PMC:4156421 / 14786-16548 JSONTXT

{"project":"2_test","denotations":[{"id":"25192356-23583980-90446763","span":{"begin":593,"end":595},"obj":"23583980"},{"id":"25192356-23583980-90446764","span":{"begin":819,"end":821},"obj":"23583980"},{"id":"25192356-24429156-90446765","span":{"begin":903,"end":905},"obj":"24429156"},{"id":"25192356-23583980-90446766","span":{"begin":1339,"end":1341},"obj":"23583980"},{"id":"25192356-23583980-90446767","span":{"begin":1416,"end":1418},"obj":"23583980"},{"id":"25192356-24429156-90446768","span":{"begin":1490,"end":1492},"obj":"24429156"},{"id":"25192356-21506748-90446769","span":{"begin":1495,"end":1497},"obj":"21506748"},{"id":"25192356-23940607-90446770","span":{"begin":1501,"end":1503},"obj":"23940607"},{"id":"25192356-23583980-90446771","span":{"begin":1580,"end":1582},"obj":"23583980"},{"id":"25192356-24429156-90446772","span":{"begin":1652,"end":1654},"obj":"24429156"},{"id":"25192356-24429156-90446773","span":{"begin":1725,"end":1727},"obj":"24429156"}],"text":"GWAS variants\nWe next cross-referenced the patient's genome with SNPs previously implicated in IPF by GWAS (Table S1). The patient was heterozygous for six variants influencing susceptibility to IPF (Table 2). Two of the six are associated with elevated risk for IPF. One of these variants (Figure 2), rs35705950, is located within the promoter region of MUC5B and has a strong association with both familial and sporadic IPF, with odds ratio (OR) estimates ranging from 2.4–6.8 for heterozygote carriers. The presence of one other variant located on chromosome 7 also increases risk for IPF [13]. Four of the six variants are associated with reduced susceptibility to IPF and include SNPs in OBFC1, a gene involved in telomere maintenance, MAPT, the gene from which the microtubule-associated protein tau is produced [13], as well as the Toll interacting protein, TOLLIP, and signal peptidase, SPPL2C [10].\nFigure 2 Integrated Genomics Viewer (IGV) screenshot of the rs35705950 variant.\nTable 2 Variants associated with IPF that were also seen in this individual. Allele frequencies accessed 4/16/2014.\nNearest Gene SNP ID Chromosome Position Variant Type Minor Allele Major Allele Patient Genotype MAF (1000 Genomes) OR Reference\nAZGP1 (AZGP1P1 pseudogene) rs4727443 7 99593346 intergenic A C C/A 0.411 1.3A 1.11B [13]\nMAPT rs1981997 17 44056767 intronic A G A/G 0.117 0.71A 0.67B [13]\nMUC5B rs35705950 11 1241221 promoter T G T/G 0.052 2.4–6.8 [10]–[14], [16]\nOBFC1 rs11191865 10 105672842 intronic G A A/G 0.584 0.8A 0.87B [13]\nTOLLIP rs5743890 11 1325829 Intronic C T C/T 0.0702 0.61 [10]\nSPPL2C rs17690703 17 43925297 Intronic T C C/T 0.1543 0.7 [10]\nA Discovery and Breplicate GWAS."}

{"project":"PubTator4TogoVar","denotations":[{"id":"27636","span":{"begin":969,"end":979},"obj":"SNP"},{"id":"27649","span":{"begin":1271,"end":1281},"obj":"SNP"},{"id":"27652","span":{"begin":1348,"end":1358},"obj":"SNP"},{"id":"27653","span":{"begin":1426,"end":1437},"obj":"SNP"}],"attributes":[{"id":"A27636","pred":"resolved_to","subj":"27636","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27649","pred":"resolved_to","subj":"27649","obj":"tmVar:rs4727443;VariantGroup:6;RS#:4727443"},{"id":"A27652","pred":"resolved_to","subj":"27652","obj":"tmVar:rs1981997;VariantGroup:25;CorrespondingGene:4137;RS#:1981997;CorrespondingSpecies:9606"},{"id":"A27653","pred":"resolved_to","subj":"27653","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"}],"text":"GWAS variants\nWe next cross-referenced the patient's genome with SNPs previously implicated in IPF by GWAS (Table S1). The patient was heterozygous for six variants influencing susceptibility to IPF (Table 2). Two of the six are associated with elevated risk for IPF. One of these variants (Figure 2), rs35705950, is located within the promoter region of MUC5B and has a strong association with both familial and sporadic IPF, with odds ratio (OR) estimates ranging from 2.4–6.8 for heterozygote carriers. The presence of one other variant located on chromosome 7 also increases risk for IPF [13]. Four of the six variants are associated with reduced susceptibility to IPF and include SNPs in OBFC1, a gene involved in telomere maintenance, MAPT, the gene from which the microtubule-associated protein tau is produced [13], as well as the Toll interacting protein, TOLLIP, and signal peptidase, SPPL2C [10].\nFigure 2 Integrated Genomics Viewer (IGV) screenshot of the rs35705950 variant.\nTable 2 Variants associated with IPF that were also seen in this individual. Allele frequencies accessed 4/16/2014.\nNearest Gene SNP ID Chromosome Position Variant Type Minor Allele Major Allele Patient Genotype MAF (1000 Genomes) OR Reference\nAZGP1 (AZGP1P1 pseudogene) rs4727443 7 99593346 intergenic A C C/A 0.411 1.3A 1.11B [13]\nMAPT rs1981997 17 44056767 intronic A G A/G 0.117 0.71A 0.67B [13]\nMUC5B rs35705950 11 1241221 promoter T G T/G 0.052 2.4–6.8 [10]–[14], [16]\nOBFC1 rs11191865 10 105672842 intronic G A A/G 0.584 0.8A 0.87B [13]\nTOLLIP rs5743890 11 1325829 Intronic C T C/T 0.0702 0.61 [10]\nSPPL2C rs17690703 17 43925297 Intronic T C C/T 0.1543 0.7 [10]\nA Discovery and Breplicate GWAS."}

{"project":"PubTatorOnTogoVar","denotations":[{"id":"27636","span":{"begin":969,"end":979},"obj":"SNP"},{"id":"27649","span":{"begin":1271,"end":1281},"obj":"SNP"},{"id":"27652","span":{"begin":1348,"end":1358},"obj":"SNP"},{"id":"27653","span":{"begin":1426,"end":1437},"obj":"SNP"},{"id":"T1","span":{"begin":969,"end":979},"obj":"SNP"},{"id":"T1","span":{"begin":1271,"end":1281},"obj":"SNP"},{"id":"T2","span":{"begin":1348,"end":1358},"obj":"SNP"},{"id":"T3","span":{"begin":1426,"end":1437},"obj":"SNP"}],"attributes":[{"id":"A27636","pred":"resolved_to","subj":"27636","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"},{"id":"A27649","pred":"resolved_to","subj":"27649","obj":"tmVar:rs4727443;VariantGroup:6;RS#:4727443"},{"id":"A27652","pred":"resolved_to","subj":"27652","obj":"tmVar:rs1981997;VariantGroup:25;CorrespondingGene:4137;RS#:1981997;CorrespondingSpecies:9606"},{"id":"A27653","pred":"resolved_to","subj":"27653","obj":"tmVar:rs35705950;VariantGroup:27;RS#:35705950"}],"text":"GWAS variants\nWe next cross-referenced the patient's genome with SNPs previously implicated in IPF by GWAS (Table S1). The patient was heterozygous for six variants influencing susceptibility to IPF (Table 2). Two of the six are associated with elevated risk for IPF. One of these variants (Figure 2), rs35705950, is located within the promoter region of MUC5B and has a strong association with both familial and sporadic IPF, with odds ratio (OR) estimates ranging from 2.4–6.8 for heterozygote carriers. The presence of one other variant located on chromosome 7 also increases risk for IPF [13]. Four of the six variants are associated with reduced susceptibility to IPF and include SNPs in OBFC1, a gene involved in telomere maintenance, MAPT, the gene from which the microtubule-associated protein tau is produced [13], as well as the Toll interacting protein, TOLLIP, and signal peptidase, SPPL2C [10].\nFigure 2 Integrated Genomics Viewer (IGV) screenshot of the rs35705950 variant.\nTable 2 Variants associated with IPF that were also seen in this individual. Allele frequencies accessed 4/16/2014.\nNearest Gene SNP ID Chromosome Position Variant Type Minor Allele Major Allele Patient Genotype MAF (1000 Genomes) OR Reference\nAZGP1 (AZGP1P1 pseudogene) rs4727443 7 99593346 intergenic A C C/A 0.411 1.3A 1.11B [13]\nMAPT rs1981997 17 44056767 intronic A G A/G 0.117 0.71A 0.67B [13]\nMUC5B rs35705950 11 1241221 promoter T G T/G 0.052 2.4–6.8 [10]–[14], [16]\nOBFC1 rs11191865 10 105672842 intronic G A A/G 0.584 0.8A 0.87B [13]\nTOLLIP rs5743890 11 1325829 Intronic C T C/T 0.0702 0.61 [10]\nSPPL2C rs17690703 17 43925297 Intronic T C C/T 0.1543 0.7 [10]\nA Discovery and Breplicate GWAS."}