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LOC112529892 Sharpr-MPRA regulatory region 4720 [ Homo sapiens (human) ]

Gene ID: 112529892, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112529892
Gene description
Sharpr-MPRA regulatory region 4720
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2018]
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Genomic context

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Location:
17p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (1438755..1439049)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1327479..1327773)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1342049..1342343)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1202102-1202696 Neighboring gene trafficking regulator of GLUT4 (SLC2A4) 1 Neighboring gene Sharpr-MPRA regulatory region 14526 Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1295206-1295734 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1302101-1302738 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1302739-1303376 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1303377-1304014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1304957-1305572 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:1305573-1306188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1335344-1335844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1335845-1336345 Neighboring gene CRK proto-oncogene, adaptor protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1357059-1357560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1358695-1359680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11449 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1366499-1367318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1371831-1372451 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7955 Neighboring gene myosin IC Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1394312-1395031 Neighboring gene uncharacterized LOC105371483 Neighboring gene inositol polyphosphate-5-phosphatase K

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_056882.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    1438755..1439049
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187613.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    380781..381075
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1327479..1327773
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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