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LOC121815944 Sharpr-MPRA regulatory region 10829 [ Homo sapiens (human) ]

Gene ID: 121815944, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121815944
Gene description
Sharpr-MPRA regulatory region 10829
Gene type
biological region
Feature type(s)
regulatory: enhancer
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). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121815944 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (70446093..70446387)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (71315524..71315818)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (72205849..72206143)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene centrosomal protein 57 like 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2447 Neighboring gene eukaryotic translation initiation factor 4E binding protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72194899-72195400 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72197102-72197282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72199683-72200292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72200293-72200900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72200901-72201510 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72202121-72202730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72210316-72210984 Neighboring gene nodal growth differentiation factor Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:72214954-72215480 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72215481-72216006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72232724-72233490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2449 Neighboring gene phosphatase domain containing paladin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72239853-72240495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72240496-72241137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72242631-72243178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72253375-72254035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72258695-72259456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72259457-72260216 Neighboring gene YY1 transcription factor pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72273197-72273732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72273733-72274267 Neighboring gene Sharpr-MPRA regulatory region 14353 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:72288493-72289410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72297349-72298033 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72298034-72298719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72301641-72302141 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72318935-72319878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72319879-72320822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72344798-72345298 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72345790-72345956 Neighboring gene Sharpr-MPRA regulatory region 12376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72356137-72356637 Neighboring gene perforin 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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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_075838.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    70446093..70446387
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    71315524..71315818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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