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LOC121847997 Sharpr-MPRA regulatory region 9835 [ Homo sapiens (human) ]

Gene ID: 121847997, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121847997
Gene description
Sharpr-MPRA regulatory region 9835
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 1:Tss, active promoter, TSS/CpG island region). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (85307603..85307897)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (91373759..91374057)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (85341209..85341503)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Gse1 coiled-coil protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:85330200-85330435 Neighboring gene Sharpr-MPRA regulatory region 9478 Neighboring gene long intergenic non-protein coding RNA 311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11270 Neighboring gene uncharacterized LOC101928502 Neighboring gene uncharacterized LOC107984830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85350968-85351763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85353355-85353865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85353866-85354375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85355126-85355656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85355657-85356187 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85361388-85361956 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85361957-85362524 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85364231-85364798 Neighboring gene microRNA 5093 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:85380301-85380577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85383235-85383873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85387813-85388516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85388517-85389218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85389454-85389954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85397928-85398554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85398555-85399181 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:85404333-85404558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85406218-85406731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85418551-85419116 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:85429395-85429960 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:85429961-85430526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85436783-85437311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85451929-85452546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85453670-85454511 Neighboring gene Sharpr-MPRA regulatory region 8888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85468128-85468788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85469448-85470107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85470108-85470766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85474018-85474538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85474539-85475058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85477805-85478693 Neighboring gene uncharacterized LOC124903738 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7806 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr16:85485239-85485738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85485752-85486252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85491854-85492505 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:85493140-85493848 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85494556-85495263 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85493849-85494555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85496679-85497386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85498095-85498800 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85507767-85508622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85508623-85509477 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:85522312-85522482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85523747-85524594 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85524595-85525442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85525443-85526290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11271 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85547643-85548327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:85548328-85549011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85549012-85549696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:85549697-85550379 Neighboring gene uncharacterized LOC124903739

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_076017.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    85307603..85307897
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    91373759..91374057
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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