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LOC121099719 Sharpr-MPRA regulatory region 6984 [ Homo sapiens (human) ]

Gene ID: 121099719, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121099719
Gene description
Sharpr-MPRA regulatory region 6984
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 unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This region also displayed weak repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 12:CtcfO). [provided by RefSeq, Apr 2021]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (2791235..2791529)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (2657398..2657692)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (2791469..2791763)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene myosin light chain kinase family member 4 Neighboring gene uncharacterized LOC124901240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2734004-2734694 Neighboring gene Sharpr-MPRA regulatory region 12436 Neighboring gene Sharpr-MPRA regulatory region 3200 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2764192-2765071 Neighboring gene Sharpr-MPRA regulatory region 3960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16831 Neighboring gene WRN helicase interacting protein 1 Neighboring gene uncharacterized LOC124901241 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:2798034-2798138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:2802330-2802830 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:2809907-2811106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16832 Neighboring gene serpin family B member 1 Neighboring gene Sharpr-MPRA regulatory region 12426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23873 Neighboring gene nonconserved acetylation island sequence 71 enhancer Neighboring gene microRNA 4645

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_074199.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    2791235..2791529
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    2657398..2657692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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