LOC122889028 (Sharpr-MPRA regulatory region 15302) - Rat Genome Database

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Gene: LOC122889028 (Sharpr-MPRA regulatory region 15302) Homo sapiens
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Symbol: LOC122889028
Name: Sharpr-MPRA regulatory region 15302
RGD ID: 150519988
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Oct 2021]
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
GRCh3839,503,245 - 9,503,539 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3739,544,929 - 9,545,223 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3pNCBI
T2T-CHM13v2.039,495,163 - 9,495,457 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:27701403  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p25.3(chr3:9142303-9793982)x3 copy number gain See cases [RCV000139348] Chr3:9142303..9793982 [GRCh38]
Chr3:9183987..9835666 [GRCh37]
Chr3:9158987..9810666 [NCBI36]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3 copy number gain See cases [RCV000051690] Chr3:52066..20280127 [GRCh38]
Chr3:93749..20321619 [GRCh37]
Chr3:68749..20296623 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-11379835)x1 copy number loss See cases [RCV000138376] Chr3:32241..11379835 [GRCh38]
Chr3:73914..11421309 [GRCh37]
Chr3:48914..11396309 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic|likely benign
GRCh38/hg38 3p26.1-25.3(chr3:8038727-11240931)x4 copy number gain See cases [RCV000135641] Chr3:8038727..11240931 [GRCh38]
Chr3:8080414..11282617 [GRCh37]
Chr3:8055414..11257617 [NCBI36]
Chr3:3p26.1-25.3		 likely pathogenic
GRCh38/hg38 3p26.1-25.2(chr3:7975734-12636917)x3 copy number gain See cases [RCV000137309] Chr3:7975734..12636917 [GRCh38]
Chr3:8017421..12678416 [GRCh37]
Chr3:7992421..12653416 [NCBI36]
Chr3:3p26.1-25.2		 likely pathogenic
GRCh38/hg38 3p25.3(chr3:8812036-9953438)x3 copy number gain See cases [RCV000137329] Chr3:8812036..9953438 [GRCh38]
Chr3:8853722..9995122 [GRCh37]
Chr3:8828722..9970122 [NCBI36]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p25.3(chr3:8941623-10151752)x3 copy number gain See cases [RCV000138535] Chr3:8941623..10151752 [GRCh38]
Chr3:8983307..10193436 [GRCh37]
Chr3:8958307..10168436 [NCBI36]
Chr3:3p25.3		 likely benign|uncertain significance
GRCh38/hg38 3p26.3-25.1(chr3:32241-13613818)x3 copy number gain See cases [RCV000138946] Chr3:32241..13613818 [GRCh38]
Chr3:73914..13655318 [GRCh37]
Chr3:48914..13630319 [NCBI36]
Chr3:3p26.3-25.1		 pathogenic
GRCh38/hg38 3p26.3-25.2(chr3:32241-12681483)x1 copy number loss See cases [RCV000138143] Chr3:32241..12681483 [GRCh38]
Chr3:73914..12722982 [GRCh37]
Chr3:48914..12697982 [NCBI36]
Chr3:3p26.3-25.2		 pathogenic
GRCh38/hg38 3p25.3-25.2(chr3:9394874-11690612)x1 copy number loss See cases [RCV000137433] Chr3:9394874..11690612 [GRCh38]
Chr3:9436558..11732086 [GRCh37]
Chr3:9411558..11707086 [NCBI36]
Chr3:3p25.3-25.2		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
GRCh38/hg38 3p25.3(chr3:9393349-9956171)x1 copy number loss See cases [RCV000051481] Chr3:9393349..9956171 [GRCh38]
Chr3:9435033..9997855 [GRCh37]
Chr3:9410033..9972855 [NCBI36]
Chr3:3p25.3		 pathogenic
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52266-11089569)x1 copy number loss See cases [RCV000051447] Chr3:52266..11089569 [GRCh38]
Chr3:93949..11131255 [GRCh37]
Chr3:68949..11106255 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:63843-9507969)x1 copy number loss See cases [RCV000051476] Chr3:63843..9507969 [GRCh38]
Chr3:105526..9549653 [GRCh37]
Chr3:80526..9524653 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p25.3(chr3:9221810-9727021)x3 copy number gain See cases [RCV000050855] Chr3:9221810..9727021 [GRCh38]
Chr3:9263494..9768705 [GRCh37]
Chr3:9238494..9743705 [NCBI36]
Chr3:3p25.3		 uncertain significance
GRCh38/hg38 3p26.3-25.3(chr3:32241-9574994)x1 copy number loss See cases [RCV000140239] Chr3:32241..9574994 [GRCh38]
Chr3:73914..9616678 [GRCh37]
Chr3:48914..9591678 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:20213-11221602)x1 copy number loss See cases [RCV000141731] Chr3:20213..11221602 [GRCh38]
Chr3:61891..11263288 [GRCh37]
Chr3:36891..11238288 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:688897-11051142)x1 copy number loss See cases [RCV000143706] Chr3:688897..11051142 [GRCh38]
Chr3:730581..11092828 [GRCh37]
Chr3:705581..11067828 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10323124)x1 copy number loss See cases [RCV000143325] Chr3:32241..10323124 [GRCh38]
Chr3:73914..10364808 [GRCh37]
Chr3:48914..10339808 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10631310)x1 copy number loss See cases [RCV000143173] Chr3:32241..10631310 [GRCh38]
Chr3:73914..10672995 [GRCh37]
Chr3:48914..10647995 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.1-25.1(chr3:7356110-14360442)x3 copy number gain See cases [RCV000143766] Chr3:7356110..14360442 [GRCh38]
Chr3:7397797..14401942 [GRCh37]
Chr3:7372797..14376946 [NCBI36]
Chr3:3p26.1-25.1		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316345GLUCO224_HGlucose level QTL 224 (human)1.270.008Glucose level3121543441Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC122889028 COSMIC
GTEx LOC122889028 GTEx
Human Proteome Map LOC122889028 Human Proteome Map
NCBI Gene LOC122889028 ENTREZGENE