LOC116225307 (CRISPRi-validated cis-regulatory element chr11.6035) - Rat Genome Database

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Gene: LOC116225307 (CRISPRi-validated cis-regulatory element chr11.6035) Homo sapiens
Analyze
Symbol: LOC116225307
Name: CRISPRi-validated cis-regulatory element chr11.6035
RGD ID: 38609653
Description: This genomic region represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. It was validated as a high-confidence cis-regulatory element for the APLP2 (amyloid beta precursor like protein 2) gene on chromosome 11 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811130,006,891 - 130,007,237 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711129,876,786 - 129,877,132 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11qNCBI
T2T-CHM13v2.011130,042,918 - 130,043,264 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
schizophrenia  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Schizophrenia  (IAGP)
References
Additional References at PubMed
PMID:22955616   PMID:22955617   PMID:30612741  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q22.1-25(chr11:100348599-135040246)x3 copy number gain See cases [RCV000053638] Chr11:100348599..135040246 [GRCh38]
Chr11:100219331..134910140 [GRCh37]
Chr11:99724541..134415350 [NCBI36]
Chr11:11q22.1-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:120515759-135075271)x1 copy number loss See cases [RCV000138373] Chr11:120515759..135075271 [GRCh38]
Chr11:120386468..134945165 [GRCh37]
Chr11:119891678..134450377 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:124205225-134998526)x1 copy number loss See cases [RCV000134731] Chr11:124205225..134998526 [GRCh38]
Chr11:124075932..134868420 [GRCh37]
Chr11:123581142..134373630 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126199589-135075271)x1 copy number loss See cases [RCV000139117] Chr11:126199589..135075271 [GRCh38]
Chr11:126069484..134945165 [GRCh37]
Chr11:125574694..134450377 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:127604660-134998454)x1 copy number loss See cases [RCV000050843] Chr11:127604660..134998454 [GRCh38]
Chr11:127474555..134868348 [GRCh37]
Chr11:126979765..134373558 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116851372-134998526)x3 copy number gain See cases [RCV000134064] Chr11:116851372..134998526 [GRCh38]
Chr11:116722088..134868420 [GRCh37]
Chr11:116227298..134373630 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.3-25(chr11:128867946-133086998)x1 copy number loss See cases [RCV000139715] Chr11:128867946..133086998 [GRCh38]
Chr11:128737841..132956893 [GRCh37]
Chr11:128243051..132462103 [NCBI36]
Chr11:11q24.3-25		 likely pathogenic
GRCh38/hg38 11q23.3-25(chr11:116851395-134998513)x3 copy number gain See cases [RCV000148276] Chr11:116851395..134998513 [GRCh38]
Chr11:116722111..134868407 [GRCh37]
Chr11:116227321..134373617 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:123799938-134998526)x1 copy number loss See cases [RCV000134708] Chr11:123799938..134998526 [GRCh38]
Chr11:123670646..134868420 [GRCh37]
Chr11:123175856..134373630 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:124155723-134998513)x1 copy number loss See cases [RCV000050865] Chr11:124155723..134998513 [GRCh38]
Chr11:124026430..134868407 [GRCh37]
Chr11:123531640..134373617 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:119424297-135075271)x1 copy number loss See cases [RCV000138947] Chr11:119424297..135075271 [GRCh38]
Chr11:119295007..134945165 [GRCh37]
Chr11:118800217..134450377 [NCBI36]
Chr11:11q23.3-25		 pathogenic|likely benign
GRCh38/hg38 11q24.1-25(chr11:121689052-135075271)x1 copy number loss See cases [RCV000139622] Chr11:121689052..135075271 [GRCh38]
Chr11:121559760..134945165 [GRCh37]
Chr11:121064970..134450377 [NCBI36]
Chr11:11q24.1-25		 pathogenic|likely benign
GRCh38/hg38 11q24.2-25(chr11:126433740-135040246)x1 copy number loss See cases [RCV000052741] Chr11:126433740..135040246 [GRCh38]
Chr11:126303635..134910140 [GRCh37]
Chr11:125808845..134415350 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126046358-134998513)x1 copy number loss See cases [RCV000136595] Chr11:126046358..134998513 [GRCh38]
Chr11:125916253..134868407 [GRCh37]
Chr11:125421463..134373617 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:127564482-135075271)x1 copy number loss See cases [RCV000137719] Chr11:127564482..135075271 [GRCh38]
Chr11:127434377..134945165 [GRCh37]
Chr11:126939587..134450377 [NCBI36]
Chr11:11q24.2-25		 pathogenic|likely benign
GRCh38/hg38 11q24.2-25(chr11:125241472-134998513)x1 copy number loss See cases [RCV000136612] Chr11:125241472..134998513 [GRCh38]
Chr11:125111368..134868407 [GRCh37]
Chr11:124616578..134373617 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116806268-135075271)x3 copy number gain See cases [RCV000138307] Chr11:116806268..135075271 [GRCh38]
Chr11:116676984..134945165 [GRCh37]
Chr11:116182194..134450377 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116868935-135075271)x3 copy number gain See cases [RCV000137453] Chr11:116868935..135075271 [GRCh38]
Chr11:116739651..134945165 [GRCh37]
Chr11:116244861..134450377 [NCBI36]
Chr11:11q23.3-25		 pathogenic|conflicting data from submitters
GRCh38/hg38 11q24.1-25(chr11:123963074-135075271)x1 copy number loss See cases [RCV000138544] Chr11:123963074..135075271 [GRCh38]
Chr11:123833781..134945165 [GRCh37]
Chr11:123338991..134450377 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q24.3-25(chr11:127915964-135068576)x1 copy number loss See cases [RCV000143755] Chr11:127915964..135068576 [GRCh38]
Chr11:127785859..134938470 [GRCh37]
Chr11:127291069..134443680 [NCBI36]
Chr11:11q24.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:119433909-134998513)x1 copy number loss See cases [RCV000050905] Chr11:119433909..134998513 [GRCh38]
Chr11:119304619..134868407 [GRCh37]
Chr11:118809829..134373617 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:124315025-134818116)x1 copy number loss See cases [RCV000139907] Chr11:124315025..134818116 [GRCh38]
Chr11:124184921..134688010 [GRCh37]
Chr11:123690131..134193220 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:124940059-135075271)x1 copy number loss See cases [RCV000138675] Chr11:124940059..135075271 [GRCh38]
Chr11:124809955..134945165 [GRCh37]
Chr11:124315165..134450377 [NCBI36]
Chr11:11q24.2-25		 pathogenic|likely benign
GRCh38/hg38 11q23.2-25(chr11:112864326-131189315)x3 copy number gain See cases [RCV000137582] Chr11:112864326..131189315 [GRCh38]
Chr11:112832130..131059210 [GRCh37]
Chr11:112240259..130564420 [NCBI36]
Chr11:11q23.2-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:120236432-135040246)x3 copy number gain See cases [RCV000053643] Chr11:120236432..135040246 [GRCh38]
Chr11:120107141..134910140 [GRCh37]
Chr11:119612351..134415350 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:116851395-134998513)x3 copy number gain See cases [RCV000050331] Chr11:116851395..134998513 [GRCh38]
Chr11:116722111..134868407 [GRCh37]
Chr11:116227321..134373617 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:121780459-135075271)x1 copy number loss See cases [RCV000138014] Chr11:121780459..135075271 [GRCh38]
Chr11:121651167..134945165 [GRCh37]
Chr11:121156377..134450377 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126046358-135075271)x1 copy number loss See cases [RCV000138163] Chr11:126046358..135075271 [GRCh38]
Chr11:125916253..134945165 [GRCh37]
Chr11:125421463..134450377 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.2-25(chr11:126445805-134998513)x3 copy number gain See cases [RCV000051162] Chr11:126445805..134998513 [GRCh38]
Chr11:126315700..134868407 [GRCh37]
Chr11:125820910..134373617 [NCBI36]
Chr11:11q24.2-25		 pathogenic
GRCh38/hg38 11q24.3-25(chr11:129700536-134998513)x1 copy number loss See cases [RCV000052742] Chr11:129700536..134998513 [GRCh38]
Chr11:129570431..134868407 [GRCh37]
Chr11:129075641..134373617 [NCBI36]
Chr11:11q24.3-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:121611476-135068576)x1 copy number loss See cases [RCV000142185] Chr11:121611476..135068576 [GRCh38]
Chr11:121482185..134938470 [GRCh37]
Chr11:120987395..134443680 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q24.1-25(chr11:121806547-135068576)x1 copy number loss See cases [RCV000142210] Chr11:121806547..135068576 [GRCh38]
Chr11:121677255..134938470 [GRCh37]
Chr11:121182465..134443680 [NCBI36]
Chr11:11q24.1-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:118789765-134998513)x3 copy number gain See cases [RCV000051213] Chr11:118789765..134998513 [GRCh38]
Chr11:118660474..134868407 [GRCh37]
Chr11:118165684..134373617 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:119215032-134998654)x1 copy number loss See cases [RCV000052715] Chr11:119215032..134998654 [GRCh38]
Chr11:119085742..134868548 [GRCh37]
Chr11:118590952..134373758 [NCBI36]
Chr11:11q23.3-25		 pathogenic
GRCh38/hg38 11q23.3-25(chr11:120507265-134576266)x1 copy number loss See cases [RCV000052716] Chr11:120507265..134576266 [GRCh38]
Chr11:120377974..134446160 [GRCh37]
Chr11:119883184..133951370 [NCBI36]
Chr11:11q23.3-25		 pathogenic
Single allele duplication Schizophrenia [RCV000754124] Chr11:118989374..135076622 [GRCh38]
Chr11:11q23.3-25		 likely pathogenic

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC116225307 COSMIC
GTEx LOC116225307 GTEx
Human Proteome Map LOC116225307 Human Proteome Map
NCBI Gene LOC116225307 ENTREZGENE