LOC112272600 (Sharpr-MPRA regulatory region 4265) - Rat Genome Database

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Gene: LOC112272600 (Sharpr-MPRA regulatory region 4265) Homo sapiens
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Symbol: LOC112272600
Name: Sharpr-MPRA regulatory region 4265
RGD ID: 38631190
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 enhancer 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 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Apr 2018]
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
GRCh381559,138,210 - 59,138,504 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371559,430,409 - 59,430,703 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map15qNCBI
T2T-CHM13v2.01556,940,302 - 56,940,596 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:27701403  


Genomics

Variants

.
Variants in LOC112272600
17 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_004998.4(MYO1E):c.3144G>A (p.Lys1048=) single nucleotide variant not provided [RCV000979625] Chr15:59138304 [GRCh38]
Chr15:59430503 [GRCh37]
Chr15:15q22.2		 likely benign
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
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
NM_004998.4(MYO1E):c.3146C>A (p.Pro1049His) single nucleotide variant not provided [RCV001574773]|not specified [RCV000591657] Chr15:59138302 [GRCh38]
Chr15:59430501 [GRCh37]
Chr15:15q22.2		 benign|likely benign
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
NM_004998.4(MYO1E):c.3141_3152del (p.Lys1048_Pro1051del) deletion not provided [RCV000723084] Chr15:59138296..59138307 [GRCh38]
Chr15:59430495..59430506 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3094_3097del (p.Thr1032fs) microsatellite Nephrotic syndrome [RCV001328212] Chr15:59138351..59138354 [GRCh38]
Chr15:59430550..59430553 [GRCh37]
Chr15:15q22.2		 likely pathogenic
NM_004998.4(MYO1E):c.3118G>C (p.Gly1040Arg) single nucleotide variant Focal segmental glomerulosclerosis 6 [RCV002492391]|not provided [RCV002024861] Chr15:59138330 [GRCh38]
Chr15:59430529 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3081-6C>T single nucleotide variant Focal segmental glomerulosclerosis 6 [RCV002497884]|not provided [RCV001953854] Chr15:59138373 [GRCh38]
Chr15:59430572 [GRCh37]
Chr15:15q22.2		 likely benign
NM_004998.4(MYO1E):c.3236A>G (p.Asp1079Gly) single nucleotide variant not provided [RCV002098405] Chr15:59138212 [GRCh38]
Chr15:59430411 [GRCh37]
Chr15:15q22.2		 likely benign
NM_004998.4(MYO1E):c.3116C>G (p.Ala1039Gly) single nucleotide variant Inborn genetic diseases [RCV002882725] Chr15:59138332 [GRCh38]
Chr15:59430531 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3101G>A (p.Ser1034Asn) single nucleotide variant Inborn genetic diseases [RCV002729868] Chr15:59138347 [GRCh38]
Chr15:59430546 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3189C>T (p.Asp1063=) single nucleotide variant not provided [RCV003078852] Chr15:59138259 [GRCh38]
Chr15:59430458 [GRCh37]
Chr15:15q22.2		 likely benign
NM_004998.4(MYO1E):c.3224A>G (p.Asn1075Ser) single nucleotide variant not provided [RCV002923494] Chr15:59138224 [GRCh38]
Chr15:59430423 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3142A>C (p.Lys1048Gln) single nucleotide variant not provided [RCV003063738] Chr15:59138306 [GRCh38]
Chr15:59430505 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3151C>T (p.Pro1051Ser) single nucleotide variant Inborn genetic diseases [RCV002718391] Chr15:59138297 [GRCh38]
Chr15:59430496 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3235G>T (p.Asp1079Tyr) single nucleotide variant not provided [RCV002967078] Chr15:59138213 [GRCh38]
Chr15:59430412 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3084C>A (p.Val1028=) single nucleotide variant not provided [RCV002585259] Chr15:59138364 [GRCh38]
Chr15:59430563 [GRCh37]
Chr15:15q22.2		 likely benign
NM_004998.4(MYO1E):c.3208C>G (p.Leu1070Val) single nucleotide variant not provided [RCV003724075] Chr15:59138240 [GRCh38]
Chr15:59430439 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3112C>A (p.Pro1038Thr) single nucleotide variant Inborn genetic diseases [RCV004456437] Chr15:59138336 [GRCh38]
Chr15:59430535 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3094A>C (p.Thr1032Pro) single nucleotide variant Inborn genetic diseases [RCV004456436] Chr15:59138354 [GRCh38]
Chr15:59430553 [GRCh37]
Chr15:15q22.2		 uncertain significance
NM_004998.4(MYO1E):c.3103C>T (p.Arg1035Trp) single nucleotide variant Inborn genetic diseases [RCV004645907] Chr15:59138345 [GRCh38]
Chr15:59430544 [GRCh37]
Chr15:15q22.2		 uncertain significance

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
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 LOC112272600 COSMIC
GTEx LOC112272600 GTEx
Human Proteome Map LOC112272600 Human Proteome Map
NCBI Gene LOC112272600 ENTREZGENE