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LOC121740645 Sharpr-MPRA regulatory region 3581 [ Homo sapiens (human) ]

Gene ID: 121740645, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740645
Gene description
Sharpr-MPRA regulatory region 3581
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121740645 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (16332098..16332392)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (16204656..16204950)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (16332329..16332623)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16957 Neighboring gene NANOG hESC enhancer GRCh37_chr6:16259269-16259823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:16262581-16263080 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:16264120-16264690 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:16264691-16265260 Neighboring gene Sharpr-MPRA regulatory region 9524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24099 Neighboring gene guanosine monophosphate reductase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16303323-16303902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24100 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16310151-16310359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16320601-16321434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16327606-16328166 Neighboring gene ataxin 1 repeat instability region Neighboring gene uncharacterized LOC127903862 Neighboring gene ataxin 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16387334-16387547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24111 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16603501-16603686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:16672541-16673042 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:16723974-16724586 Neighboring gene HNF1 motif-containing MPRA enhancer 207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16962 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16761792-16762007 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:16762145-16763344 Neighboring gene uncharacterized LOC124901268 Neighboring gene Sharpr-MPRA regulatory region 6173 Neighboring gene ATXN1 antisense RNA 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_075707.1 

    Range
    101..395
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    16332098..16332392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    16204656..16204950
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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