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LOC112577469 Sharpr-MPRA regulatory region 13538 [ Homo sapiens (human) ]

Gene ID: 112577469, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112577469
Gene description
Sharpr-MPRA regulatory region 13538
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 18:Pol2; Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jun 2018]
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Genomic context

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See LOC112577469 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1112509..1112803)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (541123..541417)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1047889..1048183)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100288175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1000857-1001357 Neighboring gene uncharacterized LOC105378948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 27 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 28 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1004678-1005443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1009379-1009878 Neighboring gene ring finger protein 223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 30 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 31 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1015879-1016581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1016582-1017283 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:1017301-1017480 Neighboring gene chromosome 1 open reading frame 159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1047169-1047670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 32 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 33 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 34 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 35 Neighboring gene uncharacterized LOC124903819 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1058337-1059155 Neighboring gene uncharacterized LOC124903820 Neighboring gene CRISPRi-validated cis-regulatory element chr1.97 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 36 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 37 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 38 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 39 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 40 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1073727-1074228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1074229-1074728 Neighboring gene long intergenic non-protein coding RNA 1342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1076651-1077172

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_060033.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    1112509..1112803
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    541123..541417
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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