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LOC113743972 Sharpr-MPRA regulatory region 12408 [ Homo sapiens (human) ]

Gene ID: 113743972, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113743972
Gene description
Sharpr-MPRA regulatory region 12408
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 DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2018]
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Genomic context

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See LOC113743972 in Genome Data Viewer
Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (2104274..2104568)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (2217895..2218189)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (2143909..2144203)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene mitotic arrest deficient 1 like 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:2019399-2020598 Neighboring gene uncharacterized LOC124901573 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2037703-2038424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2041223-2042211 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:2054673-2054929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2059628-2060447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2071047-2071728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2072411-2073090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2089101-2089704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2094763-2095278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2095767-2096320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2096321-2096873 Neighboring gene Sharpr-MPRA regulatory region 15277 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2109248-2109803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2109804-2110358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2112531-2113084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2113104-2113604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2117862-2118431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2118432-2119000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2119001-2119570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2119571-2120138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2143023-2143689 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2145023-2145690 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:2149574-2150773 Neighboring gene uncharacterized LOC105375127 Neighboring gene small nucleolar RNA, H/ACA box 114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2163326-2163826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2167782-2168380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2168381-2168978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2168979-2169576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2179597-2180202 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:2187008-2187194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2197373-2198322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2198323-2199271 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:2205752-2205962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2207917-2208590 Neighboring gene Sharpr-MPRA regulatory region 12216 Neighboring gene uncharacterized LOC105375126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2242330-2243304

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_062490.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    2104274..2104568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    2217895..2218189
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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