. 2022 Jun 23;53(5):640–656. doi: 10.1111/age.13233

TABLE 5.

SNPs of interest predicted to potentially perturb mRNA secondary structure

SNP genome coordinate	mRNA affected	Line(s) in which SNP is present	Alleles (ref/SNP)	mRNA base change	RNAsnp P‐value	SNPfold P‐value	Region affected
Chr1:106613656	IFNAR1	7₂	C/T	C/U	0.4067	0.0078	Exonic
Chr1:106622867	IFNAR1	N, 0 ^a	C/T	C/U	0.6077	#0.016	Exonic
Chr1:106623894	IFNAR1	15I, 6₁, 7₂, C, N, 0, Wl	G/A	G/A	0.0446	0.4078	Exonic
Chr1:106625990	IFNAR1	0 ^a	C/T	C/U	0.5257	0.0808	Exonic
Chr1:106631527	IFNAR1	P2a	G/A	G/A	0.8683	0.0086	3′UTR
Chr1:106632281	IFNAR1	15I, 6₁, 7₂, C, N, P2a ^a , 0 WL	T/C	U/C	0.9474	0.0093	3′UTR
Chr1:106589970	IFNAR2	15I, C, P2a ^a , 0 ^a , Wl	G/T	G/U	0.424	0.046	Exonic
Chr1:106592036	IFNAR2	15I, C, 0, Wl	T/G	U/G	0.5046	0.0275	3′UTR
Chr3:54913306	IFNGR1	15I, 6₁, 7₂, C, 0, Wl	T/C	U/C	0.084	0.3036	Exonic
Chr1:106652516	IFNGR2	N, 0 ^a	G/A	G/A	0.9103	0.0198	3′UTR
Chr1:106653379	IFNGR2	N, 0 ^a	C/T	C/U	0.1912	0.0473	3′UTR
Chr23:5823279	IFNLR1	N ^a	T/C	A/G	0.0811	0.3326	Exonic
Chr1:106604195	IL10RB	7₂ ^a , C ^a	T/G	U/G	0.045	0.2181	3′UTR
Chr1:106604577	IL10RB	15I, 0 ^a , Wl	G/A	G/A	0.0565	0.3225	3′UTR
ChrZ:34282637	IFNK	6₁, 7₂, N, P2a, 0, Wl	C/T	G/A	#0.027	0.0968	3′UTR
Chr8:28553812	JAK1	15I, 7₂, C, N ^a , P2a ^a	G/A	C/U	0.0978	0.591	Exonic
Chr8:28559109	JAK1	C	A/G	U/C	0.056	0.4255	Exonic
Chr8:28564450	JAK1	15I, 6₁, 7₂, C, N ^a , P2a ^a , Wl	T/G	A/C	0.0972	0.4388	Exonic
Chr8:28566979	JAK1	N ^a , P2a ^a , 0	A/G	U/C	0.1547	0.0105	Exonic
Chr8:28567177	JAK1	P2a ^a	T/C	A/G	0.7025	0.0056	Exonic
Chr8:28576480	JAK1	N ^a , P2a ^a , 0	C/T	G/A	0.051	0.3395	Exonic

Allele changes are listed for the forward strand; IFNLR1, IFNκ and JAK1 are found on the reverse strand so the mRNA base changes observed in these genes reflect that of the template strand.

Scores in bold can be considered significant (p > 0.1), # – scores still significant after Bonferroni correction.

^{^a}

SNP occurs in only one allele and is therefore heterozygous.