U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121838568 Sharpr-MPRA regulatory region 3114 [ Homo sapiens (human) ]

Gene ID: 121838568, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121838568
Gene description
Sharpr-MPRA regulatory region 3114
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jul 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC121838568 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (123085742..123086036)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123082284..123082578)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (123570289..123570583)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol transfer protein membrane associated 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123496109-123497029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123512108-123513066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123513067-123514024 Neighboring gene microRNA 4304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123528097-123528676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123543041-123543542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123549368-123550230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123550389-123550890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123554866-123555738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123562495-123563216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7251 Neighboring gene PITPNM2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123576672-123577193 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123577194-123577714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123579095-123579658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123579659-123580222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123580855-123581820 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123588763-123589503 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123589504-123590246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123591730-123592470 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:123602973-123603786 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:123603787-123604600 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123612195-123612806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5031 Neighboring gene M-phase phosphoprotein 9 Neighboring gene MPRA-validated peak2026 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123735127-123735916 Neighboring gene mitochondrial translation release factor in rescue Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123749585-123749777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5032 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:123754459-123755207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5033 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:123756263-123756770 Neighboring gene cyclin dependent kinase 2 associated protein 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_075931.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    123085742..123086036
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    123082284..123082578
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases