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