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LOC121099713 Sharpr-MPRA regulatory region 9502 [ Homo sapiens (human) ]

Gene ID: 121099713, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121099713
Gene description
Sharpr-MPRA regulatory region 9502
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 unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Apr 2021]
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Genomic context

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See LOC121099713 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (170623565..170623859)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (171162329..171162623)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (170050569..170050863)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:169817412-169817912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:169817913-169818413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:169818666-169819166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:169819167-169819667 Neighboring gene KCNIP1 overlapping transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23611 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16606 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:169865238-169866195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:169911974-169912474 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:169913290-169913456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:169962091-169962591 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:169979309-169979878 Neighboring gene MPRA-validated peak5573 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:170024020-170025219 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:170038765-170039501 Neighboring gene uncharacterized LOC124901132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170052347-170052846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170054080-170054580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170054581-170055081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170059758-170060339 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170063109-170063858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170065509-170066304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170066305-170067098 Neighboring gene KCNIP1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:170170758-170171517 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170172277-170173036 Neighboring gene uncharacterized LOC107986473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170173037-170173795 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170176075-170176832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170178216-170179100 Neighboring gene uncharacterized LOC107986474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170179101-170179985

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_074193.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    170623565..170623859
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    171162329..171162623
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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