Table 2 Functional mapping and annotation of UKBB GWAS and meta-analysis.
From: Genomic influences on self-reported childhood maltreatment
Sample | GWAS hit lead variant | GWAS p-value | Position (hg19) | #SNPs in LD (r2 > 0.6) | Genomic coordinated risk locus (hg19) | Predicted genes in risk locus | SNPs in LD with CADD scores > 12.37 | SNPs in LD with RegulomeDB scores < 5 | Chromatin state analysis (Roadmap Epigenomics) in neuronal cell lines/tissuesa | eQTL (28 neuronal tissue/cell lines from CommonMind Consortium, BRAINEAC or GTEx v7) |
|---|---|---|---|---|---|---|---|---|---|---|
UKBB GWAS | rs142346759 | 4.35E−08 | 3: 71362232 | 5 | chr3:71355932–71417539 | FOXP1 intronic | rs34936081 | rs13083684 (intronic) | Mainly quiecent | None |
rs10262462 | 4.36E−08 | 7: 114180062 | 77 | chr7:114015707–114287116 | FOXP2 intronic | rs7785701,rs6466488,rs10249234,rs9332390,rs66823671,rs12533005 | rs2396753 (intronic), rs12536335 (intronic) | Mainly quiecent | None | |
Meta-analysis | rs1859100 | 3.91E−08 | 7: 114194615 | 74 | chr7:114015707–114287116 | FOXP2 intronic | rs66823671,rs71149745,rs7785701,rs12533005,rs9332390,rs10249234, rs1476535, rs6466488 | rs2396753 (intronic), rs12536335 (intronic), rs9332390 (intronic) | Mainly quiecent | None |
rs917577 | 2.64E−08 | 12:126548817 | 27 | chr12:126548816–126585545 | Intergenic | None | None | Mainly quiecent | None |
