Table 1.
Genomic and Functional Context of Top SNPs in Loci with P < 5 × 10−6 for Association with Chronic Periodontitis in the HCHS/SOL Study (N = 10,935).
| Allele |
|||||||||
|---|---|---|---|---|---|---|---|---|---|
| Region | SNP | Chr Positiona | Gene (Role) or Nearest Gene | Coded | Minor | MAF | b (SE)b | Oevarc | P Value |
| 1q42.2 | rs149133391 | 1: 231580785 | TSNAX-DISC1 (intron) | T | C | 0.011 | −0.139 (0.024) | 0.94 | 7.9 × 10−9 |
| 11p15.1 | rs75715012 | 11: 21627604 | NELL1 | G | A | 0.089 | 0.045 (0.008) | >0.99 | 1.1 × 10−7 |
| 5p15.33 | rs186066047 | 5: 3875660 | IRX1; LINC01017; LINC01019 | G | A | 0.003 | 0.225 (0.043) | 0.93 | 1.7 × 10−7 |
| 6p22.3 | rs10456847d | 6: 18954940 | LOC645157; RNF144B | C | G | 0.330 | −0.026 (0.005) | >0.99 | 2.6 × 10−7 |
| 1q22 | rs79308117e | 1: 155509388 | ASH1L (intron) | A | C | 0.005 | 0.178 (0.035) | >0.99 | 2.8 × 10−7 |
Chronic periodontitis: mean interproximal attachment loss continuous trait.
Chr, chromosomal; HCHS/SOL, Hispanic Community Health Study / Study of Latinos; MAF, minor allele frequency; SNP, single-nucleotide polymorphism.
Chromosome positions are based on GRCh38.p2 annotation release 107.
Per minor allele effect size based on the linear mixed additive genetic model; standard error in parentheses.
Imputation quality metric based on the ratio of observed to expected variance of imputed dosage.
Predicted as an expression quantitative trait locus in the SCAN database: RAB37 (CEU) P = 7 × 10−5; FSCN1 (YRI) P = 10−4. SNP in linkage disequilibrium with rs1334772 (P = 1.1 × 10−6): D′ = 0.94, r2 = 0.837 and rs1891657 (P = 3.6 × 10−6): D′ = 0.89, r2 = 0.746.
SNP in linkage disequilibrium with rs13373934 (P = 4.5 × 10−7): D′ = 1.0, r2 = 1.000 is a missense intron variant of ASH1L. Ser→Pro change, predicted to be “benign” by PolyPhen-2 with HumDiv score 0.107 (sensitivity: 0.93, specificity: 0.86).