Table 4 Functional mapping and annotation of GWAS meta-analyses in the European and African ancestry data
Group | GWAS hit lead variant | #SNPs in LD (r2 > 0.6) | genomic coordinate 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 | Hi-C in 3 neuronal tissue/ cell line datasets, GSE87112 |
|---|---|---|---|---|---|---|---|---|---|
EUA | |||||||||
All | rs34517852 | 20 | chr6: 157,780,424–157,801,753 | ZDHHC14 (upstream of TSS) | rs35262389 = 15.28 | rs9348095 = 1 (TSS site) | Transcriptional active chromatin at TSS | None | Yes, with downstream elements |
rs9364611 | 12 | chr6: 162,157,139–162,168,506 | PARK2 (intronic) | None | None | Overall quiecent, some enhancer function | None | Yes, intronic within the same intron | |
Men | rs571848662 | 5 | chr19: 53,988,841–53,990,834 | ZNF813 | None | None | Weak transcription | None | None |
rs148757321 | 10 | chr1: 15,427,801–15,449,791 | KAZN and TMEM51-AS1 | None | None | None | Significant interaction with regions further upstream of KAZN | ||
AFR | |||||||||
All | rs115539978 | 61 | chr13: 55,652,129–55,759,209 | LINC02335, MIR5007, TUC338 | None | None | Overall silenced chromatin (score of 15), some SNPs map to loci with weak transcription or enhancer function | None | Interaction between risk locus and upstream region harboring LINC00458, MIR1297, and LINC00558 as well as downstream region harboring HNF4GP1 |
Men | rs142174523 | 237 | chr6: 31,257,622–31,319,815 (MHC locus) | LINC02571, HLA-B | None | manyb | Overall PolyComb repressed chromatin, heterochromatin | 16 c | None |
