Table 3 Differentially expressed genes significantly associated with the genotype of SVA RIPs at baseline (0 months) and 36 months follow up visit. The number of genes significantly differentially expressed (FDR corrected p < 0.1) are reported for each SVA RIP genotype followed by the most significant gene in brackets.

From: Reference SVA insertion polymorphisms are associated with Parkinson’s Disease progression and differential gene expression

SVA ID Nearest gene to SVA No. of significantly differentially expressed genes at baseline No. of significantly differentially expressed genes at 36 month visit Tagging SNP for SVA reported as an eQTL in GTEx portal
PP v AA PP v PA PA v AA PP v AA PP v PA PA v AA Whole blood Other tissues
SVA_7 OR14I1 (4 kb downstream) 0 686 (EVPL) 2 (HBA2) 1 (AC003102.1) 28 (RAB3B) 3 (AC003102.1) N Y
SVA_11 CASP8 (intron) 1 (FLACC1) 0 64 (IGSF3) 36 (IGLV7-46) 15 (IGLV7-43) 5 (IFI27) no tag r2 > 0.8 no tag r2 > 0.8
SVA_24 HLA-A (8 kb upstream) 4 (HLA-A) 13 (IGKV1-16) 3 (HLA-A) 10 (HLA-A) 7 (SERINC4) 13 (HLA-A) SNP not present SNP not present
SVA_36 NUPR2 (30 kb upstream) 1467 (TSPAN11) 5 (PCSK1N) 207 (FAM155B) 1474 (RPL31) 36 (ADGRG7) 823 (GIMAP2) Y Y
SVA_47 RAD23B (10 kb upstream) 0 0 12 (IL32) 75 (AC01177.3) 42 (SNORC) 11 (PLAU) N N
SVA_67 KANSL1 (12 kb upstream) 4 (PLEKHM1) 7 (ARL17A) 0 22 (AC120194.1) 25 (PLEKHM1) 13 (AC120194.1) Y Y
SVA_79 PFDN4 (30 kb downstream) na 1 (RAB3B) na na 0 na N N