PMC:4156421 / 5551-6375 JSONTXT

{"project":"2_test","denotations":[{"id":"25192356-24487276-90446713","span":{"begin":204,"end":206},"obj":"24487276"},{"id":"25192356-18974171-90446714","span":{"begin":368,"end":370},"obj":"18974171"},{"id":"25192356-24487276-90446715","span":{"begin":627,"end":629},"obj":"24487276"}],"text":"Analysis of variants in the vicinity of rs35705950 (MUC5B)\nTo 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":148,"end":158},"obj":"SNP"},{"id":"27480","span":{"begin":457,"end":467},"obj":"SNP"},{"id":"27481","span":{"begin":281,"end":291},"obj":"SNP"},{"id":"27482","span":{"begin":686,"end":696},"obj":"SNP"},{"id":"27476","span":{"begin":40,"end":50},"obj":"SNP"},{"id":"27660","span":{"begin":40,"end":50},"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"},{"id":"A27476","pred":"resolved_to","subj":"27476","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27660","pred":"resolved_to","subj":"27660","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"}],"text":"Analysis of variants in the vicinity of rs35705950 (MUC5B)\nTo 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":"27476","span":{"begin":40,"end":50},"obj":"SNP"},{"id":"27478","span":{"begin":148,"end":158},"obj":"SNP"},{"id":"27480","span":{"begin":457,"end":467},"obj":"SNP"},{"id":"27481","span":{"begin":281,"end":291},"obj":"SNP"},{"id":"27482","span":{"begin":686,"end":696},"obj":"SNP"},{"id":"27660","span":{"begin":40,"end":50},"obj":"SNP"},{"id":"T1","span":{"begin":40,"end":50},"obj":"SNP"},{"id":"T1","span":{"begin":148,"end":158},"obj":"SNP"},{"id":"T2","span":{"begin":457,"end":467},"obj":"SNP"},{"id":"T3","span":{"begin":281,"end":291},"obj":"SNP"},{"id":"T4","span":{"begin":686,"end":696},"obj":"SNP"},{"id":"T1","span":{"begin":40,"end":50},"obj":"SNP"}],"attributes":[{"id":"A27476","pred":"resolved_to","subj":"27476","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"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"},{"id":"A27660","pred":"resolved_to","subj":"27660","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"}],"text":"Analysis of variants in the vicinity of rs35705950 (MUC5B)\nTo 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."}