LOC116158510 (CRISPRi-validated cis-regulatory element chr4.3423) - Rat Genome Database

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Gene: LOC116158510 (CRISPRi-validated cis-regulatory element chr4.3423) Homo sapiens
Analyze
Symbol: LOC116158510
Name: CRISPRi-validated cis-regulatory element chr4.3423
RGD ID: 38608208
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 cis-regulatory element for the SPCS3 (signal peptidase complex subunit 3) gene on chromosome 4 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 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
GRCh384176,290,513 - 176,291,009 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh374177,211,664 - 177,212,160 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map4qNCBI
T2T-CHM13v2.04179,629,599 - 179,630,095 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:9847074   PMID:22955616   PMID:22955617   PMID:30612741  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q34.2-35.2(chr4:175483683-189975519)x1 copy number loss See cases [RCV000051215] Chr4:175483683..189975519 [GRCh38]
Chr4:176404834..190828225 [GRCh37]
Chr4:176641828..191133668 [NCBI36]
Chr4:4q34.2-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1 copy number loss See cases [RCV000141964] Chr4:167373716..190036318 [GRCh38]
Chr4:168294867..190957473 [GRCh37]
Chr4:168531442..191194467 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q33-35.2(chr4:170899124-190036318)x1 copy number loss See cases [RCV000143232] Chr4:170899124..190036318 [GRCh38]
Chr4:171820275..190957473 [GRCh37]
Chr4:172056850..191194467 [NCBI36]
Chr4:4q33-35.2		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:134935616-190036318)x3 copy number gain See cases [RCV000143559] Chr4:134935616..190036318 [GRCh38]
Chr4:135856771..190957473 [GRCh37]
Chr4:136076221..191194467 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:173754675-189343295)x1 copy number loss See cases [RCV000053353] Chr4:173754675..189343295 [GRCh38]
Chr4:174675826..190264449 [GRCh37]
Chr4:174912401..190501443 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:168970400-186936738)x1 copy number loss See cases [RCV000142368] Chr4:168970400..186936738 [GRCh38]
Chr4:169891551..187857892 [GRCh37]
Chr4:170128126..188094886 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-34.3(chr4:175013055-181652375)x1 copy number loss See cases [RCV000053355] Chr4:175013055..181652375 [GRCh38]
Chr4:175934206..182573528 [GRCh37]
Chr4:176170781..182810522 [NCBI36]
Chr4:4q34.1-34.3		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:164039530-189982708)x1 copy number loss See cases [RCV000053347] Chr4:164039530..189982708 [GRCh38]
Chr4:164960682..190828225 [GRCh37]
Chr4:165180132..191140857 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:171507704-189869726)x1 copy number loss See cases [RCV000053349] Chr4:171507704..189869726 [GRCh38]
Chr4:172428855..190790881 [GRCh37]
Chr4:172665430..191027875 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q34.1-34.3(chr4:171851295-178772816)x1 copy number loss See cases [RCV000053350] Chr4:171851295..178772816 [GRCh38]
Chr4:172772446..179693970 [GRCh37]
Chr4:173009021..179930964 [NCBI36]
Chr4:4q34.1-34.3		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:172356988-189975519)x1 copy number loss See cases [RCV000053352] Chr4:172356988..189975519 [GRCh38]
Chr4:173278139..190828225 [GRCh37]
Chr4:173514714..191133668 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:166317587-190095391)x1 copy number loss See cases [RCV000137532] Chr4:166317587..190095391 [GRCh38]
Chr4:167238739..190828225 [GRCh37]
Chr4:167458189..191250527 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:131985253-190095391)x3 copy number gain See cases [RCV000137721] Chr4:131985253..190095391 [GRCh38]
Chr4:132906408..190828225 [GRCh37]
Chr4:133125858..191250527 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic|likely benign
GRCh38/hg38 4q34.1-35.2(chr4:173599911-188624331)x1 copy number loss See cases [RCV000050771] Chr4:173599911..188624331 [GRCh38]
Chr4:174521062..189545485 [GRCh37]
Chr4:174757637..189782479 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q28.1-35.1(chr4:125432943-185761887)x3 copy number gain See cases [RCV000138578] Chr4:125432943..185761887 [GRCh38]
Chr4:126354098..186683041 [GRCh37]
Chr4:126573548..186920035 [NCBI36]
Chr4:4q28.1-35.1		 pathogenic|likely benign
GRCh38/hg38 4q31.21-35.2(chr4:145042668-189975519)x3 copy number gain See cases [RCV000135845] Chr4:145042668..189975519 [GRCh38]
Chr4:145963820..190828225 [GRCh37]
Chr4:146183270..191133668 [NCBI36]
Chr4:4q31.21-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1 copy number loss See cases [RCV000136115] Chr4:173854560..189548183 [GRCh38]
Chr4:174775711..190469337 [GRCh37]
Chr4:175012286..190706331 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q31.1-35.2(chr4:138510532-189963195)x3 copy number gain See cases [RCV000136810] Chr4:138510532..189963195 [GRCh38]
Chr4:139431686..190828225 [GRCh37]
Chr4:139651136..191121344 [NCBI36]
Chr4:4q31.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:165281036-190018185)x1 copy number loss See cases [RCV000140414] Chr4:165281036..190018185 [GRCh38]
Chr4:166202188..190939340 [GRCh37]
Chr4:166421638..191176334 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:172501374-190095332)x1 copy number loss See cases [RCV000143079] Chr4:172501374..190095332 [GRCh38]
Chr4:173422525..190828225 [GRCh37]
Chr4:173659100..191250468 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:168119317-190095391)x3 copy number gain See cases [RCV000143331] Chr4:168119317..190095391 [GRCh38]
Chr4:169040468..190828225 [GRCh37]
Chr4:169277043..191250527 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q32.2-35.2(chr4:162013220-189975519)x3 copy number gain See cases [RCV000050649] Chr4:162013220..189975519 [GRCh38]
Chr4:162934372..190828225 [GRCh37]
Chr4:163153822..191133668 [NCBI36]
Chr4:4q32.2-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.1(chr4:174080892-183195538)x1 copy number loss See cases [RCV000053354] Chr4:174080892..183195538 [GRCh38]
Chr4:175002043..184116691 [GRCh37]
Chr4:175238618..184353685 [NCBI36]
Chr4:4q34.1-35.1		 pathogenic
GRCh38/hg38 4q33-35.2(chr4:169873508-190018185)x1 copy number loss See cases [RCV000140396] Chr4:169873508..190018185 [GRCh38]
Chr4:170794659..190939340 [GRCh37]
Chr4:171031234..191176334 [NCBI36]
Chr4:4q33-35.2		 pathogenic
GRCh38/hg38 4q33-35.2(chr4:169901205-190095391)x3 copy number gain See cases [RCV000138540] Chr4:169901205..190095391 [GRCh38]
Chr4:170822356..190828225 [GRCh37]
Chr4:171058931..191250527 [NCBI36]
Chr4:4q33-35.2		 uncertain significance
GRCh38/hg38 4q32.1-35.2(chr4:160757699-190091407)x3 copy number gain See cases [RCV000140982] Chr4:160757699..190091407 [GRCh38]
Chr4:161678851..191012562 [GRCh37]
Chr4:161898301..191246543 [NCBI36]
Chr4:4q32.1-35.2		 pathogenic
GRCh38/hg38 4q34.1-34.3(chr4:171507504-181381327)x3 copy number gain See cases [RCV000051793] Chr4:171507504..181381327 [GRCh38]
Chr4:172428655..182302480 [GRCh37]
Chr4:172665230..182539474 [NCBI36]
Chr4:4q34.1-34.3		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:173989029-189975519)x1 copy number loss See cases [RCV000141490] Chr4:173989029..189975519 [GRCh38]
Chr4:174910180..190828225 [GRCh37]
Chr4:175146755..191133668 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q26-35.2(chr4:118065569-190042639)x3 copy number gain See cases [RCV000051785] Chr4:118065569..190042639 [GRCh38]
Chr4:118986724..190828225 [GRCh37]
Chr4:119206172..191200788 [NCBI36]
Chr4:4q26-35.2		 pathogenic
GRCh38/hg38 4q27-35.2(chr4:121518223-190062270)x3 copy number gain See cases [RCV000051786] Chr4:121518223..190062270 [GRCh38]
Chr4:122439378..190828225 [GRCh37]
Chr4:122658828..191220419 [NCBI36]
Chr4:4q27-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:172200228-189975519)x3 copy number gain See cases [RCV000051804] Chr4:172200228..189975519 [GRCh38]
Chr4:173121379..190828225 [GRCh37]
Chr4:173357954..191133668 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-34.3(chr4:166630207-179820960) copy number loss See cases [RCV000141653] Chr4:166630207..179820960 [GRCh38]
Chr4:167551358..180742113 [GRCh37]
Chr4:167770808..180979107 [NCBI36]
Chr4:4q32.3-34.3		 pathogenic

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC116158510 COSMIC
GTEx LOC116158510 GTEx
Human Proteome Map LOC116158510 Human Proteome Map
NCBI Gene LOC116158510 ENTREZGENE