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LOC113174986 Sharpr-MPRA regulatory region 3383 [ Homo sapiens (human) ]

Gene ID: 113174986, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113174986
Gene description
Sharpr-MPRA regulatory region 3383
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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. A subregion 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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). In addition, this genomic region was validated as a high-confidence cis-regulatory element for the WRNIP1 (WRN helicase interacting protein 1) gene on chromosome 6, and also with lower confidence for the ECI2 (enoyl-CoA delta isomerase 2) gene, based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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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 (3473044..3473524)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (3341796..3342274)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (3473278..3473758)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 22 member 23 Neighboring gene HNF4 motif-containing MPRA enhancer 213 Neighboring gene uncharacterized LOC105374890 Neighboring gene Sharpr-MPRA regulatory region 2334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3413621-3414120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3415185-3415686 Neighboring gene Sharpr-MPRA regulatory region 10234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3427759-3428672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3446415-3446962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3446963-3447509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16853 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16854 Neighboring gene uncharacterized LOC643327 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:3490051-3490550 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:3511328-3512180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3540364-3540864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3563205-3563704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3568820-3569322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3579367-3580278 Neighboring gene uncharacterized LOC100507336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3603461-3603960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3724209-3724747 Neighboring gene TOMM5 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 15708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3737712-3738338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16855 Neighboring gene PX domain containing 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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. 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)

General gene information

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Other Names

  • CRISPRi-validated cis-regulatory element chr6.239

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_061666.2 

    Range
    101..581
    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
    3473044..3473524
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    3341796..3342274
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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