Table 1. daSNVs in neuropsychiatric diseases.
Selected daSNVs of the 892 significant hits. rsIDs of daSNVs and linked lead SNVs from GWAS data are listed, along with the odds ratio value reported in GWAS Catalog. If no odds ratio is given, a +/− modifier for the beta value is listed. Diseases implicated, MPRA cell type significant, daSNV average FDR-corrected p-value from MPRAnalyze’s likelihood ratio test, average log2 fold change (alternate/reference), HiChIP-derived genes linked to daSNVs by chromatin looping as well as eQTL-linked genes (eGenes) are shown.
| daSNP | Lead SNP | OR/Beta | Diseases | MPRA Cell Type | daSNP avg p-value | daSNP Avg Log2FC | HiChIP genes | eGenes |
|---|---|---|---|---|---|---|---|---|
|
| ||||||||
| rs3814546 | rs1182 | 1.06 | ADHD|BPD|MDD|SCZ | N | 1.4E-03 | 0.57 | C9orf78|TOR1A|TOR1B|USP20 | |
| rs2276834 | rs7618915,rs11717383,rs353547 | 1.06 | BPD|SCZ | HEK293T | 4.6E-05 | 1.10 | DNAH1|GLYCTK|GNL3|ITIH4|MUSTN1|NEK4|NT5DC2|PPM1M|SFMBT1|TMEM110 | |
| rs5996094 | rs1023500 | 1.08 | SCZ | N | 3.6E-04 | −0.77 | CCDC134|CYP2D6|DESI1|NAGA|TNFRSF13C | |
| rs139784051 | rs8044995 | 1.08 | SCZ | N | 5.7E-03 | 0.53 | CTRL|ELMO3|ENKD1|GFOD2|LCAT|NFATC3|PLA2G15|PRMT7|SLC12A4|TSNAXIP1 | |
| rs1985437 | rs8044995 | 1.08 | SCZ | AST|HEK293T|N | 1.0E-03 | 1.44 | CTRL|ELMO3|ENKD1|GFOD2|LCAT|PRMT7|RANBP10|SLC12A4|TSNAXIP1 | |
| rs2071507 | rs1042779,rs736408,rs4687552,rs2302417 | 1.1 | ADHD|BPD|SCZ | HEK293T|N|NCL | 2.6E-09 | −3.36 | AC006254.1|GLT8D1|GLYCTK|GNL3|ITIH4|MUSTN1|NEK4|NT5DC2|POC1A|PPM1M|SFMBT1|TMEM110 | |
| rs72708145 | rs140505938 | 1.1 | BPD|SCZ | N|NCL | 5.6E-03 | −0.56 | RPRD2|VPS45 | RPRD2|SV2A|VPS45 |
| rs1626899 | rs2102949,rs2851447 | 1.1 | BPD|SCZ | AST|N|NCL | 6.8E-04 | 1.27 | ABCB9|CDK2AP1|MPHOSPH9|PITPNM2 | ABCB9|AC026362.1|ARL6IP4|CCDC62|CDK2AP1|MPHOSPH9|MTRFR|OGFOD2|PITPNM2 |
| rs10786713 | rs7085104,rs11191424,rs11191419 | 1.11 | BPD|SCZ}ASD | HEK293T|N|NCL | 2.0E-03 | −0.91 | ARL3|AS3MT|SFXN2 | ACTR1A|ARL3|AS3MT|BORCS7|CALHM2|CNNM2|NT5C2|PFN1P11|SFXN2|SUFU|WBP1L |
| rs907088 | rs2517959 | 1.13 | BPD | AST|HEK293T|N | 8.5E-04 | −1.12 | ERBB2|GSDMB|ORMDL3|PGAP3|PNMT | ERBB2|FBXL20|GSDMB|ORMDL3|PGAP3|PNMT |
| rs174530 | rs174576,rs28456,rs174537,rs1535,rs174535,rs4246215 | 1.13 | BPD | N | 7.4E-04 | 0.77 | FADS1|FADS2|TMEM258 | FADS1|FADS2|FADS3|TMEM258 |
| rs903503 | rs2517959 | 1.13 | BPD | AST|N | 3.6E-04 | −1.08 | ERBB2|GSDMB|ORMDL3 | ERBB2|FBXL20|GSDMB|ORMDL3|PGAP3|PNMT |
| rs9266066 | rs2596500 | 1.18 | MDD|SCZ | HEK293T|N | 1.3E-03 | 0.75 | C4A|CCHCR1|FLOT1|HLA-C|IER3|LY6G5B|MICB|MSH5|NOTCH4|RNF5|VARS2 | C4A|CCHCR1|CYP21A1P|FLOT1|HCG22|HLA-C|IER3|LY6G5B|MICB|MSH5|NOTCH4|RNF5|VARS2 |
| rs174561 | rs28456,rs174576 | 1.18 | BPD | N|NCL | 1.6E-04 | −2.37 | FADS1|FADS3 | FADS1|FADS2|FADS3|TMEM258 |
| rs762995 | rs134882,rs2239612 | 1.22 | BPD|SCZ | N | 5.7E-04 | −0.71 | CCDC134|CYP2D6|DESI1|NAGA|NDUFA6 | |
| rs35525740 | rs7914558 | 1.22 | ADHD|BPD|SCZ | N | 2.5E-04 | −1.19 | ARL3|AS3MT|CALHM2|CNNM2 | ARL3|AS3MT|CALHM2|CNNM2 |
| rs12264415 | rs7914558 | 1.22 | ADHD|BPD|SCZ | AST|N|NCL | 5.7E-04 | 1.19 | ACTR1A|ARL3|AS3MT|BORCS7|CALHM2|CNNM2 | |
| rs200948 | rs1765142,rs34706883,rs112509803 | 1.24 | MDD|SCZ|BPD | HEK293T|N | 7.5E-04 | 3.07 | PRSS16|ZSCAN23|ZSCAN9 | PGBD1|PRSS16|ZKSCAN3|ZKSCAN8|ZNF165|ZSCAN23|ZSCAN26|ZSCAN31|ZSCAN9 |
| rs200483 | rs34706883 | 1.24 | MDD|SCZ | N|NCL | 1.8E-03 | −0.53 | PGBD1|ZSCAN23|ZSCAN31|ZSCAN9 | PGBD1|PRSS16|ZKSCAN3|ZNF165|ZSCAN23|ZSCAN26|ZSCAN31|ZSCAN9 |
| rs370155 | rs34706883,rs45509595 | 1.24 | MDD|SCZ|BPD | N|NCL | 8.5E-04 | −1.01 | PGBD1|PRSS16|ZKSCAN3|ZNF165|ZSCAN23|ZSCAN31 | PGBD1|PRSS16|ZKSCAN3|ZNF165|ZSCAN23|ZSCAN26|ZSCAN31|ZSCAN9 |
| rs2428682 | rs1985762 | 1.68 | BLPD | HEK293T|N|NCL | 1.5E-04 | −1.09 | EME1 | |
| rs3134944 | rs1800625 | 3.78 | SCZ | N | 2.9E-04 | 0.69 | AGER|C4A|CYP21A1P|FKBPL|HLA-B|HLA-C|HLA-DMA|HLA-DQB1|LY6G5B|MICB|NEU1|NOTCH4|PBX2|POU5F1|RNF5|SKIV2L|ZBTB12 | |
| rs10938176 | rs34215985 | 1.04 | MDD|BPD | AST|HEK293T | 2.5E-03 | −1.33 | SLC30A9 | |
| rs301807 | rs301806,rs301805,rs159963 | 0.03 unit desc | MDD | AST|N|NCL | 3.0E-08 | −1.38 | ENO1|RERE | |
| rs6926869 | rs6930781 | 0.46 unit incr | MDD | N | 7.3E-04 | −0.64 | WASF1 | |
| rs798744 | rs4818048 | 0.895 unit incr | OCD | HEK293T|N|NCL | 7.6E-04 | −1.85 | FAM53A|FGFR3|TACC3|TMEM129 | FAM53A|FGFR3|TACC3|TMEM129 |
| rs2799077 | rs853679 | 5.30 unit desc | MDD | N | 1.4E-03 | −0.72 | PGBD1|ZKSCAN3|ZKSCAN4|ZSCAN23|ZSCAN31 | PGBD1|ZKSCAN3|ZKSCAN4|ZKSCAN8|ZNF165|ZSCAN23|ZSCAN26|ZSCAN31 |
| rs4395073 | rs4785741 | 70.99 unit incr | OCD|ASD | N | 1.9E-03 | 1.02 | CDK10|GAS8|SPATA2L | CDK10|GAS8|SPATA2L |