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LOC111828526 Sharpr-MPRA regulatory regions 5277 and 6602 [ Homo sapiens (human) ]

Gene ID: 111828526, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111828526
Gene description
Sharpr-MPRA regulatory regions 5277 and 6602
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. Two overlapping sub-regions were validated as functional enhancers 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 unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 9:DNaseU). [provided by RefSeq, Jan 2018]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (152095214..152095528)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (153296522..153296836)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (152416349..152416663)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:151969745-151970311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25284 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:152017738-152017865 Neighboring gene uncharacterized LOC107986529 Neighboring gene estrogen receptor 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:152154278-152154778 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:152221566-152222765 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:152375213-152376412 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:152414054-152414235 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:152419735-152420236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17689 Neighboring gene MPRA-validated peak6220 silencer Neighboring gene spectrin repeat containing nuclear envelope protein 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:152542272-152543471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25288 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:152630775-152631974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17690 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:152706655-152707854 Neighboring gene uncharacterized LOC124901437 Neighboring gene SYNE1 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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 5277
  • Sharpr-MPRA regulatory region 6602

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_056250.1 

    Range
    101..415
    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
    152095214..152095528
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    153296522..153296836
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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