [60].

^CCytoskeletal-associated protein tyrosine phosphatase; regulates cell growth, differentiation, mitotic cycle, and oncogenic transformation [61].

^DSorbin and SH3 domain containing 1; encodes a CBL-associated protein which functions in the signaling and stimulation of insulin [132].

^EAldehyde Dehydrogenase 18 Family, Member A1; Diseases associated with ALDH18A1 include cutis laxa, autosomal recessive, type iiia and aldh18a1-related cutis laxa [149–151].

^FSolute carrier protein 1; associated with fatty acid levels, essential tremor and other traits [56–59].

^GFibroblast growth factors 3 and 4; cell growth and breast cancer [62–64].

^HLysine acetlytransferase 2B (also known as PCAF or p300/CBP associated factor); associated with various phenotypes including inflammatory responses to S. aureus [66–70].

^IShugoshin-Like 1 cancer; associated with the cell cycle [102].

^JProtein Phosphatase 2C-Like Domain Containing 1; function unknown.

^KSGOL1 Antisense RNA 1; RNA gene. Function undefined.

^LMicroRNA 3135a; Function undefined.

^MUbiquitin-conjugating enzyme E2E; associated with gestational and type 2 diabetes [71–73].

^NRoundabout, axon guidance receptor, homolog 1; encodes a member of the immunoglobulin gene superfamily and neuronal precursor cell migration [74–77].

^ORELT-like 1; tumor necrosis receptor family member also involved in immune regulation [109].

^PPhosphoglucomutase 2; Catalyzes the conversion of the nucleoside breakdown products ribose-1-phosphate and deoxyribose-1-phosphate [genecards.org].

^QGlutathione S-Transferase Alpha 4;involved in cellular defense against toxic, carcinogenic, and pharmacologically active electrophilic compounds [genecards.org].

^RRNA, 7SK Small Nuclear; RNA gene [genecards.org].

^SIntestinal cell [MAK-like] kinase; associated with the cell cycle [101, 104].

^TRNA, 7SL, Cytoplasmic 244, Pseudogene [genecards.org].

^UF-Box Protein 9, associated with adipocyte differentiation and innate immunity [108,111].

^VRNA gene; non coding RNA [genecards.org].

^Wb-galactocerebroside; responsible for Krabbe disease [78, 79].

^XPseudogene [genecards.org]

^YZinc finger protein 532; affects adipogenesis differentiation [110].

^ZRNA; unknown function.

^AAMucosa associated lymphoid tissue lymphoma translocation gene 1; associated with immunodeficiency and multiple sclerosis [80–83]