LOC125078086 (Sharpr-MPRA regulatory region 6038) - Rat Genome Database

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Gene: LOC125078086 (Sharpr-MPRA regulatory region 6038) Homo sapiens
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Symbol: LOC125078086
Name: Sharpr-MPRA regulatory region 6038
RGD ID: 151892963
Description: This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). [provided by RefSeq, Apr 2022]
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
GRCh381558,410,470 - 58,410,764 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371558,702,669 - 58,702,963 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map15qNCBI
T2T-CHM13v2.01556,212,432 - 56,212,726 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:27701403  


Genomics

Variants

.
Variants in LOC125078086
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 15q21.3(chr15:58227724-58464615)x1 copy number loss See cases [RCV000051173] Chr15:58227724..58464615 [GRCh38]
Chr15:58519923..58756814 [GRCh37]
Chr15:56307215..56544106 [NCBI36]
Chr15:15q21.3		 uncertain significance
GRCh38/hg38 15q21.2-22.2(chr15:50864913-59646577)x1 copy number loss See cases [RCV000051621] Chr15:50864913..59646577 [GRCh38]
Chr15:51157110..59938776 [GRCh37]
Chr15:48944402..57726068 [NCBI36]
Chr15:15q21.2-22.2		 pathogenic
GRCh38/hg38 15q21.3-22.2(chr15:57567950-63019415)x1 copy number loss See cases [RCV000051622] Chr15:57567950..63019415 [GRCh38]
Chr15:57860148..63311614 [GRCh37]
Chr15:55647440..61098667 [NCBI36]
Chr15:15q21.3-22.2		 pathogenic
GRCh38/hg38 15q21.3-22.2(chr15:57456076-61907285)x1 copy number loss See cases [RCV000050884] Chr15:57456076..61907285 [GRCh38]
Chr15:57748274..62199484 [GRCh37]
Chr15:55535566..59986776 [NCBI36]
Chr15:15q21.3-22.2		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2299958PRSTS330_HProstate tumor susceptibility QTL 330 (human)1.020.0151Prostate tumor susceptibility153479023060790230Human
407076184GWAS725160_Hlevel of Sphingomyelin (d34:1) in blood serum QTL GWAS725160 (human)6e-08level of Sphingomyelin (d34:1) in blood serum155841066558410666Human
407187225GWAS836201_Hphosphatidylethanolamine measurement QTL GWAS836201 (human)6e-14phosphatidylethanolamine measurement155841066558410666Human
1559354LDLPS4_HLow density lipoprotein particle size QTL 4 (human)2.20.019LDL particle size153479023060790230Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC125078086 COSMIC
GTEx LOC125078086 GTEx
Human Proteome Map LOC125078086 Human Proteome Map
NCBI Gene LOC125078086 ENTREZGENE