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Table 3 Summary of in silico follow-up and gene prioritization score (GPS)

From: Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

        Annotation for variants in 95% credible set Biology of the gene
Locus Candidate gene Chr Pos-Start Pos-End Number of variants in 95% credible set GPS Protein Altering NMD Altered splicing eQTLa Expressed in Eye tissue § MGI Mouse eye phenotype OMIM Human eye phenotype
CD46 CD46 1 207,925,382 207,968,861 11 4 0 0 1 1 1 1 0
CD46 CR1L 1 207,818,457 207,897,036 1 1 0 0 0 0 0 1 0
CD46 PLXNA2 1 208,195,587 208,417,665 0 2 0 0 0 0 1 1 0
CD46 CR1 1 207,669,472 207,815,110 0 2 0 0 0 0 1 1 0
CD46 LOC148696 1 207,991,723 207,995,941 1 0 0 0 0 NA NA 0 0
CD46 CD34 1 208,059,882 208,084,683 0 1 0 0 0 0 1 0 0
CD46 CD55 1 207,494,816 207,534,311 0 1 0 0 0 0 1 0 0
CD46 CR2 1 207,627,644 207,663,240 0 0 0 0 0 0 0 0 0
CD46 MIR29B2 1 207,975,787 207,975,868 0 0 0 0 0 NA NA 0 0
CD46 MIR29C 1 207,975,196 207,975,284 0 0 0 0 0 NA NA 0 0
TYR TYR 11 88,911,039 89,028,927 39 4 1 0 0 0 1 1 1
TYR NOX4 11 89,057,521 89,322,779 1 3 0 1 1 0 1 0 0
TYR GRM5 11 88,237,743 88,796,846 109 1 0 0 0 0 1 0 0
TYR FOLH1B 11 89,392,464 89,431,886 0 0 0 0 0 0 0 0 0
TYR GRM5-AS1 11 88,237,743 88,257,222 0 0 0 0 0 0 NA 0 0
TYR TRIM49 11 89,530,822 89,541,743 0 0 0 0 0 0 NA 0 0
TYR TRIM77 11 89,443,466 89,451,040 0 0 0 0 0 0 NA 0 0
  1. a Variants in 95% credible set are a local expression quantitative trait locus for this gene in retina (EyeGEx) or any tissue included in the GTEx database (cis for genes in locus); § Expression in Eye Integration data; NMD nonsense-mediated mRNA decay; OMIM Online Mendelian Inheritance in Man (https://www.omim.org/); NA data not available; The gene start and end positions were extracted from the hg19 gene range list from http://www.cog-genomics.org/plink/1.9/resources
  2. The table summarizes statistical and functional evidence for 10 and seven candidate genes of the novel early AMD loci on chromosome 1 and chromosome 11, respectively. Detailed results on the individual statistical and functional analyses are shown in Tables S6-S12. For the GPS, the sum of cell entries for “annotation” and “biology” was computed per row