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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.
Term:systemic scleroderma
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Accession:DOID:418 term browser browse the term
Definition:A scleroderma that is characterized by fibrosis (or hardening) of the skin and major organs, as well as vascular alterations, and autoantibodies. (DO)
Synonyms:exact_synonym: progressive scleroderma;   progressive systemic sclerosis;   scleroderma syndrome;   systemic sclerosis
 narrow_synonym: anti-centromere-antibody-positive systemic scleroderma;   anti-topoisomerase-I-antibody-positive systemic scleroderma
 primary_id: MESH:D012595
 xref: EFO:0000717;   EFO:0008536;   EFO:0008537;   GARD:9748;   ICD10CM:M34.0;   ICD9CM:710.1;   NCI:C72070
For additional species annotation, visit the Alliance of Genome Resources.


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systemic scleroderma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ace angiotensin I converting enzyme ISO protein:decreased expression:plasma GAD
RGD		 PMID:15118671 PMID:17360781 RGD:1331525, RGD:8548889 NCBI chr11:105,858,774...105,880,790
Ensembl chr11:105,858,771...105,880,790 		JBrowse link
G Acta2 actin alpha 2, smooth muscle, aorta ISO CTD Direct Evidence: marker/mechanism CTD PMID:24706986 NCBI chr19:34,217,736...34,232,985
Ensembl chr19:34,218,490...34,232,990 		JBrowse link
G Adamts13 ADAM metallopeptidase with thrombospondin type 1 motif 13 ISO protein:decreased expression:plasma (human) RGD PMID:12935979 RGD:10449040 NCBI chr 2:26,863,363...26,899,638
Ensembl chr 2:26,863,428...26,899,640 		JBrowse link
G Ager advanced glycosylation end product-specific receptor IEP
ISO		 protein:increased expression:serum RGD PMID:18825489 PMID:18825489 RGD:8695973, RGD:8695973 NCBI chr17:34,816,545...34,819,911
Ensembl chr17:34,816,836...34,819,910 		JBrowse link
G Agt angiotensinogen ISO protein:decreased expression:plasma RGD PMID:17360781 RGD:8548889 NCBI chr 8:125,283,326...125,296,445
Ensembl chr 8:125,283,273...125,296,445 		JBrowse link
G Anxa5 annexin A5 severity ISO RGD PMID:21124692 RGD:7242029 NCBI chr 3:36,503,072...36,530,036
Ensembl chr 3:36,503,072...36,530,043 		JBrowse link
G Arpc2 actin related protein 2/3 complex, subunit 2 ISO protein:increased expression:saliva (human) RGD PMID:17722226 RGD:11049167 NCBI chr 1:74,275,656...74,307,368
Ensembl chr 1:74,275,243...74,307,368 		JBrowse link
G Bank1 B cell scaffold protein with ankyrin repeats 1 susceptibility ISO DNA:SNPs: :rs10516487,rs17266594(human) RGD PMID:19815934 RGD:9684975 NCBI chr 3:135,759,124...136,031,902
Ensembl chr 3:135,759,124...136,031,827 		JBrowse link
G Bdnf brain derived neurotrophic factor ISO protein:decreased expression:serum: RGD PMID:21085492 RGD:5144060 NCBI chr 2:109,505,045...109,557,388
Ensembl chr 2:109,505,045...109,557,352 		JBrowse link
G C3 complement component 3 ISO protein:increased expression:plasma RGD PMID:2803327 RGD:7421518 NCBI chr17:57,510,967...57,535,136
Ensembl chr17:57,510,970...57,535,136 		JBrowse link
G Cav1 caveolin 1, caveolae protein susceptibility ISO DNA:SNPs:enhancer, intron: (rs7795356, rs926198, rs959173) (human)
protein:decreased expression:lung, skin		 RGD PMID:22402147 PMID:18759267 RGD:8661768, RGD:8661773 NCBI chr 6:17,306,387...17,341,323
Ensembl chr 6:17,306,334...17,341,451 		JBrowse link
G Ccl2 C-C motif chemokine ligand 2 severity ISO protein:increased expression:respiratory system fluid/secretion
protein:increased expression:serum		 RGD PMID:19615053 PMID:21285114 PMID:21049277 RGD:4891453, RGD:5683876, RGD:5135284 NCBI chr11:81,926,403...81,928,278
Ensembl chr11:81,926,397...81,928,279 		JBrowse link
G Ccl20 C-C motif chemokine ligand 20 ISO mRNA:increased expression:skin RGD PMID:21742595 RGD:7483587 NCBI chr 1:83,094,487...83,096,888
Ensembl chr 1:83,094,487...83,096,888 		JBrowse link
G Ccl3 C-C motif chemokine ligand 3 ISO protein:increased expression:serum RGD PMID:21285114 RGD:5683876 NCBI chr11:83,538,669...83,540,204
Ensembl chr11:83,538,670...83,540,181 		JBrowse link
G Ccl4 C-C motif chemokine ligand 4 ISO protein:increased expression:serum RGD PMID:21285114 RGD:5683876 NCBI chr11:83,553,410...83,555,509
Ensembl chr11:83,553,410...83,555,509 		JBrowse link
G Ccn1 cellular communication network factor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27482699 NCBI chr 3:145,352,726...145,355,740
Ensembl chr 3:145,352,731...145,355,736 		JBrowse link
G Ccn2 cellular communication network factor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24706986 NCBI chr10:24,471,340...24,474,581
Ensembl chr10:24,471,340...24,474,581 		JBrowse link
G Ccr2 C-C motif chemokine receptor 2 IMP RGD PMID:23142052 RGD:9479741 NCBI chr 9:123,901,954...123,913,594
Ensembl chr 9:123,901,987...123,913,594 		JBrowse link
G Ccr6 C-C motif chemokine receptor 6 ISO mRNA:increased expression:skin RGD PMID:21742595 RGD:7483587 NCBI chr17:8,454,875...8,477,353
Ensembl chr17:8,454,875...8,475,973 		JBrowse link
G Cd247 CD247 antigen ISO CTD Direct Evidence: marker/mechanism CTD PMID:20383147 NCBI chr 1:165,607,514...165,698,722
Ensembl chr 1:165,616,250...165,704,846 		JBrowse link
G Cd86 CD86 antigen ISO DNA:snp:5' utr:g.-3479T>G (human) RGD PMID:16790753 RGD:4892554 NCBI chr16:36,389,318...36,486,439
Ensembl chr16:36,424,231...36,486,443 		JBrowse link
G Cfb complement factor B ISO protein:increased expression:plasma RGD PMID:2803327 RGD:7421518 NCBI chr17:35,075,350...35,081,492
Ensembl chr17:35,075,350...35,081,494 		JBrowse link
G Chi3l1 chitinase 3 like 1 ISO protein:increased secretion:serum (human) RGD PMID:16195162 RGD:4892666 NCBI chr 1:134,109,894...134,117,769
Ensembl chr 1:134,109,914...134,117,919 		JBrowse link
G Clu clusterin ISO protein:increased expression:serum RGD PMID:22350181 RGD:8898558 NCBI chr14:66,206,093...66,218,992
Ensembl chr14:66,205,932...66,218,996 		JBrowse link
G Cnr1 cannabinoid receptor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27228633 NCBI chr 4:33,923,171...33,948,831
Ensembl chr 4:33,924,593...33,948,831 		JBrowse link
G Cnr2 cannabinoid receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27228633 NCBI chr 4:135,622,500...135,647,530
Ensembl chr 4:135,622,705...135,647,518 		JBrowse link
G Col1a1 collagen, type I, alpha 1 ISO RGD PMID:1697606 RGD:5688336 NCBI chr11:94,827,050...94,843,868
Ensembl chr11:94,827,050...94,843,868 		JBrowse link
G Col1a2 collagen, type I, alpha 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24706986 NCBI chr 6:4,505,618...4,541,543
Ensembl chr 6:4,504,814...4,541,544 		JBrowse link
G Col3a1 collagen, type III, alpha 1 IAGP OMIM:181750 MouseDO NCBI chr 1:45,350,698...45,388,866
Ensembl chr 1:45,350,698...45,388,866 		JBrowse link
G Cp ceruloplasmin ISO protein:increased expression:serum RGD PMID:32630589 RGD:401827129 NCBI chr 3:20,011,097...20,063,914
Ensembl chr 3:20,011,218...20,063,309 		JBrowse link
G Csf1 colony stimulating factor 1 (macrophage) ISO mRNA:increased expression:skin RGD PMID:22700848 RGD:7257593 NCBI chr 3:107,648,364...107,668,048
Ensembl chr 3:107,648,364...107,667,785 		JBrowse link
G Cx3cl1 C-X3-C motif chemokine ligand 1 ISO protein:increased expression:serum RGD PMID:15608300 RGD:4891898 NCBI chr 8:95,498,808...95,509,055
Ensembl chr 8:95,498,637...95,509,055 		JBrowse link
G Cx3cr1 C-X3-C motif chemokine receptor 1 ISO
IMP		 protein:increased expression:lung, skin
DNA:polymorphisms: :p.V249I, p.T280M (human)		 RGD PMID:15608300 PMID:23142052 PMID:16584113 RGD:4891898, RGD:9479741, RGD:4891896 NCBI chr 9:119,877,749...119,897,362
Ensembl chr 9:119,877,749...119,898,945 		JBrowse link
G Cxcl10 C-X-C motif chemokine ligand 10 ISO protein:increased expression:serum RGD PMID:21303517 PMID:21049277 RGD:5135279, RGD:5135284 NCBI chr 5:92,494,497...92,496,748
Ensembl chr 5:92,494,497...92,496,748 		JBrowse link
G Cxcl16 C-X-C motif chemokine ligand 16 ISO protein:increased expression:serum, skin, endothelial cell RGD PMID:21303517 RGD:5135279 NCBI chr11:70,345,215...70,350,810
Ensembl chr11:70,344,809...70,350,810 		JBrowse link
G Cxcl9 C-X-C motif chemokine ligand 9 ISO protein:increased expression:serum RGD PMID:21303517 PMID:21049277 RGD:5135279, RGD:5135284 NCBI chr 5:92,469,190...92,475,938
Ensembl chr 5:92,469,206...92,475,938 		JBrowse link
G Cxcr3 C-X-C motif chemokine receptor 3 ISO protein:decreased expression:skin, endothelial cell RGD PMID:21303517 RGD:5135279 NCBI chr  X:100,775,141...100,777,753
Ensembl chr  X:100,775,141...100,777,875 		JBrowse link
G Cxcr6 C-X-C motif chemokine receptor 6 ISO protein:increased expression:skin, endothelial cell RGD PMID:21303517 RGD:5135279 NCBI chr 9:123,635,542...123,640,819
Ensembl chr 9:123,635,540...123,640,825 		JBrowse link
G Edn1 endothelin 1 ISO protein:increased secretion:plasma (human) RGD PMID:7653485 RGD:4145072 NCBI chr13:42,454,952...42,461,466
Ensembl chr13:42,454,952...42,461,466 		JBrowse link
G Eln elastin ISO RGD PMID:22563211 RGD:9585742 NCBI chr 5:134,731,449...134,776,300
Ensembl chr 5:134,731,447...134,776,177 		JBrowse link
G Esr1 estrogen receptor 1 (alpha) susceptibility ISO DNA:SNP:intron: RGD PMID:19032828 RGD:8553058 NCBI chr10:4,561,989...4,955,633
Ensembl chr10:4,561,593...4,955,614 		JBrowse link
G Esr2 estrogen receptor 2 (beta) no_association ISO DNA:SNP:exon: RGD PMID:19032828 RGD:8553058 NCBI chr12:76,167,193...76,224,033
Ensembl chr12:76,167,193...76,224,033 		JBrowse link
G F11r F11 receptor ISO RGD PMID:19153103 RGD:7488918 NCBI chr 1:171,265,129...171,292,161
Ensembl chr 1:171,265,103...171,292,171 		JBrowse link
G F2 coagulation factor II ISO protein:increased expression:plasma: RGD PMID:9374919 RGD:11565087 NCBI chr 2:91,442,742...91,466,799
Ensembl chr 2:91,455,665...91,466,759 		JBrowse link
G Fbn1 fibrillin 1 susceptibility IMP
ISO
IAGP		 DNA:insertion:5' utr
OMIM:181750		 MouseDO
RGD		 PMID:11123012 PMID:12384286 PMID:10395706 RGD:7387265, RGD:12904889, RGD:12910471 NCBI chr 2:125,142,514...125,348,417
Ensembl chr 2:125,142,514...125,349,913 		JBrowse link
G Fli1 Friend leukemia integration 1 IAGP OMIM:181750 MouseDO NCBI chr 9:32,333,500...32,454,292
Ensembl chr 9:32,333,500...32,454,157 		JBrowse link
G Flt4 FMS-like tyrosine kinase 4 ISO protein:increased expression:skin: RGD PMID:21865112 RGD:8552335 NCBI chr11:49,500,506...49,543,566
Ensembl chr11:49,500,090...49,543,566 		JBrowse link
G Fosl2 fos-like antigen 2 IAGP OMIM:181750 MouseDO NCBI chr 5:32,292,599...32,315,184
Ensembl chr 5:32,293,145...32,315,186 		JBrowse link
G Fstl1 follistatin-like 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27482699 NCBI chr16:37,597,417...37,656,878
Ensembl chr16:37,597,235...37,656,876 		JBrowse link
G Gpx3 glutathione peroxidase 3 ISO protein:decreased expression:serum RGD PMID:32630589 RGD:401827129 NCBI chr11:54,793,680...54,801,213
Ensembl chr11:54,793,279...54,801,203 		JBrowse link
G Gstm1 glutathione S-transferase, mu 1 susceptibility ISO DNA:missense mutation:cds:p.K173N (human) RGD PMID:15135176 RGD:12798510 NCBI chr 3:107,919,566...107,925,289
Ensembl chr 3:107,919,571...107,925,289 		JBrowse link
G H2-Aa histocompatibility 2, class II antigen A, alpha susceptibility ISO DNA:polymorphism::HLA-DQA1*0501; RGD PMID:11014350 RGD:8547725 NCBI chr17:34,501,718...34,506,797
Ensembl chr17:34,501,718...34,506,797 		JBrowse link
G H2-Ab1 histocompatibility 2, class II antigen A, beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:20383147 NCBI chr17:34,482,201...34,488,392
Ensembl chr17:34,476,663...34,488,393 		JBrowse link
G Hdac5 histone deacetylase 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27482699 NCBI chr11:102,085,244...102,120,968
Ensembl chr11:102,085,258...102,120,992 		JBrowse link
G Hgf hepatocyte growth factor treatment
severity		 ISO mRNA:increased expression:skin:
protein:increased expression:serum:		 RGD PMID:17049072 PMID:22286923 PMID:24387171 RGD:8548624, RGD:8548651, RGD:8548659 NCBI chr 5:16,758,493...16,827,448
Ensembl chr 5:16,758,493...16,825,150 		JBrowse link
G Hmgb1 high mobility group box 1 IEP protein:increased expression:serum RGD PMID:18825489 RGD:8695973 NCBI chr 5:148,983,512...148,989,867
Ensembl chr 5:148,983,512...149,121,299 		JBrowse link
G Hnrnpl heterogeneous nuclear ribonucleoprotein L ISO RGD PMID:21569507 RGD:9999440 NCBI chr 7:28,507,971...28,521,693
Ensembl chr 7:28,507,966...28,521,691 		JBrowse link
G Icam1 intercellular adhesion molecule 1 disease_progression ISO protein:increased expression:blood RGD PMID:18759276 PMID:1371389 PMID:8099861 RGD:8158120, RGD:8547576, RGD:8547587 NCBI chr 9:20,927,236...20,940,110
Ensembl chr 9:20,927,281...20,940,113 		JBrowse link
G Ifng interferon gamma treatment ISO RGD PMID:1418004 RGD:8157622 NCBI chr10:118,276,951...118,281,799
Ensembl chr10:118,276,951...118,281,797 		JBrowse link
G Igfbp3 insulin-like growth factor binding protein 3 ISO protein:increased expression:serum: RGD PMID:19004037 RGD:12743606 NCBI chr11:7,156,086...7,165,498
Ensembl chr11:7,156,086...7,163,923 		JBrowse link
G Il13 interleukin 13 no_association IEP
ISO		 mRNA, protein:increased expression:skin
protein:increased expression:serum
DNA:SNPs:promoter, cds:-1112C>T, p.R130Q (rs1800925, rs20541) (human)		 RGD PMID:15564778 PMID:9034992 PMID:22045834 RGD:5684370, RGD:5684371, RGD:8549502 NCBI chr11:53,522,150...53,525,529
Ensembl chr11:53,522,151...53,525,529 		JBrowse link
G Il13ra1 interleukin 13 receptor, alpha 1 no_association ISO DNA:SNP:intron:43163G>A (rs6646259) (human) RGD PMID:22045834 RGD:8549502 NCBI chr  X:35,375,761...35,434,915
Ensembl chr  X:35,375,763...35,434,912 		JBrowse link
G Il17a interleukin 17A IMP
ISO		 protein:increased expression:epidermis, endodermis, mast cell (human) RGD PMID:22833167 PMID:23335253 RGD:8696037, RGD:8696038 NCBI chr 1:20,801,129...20,804,720
Ensembl chr 1:20,801,129...20,804,720 		JBrowse link
G Il1b interleukin 1 beta susceptibility ISO DNA:polymorphisms:promoter:-31T>C,-511C>T (human) RGD PMID:17444587 RGD:4142872 NCBI chr 2:129,206,490...129,213,059
Ensembl chr 2:129,206,490...129,213,059 		JBrowse link
G Il1r1 interleukin 1 receptor, type I ISO RGD PMID:1375465 RGD:8662902 NCBI chr 1:40,261,651...40,355,361
Ensembl chr 1:40,264,240...40,356,417 		JBrowse link
G Il2 interleukin 2 ISO protein:increased expression:serum: RGD PMID:2213757 RGD:8663482 NCBI chr 3:37,174,862...37,180,103
Ensembl chr 3:37,174,672...37,180,108 		JBrowse link
G Il23r interleukin 23 receptor no_association ISO DNA:SNPs: :rs11209026, rs11465804 (human)
DNA:SNPs: :rs11209032,rs1495965(human)		 RGD PMID:19918037 PMID:18713787 RGD:5096624, RGD:8549603 NCBI chr 6:67,399,906...67,468,838
Ensembl chr 6:67,399,916...67,468,839 		JBrowse link
G Il27 interleukin 27 ISO protein:increased expression:serum RGD PMID:20705635 RGD:5128477 NCBI chr 7:126,188,181...126,194,197
Ensembl chr 7:126,188,182...126,194,113 		JBrowse link
G Il27ra interleukin 27 receptor, alpha ISO mRNA:increased expression:skin RGD PMID:20705635 RGD:5128477 NCBI chr 8:84,756,915...84,769,250
Ensembl chr 8:84,756,923...84,769,218 		JBrowse link
G Il4 interleukin 4 ISO protein:increased expression:serum
mRNA, protein:increased expression, splice variant:blood, mononuclear cell, plasma		 RGD PMID:9034992 PMID:10473513 RGD:5684371, RGD:7829819 NCBI chr11:53,503,287...53,509,492
Ensembl chr11:53,493,809...53,509,496 		JBrowse link
G Il6 interleukin 6 treatment ISO RGD PMID:23406616 RGD:12792238 NCBI chr 5:30,218,112...30,224,973
Ensembl chr 5:30,218,112...30,224,979 		JBrowse link
G Irf5 interferon regulatory factor 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:20383147 NCBI chr 6:29,526,129...29,541,874
Ensembl chr 6:29,526,624...29,541,870 		JBrowse link
G Jam3 junction adhesion molecule 3 ISO protein:increased expression:skin
protein:decreased expression:skin, endothelial cell		 RGD PMID:23001478 PMID:19439502 RGD:7488920, RGD:7488937 NCBI chr 9:27,008,680...27,066,739
Ensembl chr 9:27,008,680...27,066,717 		JBrowse link
G Kdr kinase insert domain protein receptor ISO protein:decreased expression:bone marrow:
protein:increased expression:skin:		 RGD PMID:22271757 PMID:21865112 RGD:8551843, RGD:8552335 NCBI chr 5:76,093,487...76,139,880
Ensembl chr 5:76,093,487...76,139,118 		JBrowse link
G Lta lymphotoxin A susceptibility ISO DNA:SNP:intron:252A>G (human) RGD PMID:10600011 RGD:8548796 NCBI chr17:35,422,141...35,424,568
Ensembl chr17:35,422,141...35,424,327 		JBrowse link
G Mmp1a matrix metallopeptidase 1a (interstitial collagenase) severity ISO mRNA:decreased expression:skin
protein:increased expression:serum		 RGD PMID:22286923 PMID:12051403 RGD:8548651, RGD:8693663 NCBI chr 9:7,464,141...7,476,870
Ensembl chr 9:7,464,141...7,476,857 		JBrowse link
G Mmp1b matrix metallopeptidase 1b (interstitial collagenase) severity ISO protein:increased expression:serum
mRNA:decreased expression:skin		 RGD PMID:12051403 PMID:22286923 RGD:8548651 RGD:8693663 NCBI chr 9:7,367,670...7,388,026
Ensembl chr 9:7,368,239...7,388,047 		JBrowse link
G Mmp3 matrix metallopeptidase 3 severity ISO protein:increased expression:serum RGD PMID:12051403 PMID:15498049 RGD:8693663, RGD:8693674 NCBI chr 9:7,445,845...7,455,975
Ensembl chr 9:7,445,822...7,455,975 		JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO RGD PMID:15642145 RGD:1580577 NCBI chr 2:164,782,246...164,797,770
Ensembl chr 2:164,782,700...164,797,770 		JBrowse link
G Muc1 mucin 1, transmembrane ISO protein:increased expression:serum RGD PMID:19286849 RGD:4143496 NCBI chr 3:89,136,363...89,140,688
Ensembl chr 3:89,136,364...89,140,688 		JBrowse link
G Nat2 N-acetyltransferase 2 (arylamine N-acetyltransferase) susceptibility ISO DNA:polymorphism: : RGD PMID:10599336 RGD:5147680 NCBI chr 8:67,947,527...67,955,296
Ensembl chr 8:67,947,510...67,955,236 		JBrowse link
G Nectin2 nectin cell adhesion molecule 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27482699 NCBI chr 7:19,450,569...19,483,498
Ensembl chr 7:19,450,569...19,484,408 		JBrowse link
G Ngf nerve growth factor ISO protein:increased expression:serum RGD PMID:21085492 RGD:5144060 NCBI chr 3:102,377,235...102,428,329
Ensembl chr 3:102,377,235...102,428,329 		JBrowse link
G Notch4 notch 4 ISO DNA: SNPs: non-coding :multiple RGD PMID:21779181 RGD:6480691 NCBI chr17:34,783,257...34,807,517
Ensembl chr17:34,783,242...34,807,477 		JBrowse link
G Pecam1 platelet/endothelial cell adhesion molecule 1 IEP protein:decreased expression:superficial vasculature (human) RGD PMID:20228226 RGD:11541095 NCBI chr11:106,545,039...106,606,107
Ensembl chr11:106,545,043...106,641,454 		JBrowse link
G Pf4 platelet factor 4 severity ISO RGD PMID:34556381 RGD:329901818 NCBI chr 5:90,920,362...90,921,242
Ensembl chr 5:90,920,294...90,921,242 		JBrowse link
G Ptgs2 prostaglandin-endoperoxide synthase 2 ISO RGD PMID:21979415 RGD:5508306 NCBI chr 1:149,975,851...149,983,978
Ensembl chr 1:149,975,782...149,983,978 		JBrowse link
G Ptpn22 protein tyrosine phosphatase, non-receptor type 22 (lymphoid) no_association ISO DNA: snp: cds: rs2476601
DNA:missense mutation:cds:p.R620W (rs2476601) (human)		 RGD PMID:21131644 PMID:16464986 RGD:6484551, RGD:7829741 NCBI chr 3:103,763,891...103,819,568
Ensembl chr 3:103,767,111...103,819,563 		JBrowse link
G Rbp4 retinol binding protein 4, plasma disease_progression ISO associated with Raynaud disease and interstitial lung disease; protein:decreased expression:blood serum (human) RGD PMID:22211766 RGD:329845579 NCBI chr19:38,105,068...38,113,769
Ensembl chr19:38,105,077...38,113,729 		JBrowse link
G Rhob ras homolog family member B ISO CTD Direct Evidence: marker/mechanism CTD PMID:21750679 NCBI chr12:8,547,661...8,550,009
Ensembl chr12:8,547,661...8,550,009 		JBrowse link
G S1pr5 sphingosine-1-phosphate receptor 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:29033951 NCBI chr 9:21,154,213...21,159,739
Ensembl chr 9:21,154,208...21,159,739 		JBrowse link
G Selenop selenoprotein P ISO protein:decreased expression:serum RGD PMID:32630589 RGD:401827129 NCBI chr15:3,300,249...3,309,992
Ensembl chr15:3,298,029...3,309,990 		JBrowse link
G Serpine1 serine (or cysteine) peptidase inhibitor, clade E, member 1 ISO protein:increased expression:dermis,microvessel: RGD PMID:26414805 RGD:11343779 NCBI chr 5:137,090,358...137,101,126
Ensembl chr 5:137,090,358...137,101,122 		JBrowse link
G Serpinf2 serine (or cysteine) peptidase inhibitor, clade F, member 2 ISO protein:increased expression:plasma RGD PMID:12595617 RGD:1625530 NCBI chr11:75,322,562...75,330,327
Ensembl chr11:75,322,558...75,330,417 		JBrowse link
G Sirt1 sirtuin 1 ISO CTD Direct Evidence: therapeutic CTD PMID:25707573 NCBI chr10:63,154,784...63,174,814
Ensembl chr10:63,154,784...63,217,483 		JBrowse link
G Sirt7 sirtuin 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25707573 NCBI chr11:120,509,197...120,515,840
Ensembl chr11:120,509,198...120,516,066 		JBrowse link
G Slc11a1 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 ISO DNA:repeat, polymorphism:promoter, intron: (human) RGD PMID:17876529 RGD:5684940 NCBI chr 1:74,414,318...74,429,974
Ensembl chr 1:74,414,354...74,425,221 		JBrowse link
G Stat4 signal transducer and activator of transcription 4 susceptibility ISO DNA:SNP:intron: (rs7574865) (human)
CTD Direct Evidence: marker/mechanism
DNA:SNP:intron: (rs11889341) (human)		 CTD
RGD		 PMID:20383147 PMID:19644887 PMID:19950257 RGD:8661700, RGD:8661711 NCBI chr 1:52,026,265...52,146,348
Ensembl chr 1:52,026,307...52,146,348 		JBrowse link
G Tgfbr1 transforming growth factor, beta receptor I IAGP OMIM:181750 MouseDO NCBI chr 4:47,353,258...47,414,926
Ensembl chr 4:47,353,222...47,414,931 		JBrowse link
G Tnip1 TNFAIP3 interacting protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21750679 NCBI chr11:54,801,613...54,853,766
Ensembl chr11:54,801,611...54,853,743 		JBrowse link
G Vegfa vascular endothelial growth factor A ISO protein:increased expression:skin
mRNA,protein:increased expression:skin:
protein:increased expression:serum:
protein:increased expression:bone marrow:		 RGD PMID:16426919 PMID:21636803 PMID:24387171 PMID:22271757 RGD:5684416, RGD:7421579, RGD:8548659, RGD:8551843 NCBI chr17:46,327,919...46,343,303
Ensembl chr17:46,327,919...46,343,295 		JBrowse link
G Vwf Von Willebrand factor severity ISO RGD PMID:22596213 RGD:7205639 NCBI chr 6:125,529,911...125,663,642
Ensembl chr 6:125,523,737...125,663,642 		JBrowse link
CREST syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cenpc1 centromere protein C1 ISO associated with Anticentromere antibody positivity RGD PMID:25220385 RGD:27372886 NCBI chr 5:86,159,877...86,214,325
Ensembl chr 5:86,159,883...86,213,442 		JBrowse link
G Fbn1 fibrillin 1 ISO RGD PMID:10395706 RGD:12910471 NCBI chr 2:125,142,514...125,348,417
Ensembl chr 2:125,142,514...125,349,913 		JBrowse link
diffuse scleroderma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Adipoq adiponectin, C1Q and collagen domain containing severity ISO protein:decreased expression:serum RGD PMID:21615510 RGD:8694418 NCBI chr16:22,965,286...22,976,718
Ensembl chr16:22,965,286...22,976,778 		JBrowse link
G Agt angiotensinogen ISO protein:increased expression:serum RGD PMID:14730619 RGD:8548886 NCBI chr 8:125,283,326...125,296,445
Ensembl chr 8:125,283,273...125,296,445 		JBrowse link
G Bank1 B cell scaffold protein with ankyrin repeats 1 susceptibility ISO DNA:SNPs: :rs10516487,rs17266594,rs3733197(human) RGD PMID:19815934 RGD:9684975 NCBI chr 3:135,759,124...136,031,902
Ensembl chr 3:135,759,124...136,031,827 		JBrowse link
G Cav1 caveolin 1, caveolae protein susceptibility
no_association		 ISO DNA:SNPs:intron, 3' utr: (rs729949, rs3815412, rs9920) (human)
DNA:SNPs:enhancer, intron:multiple		 RGD PMID:22402147 PMID:22402147 RGD:8661768, RGD:8661768 NCBI chr 6:17,306,387...17,341,323
Ensembl chr 6:17,306,334...17,341,451 		JBrowse link
G Cxcl5 C-X-C motif chemokine ligand 5 ISO RGD PMID:18432520 RGD:5135258 NCBI chr 5:90,907,157...90,909,484
Ensembl chr 5:90,907,219...90,909,483 		JBrowse link
G H2-Aa histocompatibility 2, class II antigen A, alpha susceptibility ISO DNA:polymorphism::HLA-DQA1*0501; RGD PMID:11014350 RGD:8547725 NCBI chr17:34,501,718...34,506,797
Ensembl chr17:34,501,718...34,506,797 		JBrowse link
G Il10 interleukin 10 ISO protein:increased expression:serum RGD PMID:9034992 RGD:5684371 NCBI chr 1:130,947,459...130,952,707
Ensembl chr 1:130,947,582...130,952,711 		JBrowse link
G Il13 interleukin 13 ISO DNA:SNPs:5' utr, enhancer: (rs1800925, rs2243204) (human) RGD PMID:16832637 RGD:5684369 NCBI chr11:53,522,150...53,525,529
Ensembl chr11:53,522,151...53,525,529 		JBrowse link
G Il6 interleukin 6 treatment ISO RGD PMID:20338043 RGD:12792275 NCBI chr 5:30,218,112...30,224,973
Ensembl chr 5:30,218,112...30,224,979 		JBrowse link
G Irak1 interleukin-1 receptor-associated kinase 1 susceptibility ISO DNA:missense mutation:cds:p.F196S (rs1059702) (human) RGD PMID:21898345 RGD:7495782 NCBI chr  X:73,057,520...73,067,527
Ensembl chr  X:73,057,520...73,067,524 		JBrowse link
G Kdr kinase insert domain protein receptor ISO protein:increased expression:serum: RGD PMID:19886888 RGD:8551850 NCBI chr 5:76,093,487...76,139,880
Ensembl chr 5:76,093,487...76,139,118 		JBrowse link
G Stat4 signal transducer and activator of transcription 4 susceptibility
no_association		 ISO DNA:SNP:introns: (rs7574865, rs10168266) (human)
DNA:SNP:intron: (rs7574865) (human)
DNA:SNP:intron: (rs3821236) (human)		 RGD PMID:23755762 PMID:19286670 PMID:23755762 RGD:8661701, RGD:8661714, RGD:8661701 NCBI chr 1:52,026,265...52,146,348
Ensembl chr 1:52,026,307...52,146,348 		JBrowse link
G Tap1 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) susceptibility ISO RGD PMID:16112028 RGD:1578361 NCBI chr17:34,406,530...34,416,199
Ensembl chr17:34,406,527...34,416,199 		JBrowse link
G Tap2 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) susceptibility ISO RGD PMID:16112028 RGD:1578361 NCBI chr17:34,423,453...34,435,295
Ensembl chr17:34,422,501...34,435,295 		JBrowse link
G Tgfbr1 transforming growth factor, beta receptor I ISO CTD Direct Evidence: marker/mechanism CTD PMID:27228633 NCBI chr 4:47,353,258...47,414,926
Ensembl chr 4:47,353,222...47,414,931 		JBrowse link
G Tlr2 toll-like receptor 2 disease_progression ISO DNA:polymorphism:cds:p.P631H(rs5743704)(human) RGD PMID:21905008 RGD:8553044 NCBI chr 3:83,743,579...83,749,045
Ensembl chr 3:83,743,579...83,749,074 		JBrowse link
G Wrn Werner syndrome RecQ like helicase ISO RGD PMID:16906373 RGD:10042980 NCBI chr 8:33,724,400...33,875,591
Ensembl chr 8:33,724,412...33,875,555 		JBrowse link
limited scleroderma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cav1 caveolin 1, caveolae protein susceptibility
no_association		 ISO DNA:SNPs:enhancer, intron:multiple
DNA:SNPs:3' utr, intron: (rs9920, rs729949, rs3815412) (human)		 RGD PMID:22402147 PMID:22402147 RGD:8661768, RGD:8661768 NCBI chr 6:17,306,387...17,341,323
Ensembl chr 6:17,306,334...17,341,451 		JBrowse link
G Ccl2 C-C motif chemokine ligand 2 IMP
IEP		 mRNA,protein:increased expression:skin: RGD PMID:12925209 PMID:12925209 RGD:8661733, RGD:8661733 NCBI chr11:81,926,403...81,928,278
Ensembl chr11:81,926,397...81,928,279 		JBrowse link
G Ccr2 C-C motif chemokine receptor 2 IEP mRNA,protein:increased expression:skin: RGD PMID:12925209 RGD:8661733 NCBI chr 9:123,901,954...123,913,594
Ensembl chr 9:123,901,987...123,913,594 		JBrowse link
G Fas Fas cell surface death receptor IMP RGD PMID:17102953 RGD:12903974 NCBI chr19:34,267,926...34,305,175
Ensembl chr19:34,268,066...34,305,172 		JBrowse link
G Fasl Fas ligand IMP RGD PMID:17102953 RGD:12903974 NCBI chr 1:161,608,260...161,616,064
Ensembl chr 1:161,608,258...161,616,064 		JBrowse link
G Il2 interleukin 2 susceptibility ISO DNA:polymorphism::-384T>G(human) RGD PMID:17444587 RGD:4142872 NCBI chr 3:37,174,862...37,180,103
Ensembl chr 3:37,174,672...37,180,108 		JBrowse link
G Jak2 Janus kinase 2 ISO RGD PMID:20808962 RGD:4892610 NCBI chr19:29,229,006...29,290,495
Ensembl chr19:29,229,228...29,290,480 		JBrowse link
G Kdr kinase insert domain protein receptor ISO protein:increased expression:serum: RGD PMID:19886888 RGD:8551850 NCBI chr 5:76,093,487...76,139,880
Ensembl chr 5:76,093,487...76,139,118 		JBrowse link
G Pgf placental growth factor ISO protein:increased expression:plasma RGD PMID:22461185 RGD:6483571 NCBI chr12:85,213,413...85,224,087
Ensembl chr12:85,213,409...85,224,564 		JBrowse link
G Serpine1 serine (or cysteine) peptidase inhibitor, clade E, member 1 IEP mRNA,protein:increased expression:skin: RGD PMID:15730388 RGD:13208597 NCBI chr 5:137,090,358...137,101,126
Ensembl chr 5:137,090,358...137,101,122 		JBrowse link
G Stat4 signal transducer and activator of transcription 4 no_association
susceptibility		 ISO DNA:SNPs:introns: (rs10168266, rs3821236) (human)
DNA:SNP:intron: (rs7574865) (human)		 RGD PMID:23755762 PMID:23755762 PMID:19286670 RGD:8661701, RGD:8661701, RGD:8661714 NCBI chr 1:52,026,265...52,146,348
Ensembl chr 1:52,026,307...52,146,348 		JBrowse link
G Tap2 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) susceptibility ISO RGD PMID:16112028 RGD:1578361 NCBI chr17:34,423,453...34,435,295
Ensembl chr17:34,422,501...34,435,295 		JBrowse link
Reynolds Syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Lbr lamin B receptor ISO ClinVar Annotator: match by term: PRIMARY BILIARY CIRRHOSIS, SCLERODERMA, RAYNAUD DISEASE, AND TELANGIECTASIA | ClinVar Annotator: match by term: Reynolds syndrome OMIM
ClinVar		 PMID:18382993 PMID:20522425 PMID:23824842 PMID:24033266 PMID:25348816 More... NCBI chr 1:181,642,880...181,669,933
Ensembl chr 1:181,642,900...181,670,611 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16263
    disease of anatomical entity 15856
      musculoskeletal system disease 8124
        autoimmune disease of musculoskeletal system 938
          rheumatic disease 721
            scleroderma 124
              systemic scleroderma 116
                Familial Progressive Scleroderma 0
                Juvenile Systemic Scleroderma 0
                Juvenile-Onset Scleroderma 0
                Reynolds Syndrome 1
                diffuse scleroderma 17
                limited scleroderma + 14
                pulmonary systemic sclerosis 0
Path 2
Term Annotations click to browse term
  disease 16263
    disease of anatomical entity 15856
      Immune & Inflammatory Diseases 5360
        immune system disease 4765
          primary immunodeficiency disease 4189
            autoimmune disease 2123
              autoimmune disease of musculoskeletal system 938
                rheumatic disease 721
                  scleroderma 124
                    systemic scleroderma 116
                      Familial Progressive Scleroderma 0
                      Juvenile Systemic Scleroderma 0
                      Juvenile-Onset Scleroderma 0
                      Reynolds Syndrome 1
                      diffuse scleroderma 17
                      limited scleroderma + 14
                      pulmonary systemic sclerosis 0
paths to the root