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LOC112695103 Sharpr-MPRA regulatory region 5228 [ Homo sapiens (human) ]

Gene ID: 112695103, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112695103
Gene description
Sharpr-MPRA regulatory region 5228
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 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (45140088..45140382)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (45624574..45624868)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (45535969..45536263)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene PHD finger protein 21B Neighboring gene ribosomal protein L6 pseudogene 28 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45328117-45328618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45334716-45335643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45338425-45339352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45340279-45341206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45348327-45349097 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45349098-45349867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45352179-45352948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45355867-45356450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45359222-45359844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45359845-45360468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45360469-45361090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45361091-45361714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45361715-45362336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45362337-45362959 Neighboring gene Sharpr-MPRA regulatory region 3533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45375229-45375808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45377983-45378603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45387215-45388036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45390633-45391132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45395779-45396638 Neighboring gene uncharacterized LOC101927551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45398138-45398996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45398997-45399855 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:45404265-45404866 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:45427253-45427890 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:45427891-45428528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45445441-45446014 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45447813-45448616 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45448617-45449421 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45449422-45450225 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:45468530-45469729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45489639-45490138 Neighboring gene NUP50 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 5104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13872 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:45559735-45560257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13874 Neighboring gene uncharacterized LOC105373064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45586750-45587250 Neighboring gene nucleoporin 50 Neighboring gene KIAA0930 Neighboring gene microRNA 1249

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_060881.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    45140088..45140382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    45624574..45624868
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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