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LOC124646394 Sharpr-MPRA regulatory region 14866 [ Homo sapiens (human) ]

Gene ID: 124646394, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124646394
Gene description
Sharpr-MPRA regulatory region 14866
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124646394 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (104523331..104523625)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (104484989..104485283)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6910 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:104808107-104809018 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23909 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104846113-104846615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4795 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4797 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104876710-104877210 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104885786-104885989 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6920 Neighboring gene carbohydrate sulfotransferase 11 Neighboring gene ATP synthase F(0) complex subunit C1, mitochondrial-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6921 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:104920569-104921159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104949096-104949598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104950760-104951594 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6926 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104997281-104997908 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104997909-104998535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104998957-104999544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104999545-105000132 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:105017531-105018268 Neighboring gene microRNA 3922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:105026139-105026640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105065189-105065793 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:105081721-105081916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6931 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105102028-105102832 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105102833-105103637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:105114284-105114912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105116877-105117495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105136527-105137148 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:105144840-105145417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6936 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24027 Neighboring gene Sharpr-MPRA regulatory region 12146 Neighboring gene solute carrier family 41 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6937 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24038 Neighboring gene Sharpr-MPRA regulatory region 3023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4800

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

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_079802.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    104523331..104523625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    104484989..104485283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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