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LOC121627861 Sharpr-MPRA regulatory region 10590 [ Homo sapiens (human) ]

Gene ID: 121627861, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627861
Gene description
Sharpr-MPRA regulatory region 10590
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (17139239..17139533)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (17274116..17274410)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (17250049..17250343)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9643 Neighboring gene HAUS augmin like complex subunit 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10319 Neighboring gene Sharpr-MPRA regulatory region 7940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17190569-17191106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17192643-17193192 Neighboring gene myosin IXB Neighboring gene small nucleolar RNA, H/ACA box 118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17221215-17221716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17227113-17227612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17241751-17242749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17245192-17245801 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17245802-17246410 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17246411-17247020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17260531-17261223 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:17263413-17264160 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17269991-17270808 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17270809-17271626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17271627-17272442 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:17288573-17288756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17291382-17291974 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:17291975-17292566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:17321117-17321622 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:17325806-17326386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17336955-17337629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:17337630-17338303 Neighboring gene unconventional SNARE in the ER 1 Neighboring gene occludin/ELL domain containing 1

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_075052.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    17139239..17139533
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    17274116..17274410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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