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. 2020 Jun 8;21(4):240–248. doi: 10.1038/s41435-020-0101-0

Table 2.

Comparison of minor allele frequencies between subjects with short-term and persistent S. aureus bacteremia.

Gene SNP Major/minor allele Putative functional effect of SNP Minor allele frequency Comparison of minor allele frequencies
GnomAD population with European ancestry (n = 77,165) Patients with short-term bacteremia (n = 158) Patients with persistent bacteremia (n = 44) P value comparing short-term bacteremia and GnomAD populationa P value comparing persistent and short-term bacteremiab
CISH rs175634 T/C eQTL, DNase I hypersensitivity site, transcription factor binding site, creates new microRNA target site 0.155 0.158 0.182 0.88 0.81
CISH rs148685070 G/T Histone H3K27Ac binding site, transcription factor binding site 0.000583 0.00338 0 0.17 0.99
IRAK4 rs4251545 G/A SNP located in enhancer/silencer region of gene 0.0885 0.0918 0.0796 0.84 0.63
NOD2 rs2067085 C/G eQTL, DNase I hypersensitivity site, transcription factor binding site 0.402 0.424 0.386 0.46 0.71
NOD2 rs2066842 C/T eQTL 0.249 0.269 0.307 0.43 0.64
NOD2 rs5743271 A/G Possibly damaging missense variant p.N262S, p.N289S 0.00566 0.00633 0.0114 0.70 0.50
NOD2 rs1861759 T/G eQTL, histone H3K4Me1 binding site, transcription factor binding site 0.396 0.421 0.398 0.36 0.97
NOD2 rs5743279 G/A Transcription factor binding site 0.0000262 0.00317 0 0.010 0.76
NOD2 rs2066847 -/insC Frameshift variant in transcription factor binding site 0.0221 0.0411 0.0341 0.032 0.99
TIRAP rs655540 T/C RNA polymerase II binding site 0.236 0.231 0.330 0.89 0.020
TIRAP rs8177342 C/G RNA polymerase II binding site 0.0522 0.0443 0 0.61 0.037
TIRAP rs563011 T/G RNA polymerase II binding site 0.238 0.218 0.318 0.46 0.020
TIRAP rs79946960 G/A DNase I hypersensitivity site, transcription factor binding site 0.000635 0.00331 0 0.19 0.66
TIRAP rs4937114 G/T Histone H3K4Me1 binding site, transcription factor binding site 0.0515 0.0467 0 0.79 0.042
TIRAP rs10893493 A/G Histone H3K4Me1 binding site, transcription factor binding site 0.115 0.123 0.0833 0.65 0.66
TIRAP rs8177368 C/T DNase I hypersensitivity site 0.000635 0.00317 0 0.19 0.65
TIRAP rs184774567 G/A Transcription factor binding site 0.00659 0 0.0114 0.28 0.056
TIRAP rs8177399 C/T Transcription factor binding site 0.0227 0.0253 0.0341 0.70 0.48
TIRAP rs3802813 G/A Transcription factor binding site 0.0459 0.0443 0 1.00 0.037
TIRAP rs8177376 T/G Histone H3K4Me1 binding site, transcription factor binding site, microRNA target site 0.231 0.228 0.318 0.95 0.021
TIRAP rs625413 C/T eQTL, RNA polymerase II binding site 0.222 0.215 0.307 0.84 0.11
TIRAP rs4937115 A/G eQTL 0.0522 0.0411 0 0.44 0.043
TLR2 rs3804100 T/C Activation of a cryptic splice site 0.0640 0.0696 0.0909 0.65 0.51
TLR2 rs5743704 C/A Possibly damaging missense variant p.P631H, DNase I hypersensitivity site, transcription factor binding site 0.0420 0.0222 0.0341 0.090 0.15
TLR4 rs5030724 C/A Histone H3K4Me1 binding site, transcription factor binding site 0.000910 0.00633 0 0.035 0.54
TLR4 rs5030718 G/A Stop-gain variant possibly leading to truncated protein p.E474*, p.E434* 0.000137 0.00633 0 0.0010 0.96
TLR4 rs200020265 G/A DNase I hypersensitivity site, histone H3K4Me1 binding site, transcription factor binding site 0 0.00317 0 0.0021 0.76
TRAF6 rs200798752 -/insGAA Transcription factor binding site 0.0108 0.0253 0.0227 0.025 0.87

eQTL expression quantitative trait locus, GnomAD Genome Aggregation Database, H3K4Me1 mono-methylation of histone H3 at lysine 4, H3K27Ac acetylation of histone H3 at lysine 27, SNP single nucleotide polymorphism.

aMinor allele frequencies compared using Fisher’s exact test.

bMinor allele frequencies compared using Firth logistic regression.