PMC:4156421 / 5610-6375 JSONTXT

{"project":"2_test","denotations":[{"id":"25192356-24487276-90446713","span":{"begin":145,"end":147},"obj":"24487276"},{"id":"25192356-18974171-90446714","span":{"begin":309,"end":311},"obj":"18974171"},{"id":"25192356-24487276-90446715","span":{"begin":568,"end":570},"obj":"24487276"}],"text":"To assess the possibility of causal variants underlying the MUC5B GWAS signal in LD with rs35705950, we used the recently described CADD method [21] to generate “C-scores” for each of the patient's variants within 1 Mb of rs35705950 (Chr11∶1,241,221). LD data from the SNP Annotation and Proxy Search (SNAP) [22] did not identify any variants in the CEU population in high LD (r-squared \u003e0.6) with rs35705950 within 1 Mb. Nonetheless, we ranked variants by C-scores, which are an integrated measure of “deleteriousness” outputted on a “phred-like” scale from 0 to 99 [21]. We additionally investigated a region within 20 kB of rs35705950 to identify any rare (AF\u003c2%) variants that overlapped with DNase hypersensitive or putative transcription factor binding sites."}

{"project":"PubTator4TogoVar","denotations":[{"id":"27478","span":{"begin":89,"end":99},"obj":"SNP"},{"id":"27480","span":{"begin":398,"end":408},"obj":"SNP"},{"id":"27481","span":{"begin":222,"end":232},"obj":"SNP"},{"id":"27482","span":{"begin":627,"end":637},"obj":"SNP"}],"attributes":[{"id":"A27478","pred":"resolved_to","subj":"27478","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27480","pred":"resolved_to","subj":"27480","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27481","pred":"resolved_to","subj":"27481","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27482","pred":"resolved_to","subj":"27482","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"}],"text":"To assess the possibility of causal variants underlying the MUC5B GWAS signal in LD with rs35705950, we used the recently described CADD method [21] to generate “C-scores” for each of the patient's variants within 1 Mb of rs35705950 (Chr11∶1,241,221). LD data from the SNP Annotation and Proxy Search (SNAP) [22] did not identify any variants in the CEU population in high LD (r-squared \u003e0.6) with rs35705950 within 1 Mb. Nonetheless, we ranked variants by C-scores, which are an integrated measure of “deleteriousness” outputted on a “phred-like” scale from 0 to 99 [21]. We additionally investigated a region within 20 kB of rs35705950 to identify any rare (AF\u003c2%) variants that overlapped with DNase hypersensitive or putative transcription factor binding sites."}

{"project":"PubTatorOnTogoVar","denotations":[{"id":"27478","span":{"begin":89,"end":99},"obj":"SNP"},{"id":"27480","span":{"begin":398,"end":408},"obj":"SNP"},{"id":"27481","span":{"begin":222,"end":232},"obj":"SNP"},{"id":"27482","span":{"begin":627,"end":637},"obj":"SNP"},{"id":"T1","span":{"begin":89,"end":99},"obj":"SNP"},{"id":"T2","span":{"begin":398,"end":408},"obj":"SNP"},{"id":"T3","span":{"begin":222,"end":232},"obj":"SNP"},{"id":"T4","span":{"begin":627,"end":637},"obj":"SNP"}],"attributes":[{"id":"A27478","pred":"resolved_to","subj":"27478","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27480","pred":"resolved_to","subj":"27480","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27481","pred":"resolved_to","subj":"27481","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27482","pred":"resolved_to","subj":"27482","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"}],"text":"To assess the possibility of causal variants underlying the MUC5B GWAS signal in LD with rs35705950, we used the recently described CADD method [21] to generate “C-scores” for each of the patient's variants within 1 Mb of rs35705950 (Chr11∶1,241,221). LD data from the SNP Annotation and Proxy Search (SNAP) [22] did not identify any variants in the CEU population in high LD (r-squared \u003e0.6) with rs35705950 within 1 Mb. Nonetheless, we ranked variants by C-scores, which are an integrated measure of “deleteriousness” outputted on a “phred-like” scale from 0 to 99 [21]. We additionally investigated a region within 20 kB of rs35705950 to identify any rare (AF\u003c2%) variants that overlapped with DNase hypersensitive or putative transcription factor binding sites."}