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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-78 Sentence denotes MHC region and risk of systemic lupus erythematosus in African American women.
T2 79-221 Sentence denotes The major histocompatibility complex (MHC) on chromosome 6p21 is a key contributor to the genetic basis of systemic lupus erythematosus (SLE).
T3 222-415 Sentence denotes Although SLE affects African Americans disproportionately compared to European Americans, there has been no comprehensive analysis of the MHC region in relationship to SLE in African Americans.
T4 416-664 Sentence denotes We conducted a screening of the MHC region for 1,536 single nucleotide polymorphisms (SNPs) and the deletion of the C4A gene in a SLE case-control study (380 cases, 765 age-matched controls) nested within the prospective Black Women's Health Study.
T5 665-840 Sentence denotes We also genotyped 1,509 ancestral informative markers throughout the genome to estimate European ancestry to control for population stratification due to population admixture.
T6 841-966 Sentence denotes The most strongly associated SNP with SLE was the rs9271366 (odds ratio, OR = 1.70, p = 5.6 × 10(-5)) near the HLA-DRB1 gene.
T7 967-1210 Sentence denotes Conditional haplotype analysis revealed three other SNPs, rs204890 (OR = 1.86, p = 1.2 × 10(-4)), rs2071349 (OR = 1.53, p = 1.0 × 10(-3)), and rs2844580 (OR = 1.43, p = 1.3 × 10(-3)), to be associated with SLE independent of the rs9271366 SNP.
T8 1211-1376 Sentence denotes In univariate analysis, the OR for the C4A deletion was 1.38, p = 0.075, but after simultaneous adjustment for the other four SNPs the odds ratio was 1.01, p = 0.98.
T9 1377-1549 Sentence denotes A genotype score combining the four newly identified SNPs showed an additive risk according to the number of high-risk alleles (OR = 1.67 per high-risk allele, p < 0.0001).
T10 1550-1694 Sentence denotes Our strongest signal, the rs9271366 SNP, was also associated with higher risk of SLE in a previous Chinese genome-wide association study (GWAS).
T11 1695-1898 Sentence denotes In addition, two SNPs found in a GWAS of European ancestry women were confirmed in our study, indicating that African Americans share some genetic risk factors for SLE with European and Chinese subjects.
T12 1899-2017 Sentence denotes In summary, we found four independent signals in the MHC region associated with risk of SLE in African American women.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
8725 0-3 GeneOrGeneProduct denotes MHC NCBIGene:3123|NCBIGene:720
8726 23-51 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus MESH:D008180
8727 72-77 OrganismTaxon denotes women NCBITaxon:9606
8728 83-115 GeneOrGeneProduct denotes major histocompatibility complex NCBIGene:3123|NCBIGene:720
8729 117-120 GeneOrGeneProduct denotes MHC NCBIGene:3123|NCBIGene:720
8730 186-214 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus MESH:D008180
8731 216-219 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8732 231-234 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8733 360-363 GeneOrGeneProduct denotes MHC NCBIGene:3123|NCBIGene:720
8734 390-393 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8735 448-451 GeneOrGeneProduct denotes MHC NCBIGene:3123|NCBIGene:720
8736 532-535 GeneOrGeneProduct denotes C4A NCBIGene:720
8737 546-549 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8738 643-648 OrganismTaxon denotes Women NCBITaxon:9606
8739 879-882 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8740 891-900 SequenceVariant denotes rs9271366 DBSNP:rs9271366
8741 952-960 GeneOrGeneProduct denotes HLA-DRB1 NCBIGene:3123
8742 1025-1033 SequenceVariant denotes rs204890 DBSNP:rs204890
8743 1065-1074 SequenceVariant denotes rs2071349 DBSNP:rs2071349
8744 1110-1119 SequenceVariant denotes rs2844580 DBSNP:rs2844580
8745 1173-1176 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8746 1196-1205 SequenceVariant denotes rs9271366 DBSNP:rs9271366
8747 1250-1253 GeneOrGeneProduct denotes C4A NCBIGene:720
8748 1576-1585 SequenceVariant denotes rs9271366 DBSNP:rs9271366
8749 1631-1634 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8750 1754-1759 OrganismTaxon denotes women NCBITaxon:9606
8751 1859-1862 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8752 1952-1955 GeneOrGeneProduct denotes MHC NCBIGene:3123|NCBIGene:720
8753 1987-1990 DiseaseOrPhenotypicFeature denotes SLE MESH:D008180
8754 2011-2016 OrganismTaxon denotes women NCBITaxon:9606

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 23-51 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus 0007915
T2 32-51 DiseaseOrPhenotypicFeature denotes lupus erythematosus 0004670
T3 186-214 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus 0007915
T4 195-214 DiseaseOrPhenotypicFeature denotes lupus erythematosus 0004670

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 516-531 SequenceVariant denotes deletion of the
T2 532-535 SequenceVariant denotes C4A
T3 891-900 SequenceVariant denotes rs9271366
T4 1025-1033 SequenceVariant denotes rs204890
T5 1065-1074 SequenceVariant denotes rs2071349
T6 1110-1119 SequenceVariant denotes rs2844580
T7 1196-1205 SequenceVariant denotes rs9271366
T8 1250-1253 SequenceVariant denotes C4A
T9 1576-1585 SequenceVariant denotes rs9271366

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 0-3 GeneOrGeneProduct denotes MHC
T2 83-115 GeneOrGeneProduct denotes major histocompatibility complex
T3 117-120 GeneOrGeneProduct denotes MHC
T4 177-182 GeneOrGeneProduct denotes basis
T5 360-363 GeneOrGeneProduct denotes MHC
T6 448-451 GeneOrGeneProduct denotes MHC
T7 536-545 GeneOrGeneProduct denotes gene in a
T8 550-554 GeneOrGeneProduct denotes case
T9 574-579 GeneOrGeneProduct denotes cases
T10 607-613 GeneOrGeneProduct denotes nested
T11 637-642 GeneOrGeneProduct denotes Black
T12 925-932 GeneOrGeneProduct denotes p = 5.6
T13 952-960 GeneOrGeneProduct denotes HLA-DRB1
T14 1013-1018 GeneOrGeneProduct denotes other
T15 1326-1331 GeneOrGeneProduct denotes other
T16 1486-1490 GeneOrGeneProduct denotes high
T17 1515-1518 GeneOrGeneProduct denotes per
T18 1519-1523 GeneOrGeneProduct denotes high
T19 1635-1639 GeneOrGeneProduct denotes in a
T20 1723-1727 GeneOrGeneProduct denotes in a
T21 1847-1858 GeneOrGeneProduct denotes factors for
T22 1952-1955 GeneOrGeneProduct denotes MHC

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 0-3 GeneOrGeneProduct denotes MHC
T2 83-115 GeneOrGeneProduct denotes major histocompatibility complex
T3 117-120 GeneOrGeneProduct denotes MHC
T4 360-363 GeneOrGeneProduct denotes MHC
T5 448-451 GeneOrGeneProduct denotes MHC
T6 607-613 GeneOrGeneProduct denotes nested
T7 637-642 GeneOrGeneProduct denotes Black
T8 925-932 GeneOrGeneProduct denotes p = 5.6
T9 952-960 GeneOrGeneProduct denotes HLA-DRB1
T10 1013-1018 GeneOrGeneProduct denotes other
T11 1326-1331 GeneOrGeneProduct denotes other
T12 1486-1490 GeneOrGeneProduct denotes high
T13 1519-1523 GeneOrGeneProduct denotes high
T14 1952-1955 GeneOrGeneProduct denotes MHC

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 23-51 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus D008180
T2 186-214 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus D008180
T3 216-219 DiseaseOrPhenotypicFeature denotes SLE D008180
T4 231-234 DiseaseOrPhenotypicFeature denotes SLE D008180
T5 390-393 DiseaseOrPhenotypicFeature denotes SLE D008180
T6 546-549 DiseaseOrPhenotypicFeature denotes SLE D008180
T7 879-882 DiseaseOrPhenotypicFeature denotes SLE D008180
T8 1173-1176 DiseaseOrPhenotypicFeature denotes SLE D008180
T9 1631-1634 DiseaseOrPhenotypicFeature denotes SLE D008180
T10 1859-1862 DiseaseOrPhenotypicFeature denotes SLE D008180
T11 1987-1990 DiseaseOrPhenotypicFeature denotes SLE D008180

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 925-932 GeneOrGeneProduct denotes p = 5.6
T2 952-960 GeneOrGeneProduct denotes HLA-DRB1

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 23-51 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus 0007915
T2 186-214 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus 0007915
T3 216-219 DiseaseOrPhenotypicFeature denotes SLE 0007915
T4 231-234 DiseaseOrPhenotypicFeature denotes SLE 0007915
T5 390-393 DiseaseOrPhenotypicFeature denotes SLE 0007915
T6 546-549 DiseaseOrPhenotypicFeature denotes SLE 0007915
T7 879-882 DiseaseOrPhenotypicFeature denotes SLE 0007915
T8 1173-1176 DiseaseOrPhenotypicFeature denotes SLE 0007915
T9 1631-1634 DiseaseOrPhenotypicFeature denotes SLE 0007915
T10 1859-1862 DiseaseOrPhenotypicFeature denotes SLE 0007915
T11 1987-1990 DiseaseOrPhenotypicFeature denotes SLE 0007915

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 23-51 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus D008180
T2 186-214 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus D008180
T3 216-219 DiseaseOrPhenotypicFeature denotes SLE D008180
T4 231-234 DiseaseOrPhenotypicFeature denotes SLE D008180
T5 390-393 DiseaseOrPhenotypicFeature denotes SLE D008180
T6 546-549 DiseaseOrPhenotypicFeature denotes SLE D008180
T7 879-882 DiseaseOrPhenotypicFeature denotes SLE D008180
T8 1173-1176 DiseaseOrPhenotypicFeature denotes SLE D008180
T9 1631-1634 DiseaseOrPhenotypicFeature denotes SLE D008180
T10 1859-1862 DiseaseOrPhenotypicFeature denotes SLE D008180
T11 1987-1990 DiseaseOrPhenotypicFeature denotes SLE D008180

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 23-51 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus D008180
T2 186-214 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus D008180
T3 216-219 DiseaseOrPhenotypicFeature denotes SLE D008180
T4 231-234 DiseaseOrPhenotypicFeature denotes SLE D008180
T5 390-393 DiseaseOrPhenotypicFeature denotes SLE D008180
T6 546-549 DiseaseOrPhenotypicFeature denotes SLE D008180
T7 879-882 DiseaseOrPhenotypicFeature denotes SLE D008180
T8 1173-1176 DiseaseOrPhenotypicFeature denotes SLE D008180
T9 1631-1634 DiseaseOrPhenotypicFeature denotes SLE D008180
T10 1859-1862 DiseaseOrPhenotypicFeature denotes SLE D008180
T11 1987-1990 DiseaseOrPhenotypicFeature denotes SLE D008180

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 72-77 OrganismTaxon denotes women
T2 1754-1759 OrganismTaxon denotes women
T3 2011-2016 OrganismTaxon denotes women

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label
T2 952-960 GeneOrGeneProduct denotes HLA-DRB1
T1 925-932 GeneOrGeneProduct denotes p = 5.6
T11 1987-1990 DiseaseOrPhenotypicFeature denotes SLE D008180
T10 1859-1862 DiseaseOrPhenotypicFeature denotes SLE D008180
T9 1631-1634 DiseaseOrPhenotypicFeature denotes SLE D008180
T8 1173-1176 DiseaseOrPhenotypicFeature denotes SLE D008180
T7 879-882 DiseaseOrPhenotypicFeature denotes SLE D008180
T6 546-549 DiseaseOrPhenotypicFeature denotes SLE D008180
T5 390-393 DiseaseOrPhenotypicFeature denotes SLE D008180
T4 231-234 DiseaseOrPhenotypicFeature denotes SLE D008180
T3 216-219 DiseaseOrPhenotypicFeature denotes SLE D008180
T79530 186-214 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus D008180
T93336 23-51 DiseaseOrPhenotypicFeature denotes systemic lupus erythematosus D008180
T78271 2011-2016 OrganismTaxon denotes women
T68839 1754-1759 OrganismTaxon denotes women
T15424 72-77 OrganismTaxon denotes women
T15492 1576-1585 SequenceVariant denotes rs9271366
T44578 1250-1253 SequenceVariant denotes C4A
T88976 1196-1205 SequenceVariant denotes rs9271366
T34867 1110-1119 SequenceVariant denotes rs2844580
T92732 1065-1074 SequenceVariant denotes rs2071349
T95789 1025-1033 SequenceVariant denotes rs204890
T68114 891-900 SequenceVariant denotes rs9271366
T95679 532-535 SequenceVariant denotes C4A
T53543 516-531 SequenceVariant denotes deletion of the

DisGeNET

Id Subject Object Predicate Lexical cue
T0 532-535 gene:100293534 denotes C4A
T1 546-549 disease:C0024141 denotes SLE
T2 532-535 gene:720 denotes C4A
T3 546-549 disease:C0024141 denotes SLE
T4 532-535 gene:721 denotes C4A
T5 546-549 disease:C0024141 denotes SLE
T6 952-960 gene:3123 denotes HLA-DRB1
T7 879-882 disease:C0024141 denotes SLE
R1 T0 T1 associated_with C4A,SLE
R2 T2 T3 associated_with C4A,SLE
R3 T4 T5 associated_with C4A,SLE
R4 T6 T7 associated_with HLA-DRB1,SLE

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 186-214 HP_0002725 denotes systemic lupus erythematosus

Allie

Id Subject Object Predicate Lexical cue
SS1_21695597_1_0 83-115 expanded denotes major histocompatibility complex
SS2_21695597_1_0 117-120 abbr denotes MHC
SS1_21695597_1_1 186-214 expanded denotes systemic lupus erythematosus
SS2_21695597_1_1 216-219 abbr denotes SLE
SS1_21695597_3_0 469-500 expanded denotes single nucleotide polymorphisms
SS2_21695597_3_0 502-506 abbr denotes SNPs
SS1_21695597_9_0 1657-1686 expanded denotes genome-wide association study
SS2_21695597_9_0 1688-1692 abbr denotes GWAS
AE1_21695597_1_0 SS1_21695597_1_0 SS2_21695597_1_0 abbreviatedTo major histocompatibility complex,MHC
AE1_21695597_1_1 SS1_21695597_1_1 SS2_21695597_1_1 abbreviatedTo systemic lupus erythematosus,SLE
AE1_21695597_3_0 SS1_21695597_3_0 SS2_21695597_3_0 abbreviatedTo single nucleotide polymorphisms,SNPs
AE1_21695597_9_0 SS1_21695597_9_0 SS2_21695597_9_0 abbreviatedTo genome-wide association study,GWAS

DisGeNET5_variant_disease

Id Subject Object Predicate Lexical cue
21695597-6#58#66#geners204890 1025-1033 geners204890 denotes rs204890
21695597-6#143#152#geners2844580 1110-1119 geners2844580 denotes rs2844580
21695597-6#98#107#geners2071349 1065-1074 geners2071349 denotes rs2071349
21695597-6#206#209#diseaseC0024141 1173-1176 diseaseC0024141 denotes SLE
21695597-9#26#35#geners9271366 1576-1585 geners9271366 denotes rs9271366
21695597-9#81#84#diseaseC0024141 1631-1634 diseaseC0024141 denotes SLE
58#66#geners204890206#209#diseaseC0024141 21695597-6#58#66#geners204890 21695597-6#206#209#diseaseC0024141 associated_with rs204890,SLE
143#152#geners2844580206#209#diseaseC0024141 21695597-6#143#152#geners2844580 21695597-6#206#209#diseaseC0024141 associated_with rs2844580,SLE
98#107#geners2071349206#209#diseaseC0024141 21695597-6#98#107#geners2071349 21695597-6#206#209#diseaseC0024141 associated_with rs2071349,SLE
26#35#geners927136681#84#diseaseC0024141 21695597-9#26#35#geners9271366 21695597-9#81#84#diseaseC0024141 associated_with rs9271366,SLE

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
21695597-3#116#119#gene720 532-535 gene720 denotes C4A
21695597-3#130#133#diseaseC0024141 546-549 diseaseC0024141 denotes SLE
21695597-5#111#119#gene3123 952-960 gene3123 denotes HLA-DRB1
21695597-5#38#41#diseaseC0024141 879-882 diseaseC0024141 denotes SLE
116#119#gene720130#133#diseaseC0024141 21695597-3#116#119#gene720 21695597-3#130#133#diseaseC0024141 associated_with C4A,SLE
111#119#gene312338#41#diseaseC0024141 21695597-5#111#119#gene3123 21695597-5#38#41#diseaseC0024141 associated_with HLA-DRB1,SLE

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 891-900 SNP:rs9271366 denotes rs9271366
T2 1025-1033 SNP:rs204890 denotes rs204890
T3 1065-1074 SNP:rs2071349 denotes rs2071349
T4 1110-1119 SNP:rs2844580 denotes rs2844580
T5 1196-1205 SNP:rs9271366 denotes rs9271366
T6 1576-1585 SNP:rs9271366 denotes rs9271366