Table 1. Genome-wide significant loci from ASD scans and MTAG analyses.
Panel a shows the loci reaching genome-wide significance in analysis of the ASD phenotype alone. The column “Analysis” indicates the minimum p-value arising from the original scan (ASD) and the combined analysis with the follow-up sample (Comb ASD). The columns “Support from other scans” list the other analyses (including MTAG) that further support the locus at genome-wide significance. For the ASD scan results, this shows the genome-wide significant results in the locus from the other scans, and for Comb ASD it displays the result from ASD. Panel b presents additional genome-wide significant loci identified in the three MTAG analyses. The three analyses are ASD with schizophrenia (SCZ)15, educational attainment (Edu)20 and major depression (MD)21. Here the “Analysis” column points to which MTAG analysis gave the results (ASD-Edu or ASD-MD), and the columns “Support from other scans” provide the corresponding scan results in ASD alone. In both panels, independent loci are defined to have r2 < 0.1 and distance > 400 kb and the index variant is displayed in the column “Index var”. Other columns are: chromosome (CHR), chromosomal position (BP), alleles (A1/A2), allele frequency of A1 (FRQ), estimate of effect (β) with respect to A1, standard error of β (SE), and the association p-value of the index variant (P). The column “Nearest genes” lists nearest genes from within 50 kb of the region spanned by all SNPs with r2 ≥ 0.6 to the index variant.
*Indicate different lead SNP than the index variant
| Index var | CHR | BP | Analysis | P | β | SE | A1/A2 | FRQ | Support from other scans | Nearest genes | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Scan | P | β | |||||||||||
| a | rs910805 | 20 | 21248116 | ASD | 2.04 × 10−9 | −0.096 | 0.016 | A/G | 0.76 | ASD-SCZ ASD-Edu* |
1.5 × 10−10 2.0 × 10−8 |
−0.069 −0.061 |
KIZ, XRN2, NKX2–2, NKX2–4 |
| rs10099100 | 8 | 10576775 | ASD | 1.07 × 10−8 | 0.084 | 0.015 | C/G | 0.331 | Comb ASD ASD-Edu |
9.6 × 10−9 1.6 × 10−8 |
0.078 0.056 |
C8orf74, SOX7, PINX1 | |
| rs201910565 | 1 | 96561801 | Comb ASD | 2.48 × 10−8 | −0.077 | 0.014 | A/AT | 0.689 | ASD | 3.4 × 10−7 | −0.033 | LOC102723661, PTBP2 | |
| rs71190156 | 20 | 14836243 | ASD | 2.75 × 10−8 | −0.078 | 0.014 | GTTTT TTT/G |
0.481 | Comb ASD ASD-Edu |
3.0 × 10−8 1.2 × 10−8 |
−0.072 0.053 |
MACROD2 | |
| rs111931861 | 7 | 104744219 | Comb ASD | 3.53 × 10−8 | −0.216 | 0.039 | A/G | 0.966 | ASD | 1.1 × 10−7 | −0.094 | KMT2E, SRPK2 | |
| b | rs2388334 | 6 | 98591622 | ASD-Edu | 3.34 × 10−12 | −0.065 | 0.009 | A/G | 0.517 | ASD | 1.0 × 10−6 | −0.068 | MMS22L, POU3F2 |
| rs325506 | 5 | 104012303 | ASD-MD | 3.26 × 10−11 | 0.057 | 0.009 | C/G | 0.423 | ASD | 3.5 × 10−7 | 0.071 | NUD12 | |
| rs11787216 | 8 | 142615222 | ASD-Edu | 1.99 × 10−9 | −0.058 | 0.010 | T/C | 0.364 | ASD | 2.6 × 10−6 | −0.030 | MROH5 | |
| rs1452075 | 3 | 62481063 | ASD-Edu | 3.17 × 10−9 | 0.061 | 0.010 | T/C | 0.721 | ASD | 2.1 × 10−7 | 0.035 | CADPS | |
| rs1620977 | 1 | 72729142 | ASD-MD | 6.66 × 10−9 | 0.056 | 0.010 | A/G | 0.26 | ASD | 1.2 × 10−4 | 0.062 | NEGR1 | |
| rs10149470 | 14 | 104017953 | ASD-MD | 8.52 × 10−9 | −0.049 | 0.008 | A/G | 0.487 | ASD | 8.5 × 10−5 | −0.056 | MARK3, CKB, TRMT61A, BAG5, APOPT1, KLC1, XRCC3 | |
| rs16854048 | 4 | 42123728 | ASD-MD | 1.29 × 10−8 | 0.069 | 0.012 | A/C | 0.858 | ASD | 5.9 × 10−5 | 0.082 | SLC30A9, BEND4, TMEM33, DCAF4L1 | |