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LOC121740671 Sharpr-MPRA regulatory region 4140 [ Homo sapiens (human) ]

Gene ID: 121740671, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740671
Gene description
Sharpr-MPRA regulatory region 4140
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. 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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121740671 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (158537077..158537371)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159782056..159782350)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (158958109..158958403)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene TUB like protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25355 Neighboring gene RNA, 7SL, cytoplasmic 173, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:158884819-158885810 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:158885811-158886802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158890813-158891694 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158895792-158896364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158900383-158900884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158927517-158928017 Neighboring gene calcyclin binding protein pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 10808 Neighboring gene Sharpr-MPRA regulatory region 807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17739 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158982153-158982654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158982655-158983154 Neighboring gene transmembrane protein 181 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:159000120-159000332 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:159030351-159030852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159051575-159052076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159052077-159052576 Neighboring gene TatD DNase domain containing 2 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:159053255-159053416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159065146-159066089 Neighboring gene microRNA 7161 Neighboring gene dynein light chain Tctex-type 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_075733.1 

    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
    158537077..158537371
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    159782056..159782350
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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