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LOC122819148 Sharpr-MPRA regulatory region 398 [ Homo sapiens (human) ]

Gene ID: 122819148, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122819148
Gene description
Sharpr-MPRA regulatory region 398
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element 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 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Oct 2021]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (120785773..120786067)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (121221497..121221791)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (121543349..121543643)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:121301087-121302286 Neighboring gene uncharacterized LOC105373585 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121317507-121318008 Neighboring gene NANOG hESC enhancer GRCh37_chr2:121332587-121333189 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121345700-121346593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121352388-121352896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121355088-121355588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121355589-121356089 Neighboring gene Sharpr-MPRA regulatory region 1201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121366968-121367468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121412505-121413005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121419009-121419957 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:121426571-121427770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121463233-121463948 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121466954-121467822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121467823-121468690 Neighboring gene uncharacterized LOC124906073 Neighboring gene uncharacterized LOC124907881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121492073-121492720 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52581 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:121494648-121495148 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:121495149-121495649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121496056-121496893 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121496894-121497730 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:121497887-121498529 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:121498530-121499171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121503217-121503718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121510854-121511369 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121515981-121516842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121526109-121526644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121531159-121531669 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121540897-121541818 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121543663-121544585 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121545508-121546430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121547621-121548252 Neighboring gene GLI family zinc finger 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121552862-121553525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121562057-121562706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121565847-121566347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121579379-121580044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121580881-121581688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121581689-121582496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121582497-121583304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121590494-121591486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121603734-121604234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121613936-121614585 Neighboring gene uncharacterized LOC124907880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121629417-121630339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121644446-121645013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121665103-121665838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121665839-121666575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121668884-121669827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121672119-121672892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121672893-121673666 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:121692033-121693232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121700728-121701316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121701317-121701903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121717481-121717980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:121721921-121722462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121722463-121723004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121723005-121723545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121740347-121740857 Neighboring gene NANOG hESC enhancer GRCh37_chr2:121759954-121760517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121776165-121776784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121776785-121777404 Neighboring gene uncharacterized LOC105373587

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_077008.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    120785773..120786067
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    121221497..121221791
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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