Table 1.
Summary of JIA GWAS loci targeted genes in neutrophils.
| DEG |
Methylation |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Chr | Pos (hg19) | Gene | Location | GWAS_Pval | GTEx_Pval | PFP | FC | Histone Mark | Probe | Pval | |
| rs4648881 | 1 | 25197155 | MTFR1L | 5′ | 5.E-07 | 4.0E-03 | 2.33E-02 | -1.30 | none | |||
| rs9633402 | 1 | 247946160 | TRIM58 | 5′ | 3.E-06 | 5.4E-04 | 1.15E-02 | 1.21 | none | cg12689806 | 8.45E-02 | |
| rs79893749 | 3 | 46253650 | CCR3 | intron | 2.E-07 | 2.5E-04 | 1.68E-02 | -1.27 | H3K4me1_Enh | cg04111761 | 7.78E-03 | |
| rs4869313 | 5 | 96223880 | ELL2 | 5′ | 9.E-08 | 2.4E-02 | 4.04E-02 | -1.26 | none | |||
| rs41291794 | 6 | 32425762 | HLA-DPA1 | 3′ | ∗4.E-15 | 1.4E-02 | 8.20E-04 | 1.33 | none | cg13906813 | 1.64E-02 | |
| rs7069750 | 10 | 90762376 | ACTA2 | 5′ | ∗3.E-08 | 4.9E-20 | 3.60E-03 | 1.27 | none | cg03111039 | ∗∗6.52E-08 | |
| rs7069750 | 10 | 90762376 | ANKRD22 | 5′ | ∗3.E-08 | 4.0E-03 | 3.64E-02 | 1.21 | none | cg15103050 | 1.52E-01 | |
| rs12598357 | 16 | 28340945 | SH2B1 | 5′ | ∗4.E-09 | 4.4E-06 | 3.83E-04 | 1.68 | none | cg07884168 | 1.55E-02 | |
| rs12598357 | 16 | 28340945 | SULT1A1 | 3′ | ∗4.E-09 | 9.6E-07 | 5.51E-03 | -1.31 | none | cg09685060 | ∗∗1.41E-09 | |
| rs12928404 | 16 | 28847246 | SH2B1 | 5′ | 6.E-07 | 1.9E-04 | 3.83E-04 | 1.68 | none | cg06932837 | ∗∗5.13E-05 | |
| rs12928404 | 16 | 28847246 | SULT1A1 | 5′ | 6.E-07 | 5.0E-06 | 5.51E-03 | -1.31 | none | cg26603685 | ∗∗1.72E-07 | |
| rs2847293 | 18 | 12782448 | MPPE1 | 5′ | ∗1.E-12 | 3.9E-02 | 2.01E-02 | -1.36 | none | cg14599440 | 2.01E-03 | |
| rs149850873 | 18 | 12885120 | CEP192 | 5′ | 5.E-07 | 6.0E-03 | 4.90E-03 | -1.37 | H3K4me1_Enh H3K4me3_Pro | cg00686761 | 1.78E-01 | |
SNP = single nucleotide polymorphism; Chr = chromosome; Pos (hg19) = position on human genome build hg19; Gene = likely targeted gene at each GWAS locus; Location = The SNP is located within intron, 5′ upstream or 3′ downstream of its target gene. GWAS_Pval = P-value of each SNP in GWAS analyses extracted from GWAS catalog; GTEx_Pval = P-value of correlation between gene expression level and GWAS SNP genotype in GTEx database; DEG_PFP = the probability of being false positive for the differentially expressed gene in the microarray analysis; DEG_FC = fold change of the differentially expressed gene in a microarray analysis; Histone Mark = histone marks overlap with each SNP in cell line E030 BLD.CD15.PC; Methylation_probe = the methylation probe with the minimum P-value in the target gene for association testing with the GWAS SNP; Methylation_Pval = the P-value of the methylation probe in methylation analysis; ∗GWAS_Pval < 5.E-08; ∗∗Methylation P-value < 3.5E-04; none = no histone modification was found in cell line E030 BLD.CD15.PC.