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LOC121627820 Sharpr-MPRA regulatory region 4733 [ Homo sapiens (human) ]

Gene ID: 121627820, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627820
Gene description
Sharpr-MPRA regulatory region 4733
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82215113..82215407)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (83083037..83083331)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80172989..80173283)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80054421-80055336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9194 Neighboring gene fatty acid synthase Neighboring gene small nucleolar RNA, C/D box 134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80061739-80062652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80062653-80063566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80065397-80066310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80074745-80075652 Neighboring gene coiled-coil domain containing 57 Neighboring gene uncharacterized LOC124904119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12990 Neighboring gene Sharpr-MPRA regulatory region 9641 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80131430-80132220 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80133010-80133799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80137557-80138524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80138525-80139491 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:80163065-80163866 and GRCh37_chr17:80163867-80164668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9195 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80171129-80172071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12994 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:80183365-80183517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9202 Neighboring gene solute carrier family 16 member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12995 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80195135-80195906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80196677-80197447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12996 Neighboring gene microRNA 6787 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:80210177-80211376 Neighboring gene casein kinase 1 delta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80223561-80224292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9205 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9206

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_075010.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    82215113..82215407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    83083037..83083331
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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