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LOC121530617 Sharpr-MPRA regulatory region 12604 [ Homo sapiens (human) ]

Gene ID: 121530617, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121530617
Gene description
Sharpr-MPRA regulatory region 12604
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 non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). This region also displayed weak repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121530617 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11113032..11113326)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (11149312..11149606)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (11206889..11207183)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene class II major histocompatibility complex transactivator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10406 Neighboring gene Dexi homolog Neighboring gene C-type lectin domain containing 16A Neighboring gene Sharpr-MPRA regulatory region 12638 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11066007-11066184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11073759-11074260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11074261-11074760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7196 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11099817-11100053 Neighboring gene NANOG hESC enhancer GRCh37_chr16:11101530-11102234 Neighboring gene Sharpr-MPRA regulatory region 10204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11144189-11144765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11144766-11145343 Neighboring gene ribosomal protein L7 pseudogene 46 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10411 Neighboring gene uncharacterized LOC105371081 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11234005-11234583 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11234584-11235161 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11235162-11235740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11238795-11239462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11268031-11268544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11275481-11276366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11276367-11277253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11290798-11291307 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11291308-11291816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11292853-11293353 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:11295121-11296320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11296313-11297109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11304646-11305240 Neighboring gene uncharacterized LOC107984859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10422

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_074816.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    11113032..11113326
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    11149312..11149606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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