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LOC112577545 Sharpr-MPRA regulatory region 12356 [ Homo sapiens (human) ]

Gene ID: 112577545, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577545
Gene description
Sharpr-MPRA regulatory region 12356
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 5:Enh, candidate strong enhancer, open chromatin), with weak activity in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (226828088..226828382)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (226015967..226016261)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (227015789..227016083)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene inositol-trisphosphate 3-kinase B Neighboring gene uncharacterized LOC124904529 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226850479-226851004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2662 Neighboring gene ITPKB intronic transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2665 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226872731-226873232 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226876299-226876798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1889 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:226896320-226896495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226905393-226905892 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226911101-226911856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226925617-226926116 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:226942001-226942500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2671 Neighboring gene ribosomal protein S27 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2672 Neighboring gene uncharacterized LOC124904530 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:227038591-227039325 Neighboring gene uncharacterized LOC105373119 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:227051075-227051623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1893 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1894 Neighboring gene MPRA-validated peak736 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2673 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:227083595-227083826 Neighboring gene presenilin 2

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_060465.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    226828088..226828382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    226015967..226016261
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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