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Chunk #31 — Methods — SNP functional annotations

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Meta-analysis and genome-wide interpretation of genetic susceptibility to drug addiction.
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yes

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Coordinates of the SNPs were retrieved from NCBI dbSNP database (Build 130) [48]. Genomic coordinates of 3' UTR, 5' UTR, intron region, intergenic regions, synonymous, non-synonymous, and splicing sites were retrieved from the UCSC Genome Browser Database (NCBI36/hg18) [49]. Regulatory elements including transcription factor binding sites and experimentally validated and putative miRNA targets were retrieved from TransFac [50], Argonaute [51], TarBase [14] and PicTar [52]. Information for SNPs under negative selection or positive selection was retrieved from published data [34,49]. The correlation between SNPs and gene expression were retrieved from high-throughput studies correlating human gene expression and genotypes. The full text papers of 11 such studies were manually curated for fulfillment of inclusion criteria of (i) neuropathologically normal samples, (ii) association design and iii) available statistics data. In all, four studies met the inclusion criteria [53-56]. A total list of 33,731 significantly correlated SNP-expression pairs was identified, involving 22,178 SNPs and 3,640 transcripts [53-56]. Then, for the addiction vulnerable SNPs, We estimated the magnitude of the contributions of different molecular mechanisms to the effects of addiction susceptibility. We further compared