Table 2 Association results of the top SNPs in the meta-analysis
From: Genome-wide association study of periodontal pocketing in Finnish adults
N | Chr | Position | SNP | Nearest gene (function) | GTEX | Effect allele | EAF | Beta (95% CI) | SE | P value | |
|---|---|---|---|---|---|---|---|---|---|---|---|
(a) | 3245 | 1 | 79069409 | rs187209330 | IFI44L (intergenic) | G | 0.015 | − 0.55 (− 0.78; − 0.32) | 0.12 | 1.81 × 10–6 | |
2 | 201819623 | rs867275005 | ORC2 (intron) | GAATA | 0.040 | − 0.33 (− 0.47; − 0.19) | 0.071 | 3.83 × 10–6 | |||
3 | 5859909 | rs12494721 | AC027119.1 | T | 0.14 | 0.18 (0.11; 0.26) | 0.039 | 3.11 × 10–6 | |||
4 | 183159364 | rs12508476 | TENM3 (intron) | C | 0.83 | 0.16 (0.096; 0.23) | 0.034 | 2.01 × 10–6 | |||
7 | 75505491 | rs56045460 | RHBDD2 (upstream) | TMEM120A (skin) | A | 0.088 | − 0.23 (− 0.33; − 0.14) | 0.049 | 2.17 × 10–6 | ||
7 | 37556237 | rs1364731 | ELMO1 (intergenic) | NME8 (skin, thyroid) | T | 0.37 | 0.12 (0.070; 0.17) | 0.026 | 3.92 × 10–6 | ||
9 | 6868737 | rs77366980 | KDM4C (intron) | KDM4C,GLDC (brain) | T | 0.14 | − 0.17 (− 0.25; − 0.10) | 0.038 | 3.91 × 10–6 | ||
13 | 112056064 | rs7324141 | TEX29 (intergenic) | ARHGEF7 (nerve, blood, adipose) | A | 0.50 | − 0.12 (− 0.17; − 0.069) | 0.025 | 2.34 × 10–6 | ||
(b) | 2925 | 6 | 7452509 | rs200392355 | HNRNPLP1 (indel) | CT | 0.46 | 0.14 (0.084; 0.20) | 0.030 | 2.23 × 10–6 | |
8 | 139663617 | rs3923549 | COL22A1 (intron) | G | 0.91 | − 0.21 (− 0.30; − 0.12) | 0.045 | 3.01 × 10–6 | |||
10 | 72481095 | rs72814570 | ADAMTS14 (intron) | ADAMTS14 (skin, mucosa, fibroblasts) | A | 0.23 | − 0.16 (− 0.22; − 0.093) | 0.032 | 1.10 × 10–6 | ||
14 | 91608044 | rs147203970 | C14orf159 (intron) | T | 0.033 | 0.37 (0.22; 0.52) | 0.075 | 8.06 × 10–7 | |||
15 | 59799643 | rs16941452 | FAM81A (intron) | G | 0.022 | − 0.45 (− 0.63; − 0.26) | 0.096 | 3.24 × 10–6 | |||
(c) | 2650 | 6 | 7452509 | rs200392355 | HNRNPLP1 (indel) | CT | 0.46 | 0.16 (0.093; 0.22) | 0.032 | 1.22 × 10–6 | |
8 | 10958526 | rs2409703 | XKR6 (intron) | C | 0.079 | 0.28 (0.16; 0.39) | 0.058 | 1.61 × 10–6 | |||
15 | 76021782 | rs11630851 | ODF3L1 (downstream) | LMAN1L (colon), NRG4 (lung, pituitary) | T | 0.067 | 0.30 (0.18;0.42) | 0.061 | 9.39 × 10–7 | ||
20 | 13340138 | rs4444613 | BANF2 (intergenic) | ISM1 (brain) | A | 0.087 | − 0.28 (− 0.38; − 0.18) | 0.053 | 1.35 × 10–7 | ||
20 | 37763743 | rs2003705 | RP11-101E14.3 (intergenic) | DHX35 (colon, oesophagus, testis), FAM83D (artery, colon, oesophagus, skin), RP4-616B8.5 (oesophagus) | T | 0.20 | − 0.16 (− 0.23; − 0.097) | 0.034 | 1.68 × 10–6 |