LOC128772272 (melanoma risk locus-associated MPRA allelic enhancer 5:90277675) - Rat Genome Database

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Gene: LOC128772272 (melanoma risk locus-associated MPRA allelic enhancer 5:90277675) Homo sapiens
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Symbol: LOC128772272
Name: melanoma risk locus-associated MPRA allelic enhancer 5:90277675
RGD ID: 156451468
Description: This genomic sequence includes a genetic variant, rs11742679, that is in strong linkage disequilibrium with a melanoma risk locus identified at 5q14.3 in genome-wide association studies (GWASs), and for which the reference allele has a risk effect. This region was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in UACC903 melanoma cells, where differences in transcriptional activity were observed between the reference and alternative rs11742679 alleles. [provided by RefSeq, Mar 2023]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38590,981,786 - 90,981,930 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37590,277,603 - 90,277,747 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.0591,468,272 - 91,468,416 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LOC128772272Humanfamilial febrile seizures 4  IAGPRGD:1272617558554872ClinVar Annotator: match by term: Febrile seizures, familial, 4ClinVar 
LOC128772272HumanUsher syndrome type 2C  IAGPRGD:85595538554872ClinVar Annotator: match by term: Usher syndrome type 2CClinVarPMID:19357116

PMID:32341527   PMID:36423637  



.

1 to 10 of 16 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 5q13.3-22.1(chr5:74163186-110809453)x3 copy number gain See cases [RCV000051839] Chr5:74163186..110809453 [GRCh38]
Chr5:73459011..110145153 [GRCh37]
Chr5:73494767..110173052 [NCBI36]
Chr5:5q13.3-22.1		 pathogenic
GRCh38/hg38 5q14.3-15(chr5:87124838-93383020)x3 copy number gain See cases [RCV000051840] Chr5:87124838..93383020 [GRCh38]
Chr5:86420655..92718726 [GRCh37]
Chr5:86456411..92744482 [NCBI36]
Chr5:5q14.3-15		 pathogenic
GRCh38/hg38 5q14.3-15(chr5:88936770-94102018)x1 copy number loss See cases [RCV000053480] Chr5:88936770..94102018 [GRCh38]
Chr5:88232587..93437723 [GRCh37]
Chr5:88268343..93463479 [NCBI36]
Chr5:5q14.3-15		 pathogenic
GRCh38/hg38 5q14.3-21.2(chr5:89081352-104687248)x1 copy number loss See cases [RCV000053516] Chr5:89081352..104687248 [GRCh38]
Chr5:88377169..104022949 [GRCh37]
Chr5:88412925..104050848 [NCBI36]
Chr5:5q14.3-21.2		 pathogenic
GRCh38/hg38 5q14.3(chr5:86743723-92337264)x1 copy number loss See cases [RCV000053477] Chr5:86743723..92337264 [GRCh38]
Chr5:86039540..91633081 [GRCh37]
Chr5:86075296..91668837 [NCBI36]
Chr5:5q14.3		 pathogenic
NG_007083.1:g.371658_507674del deletion Usher syndrome type 2C [RCV000007205] Chr5:90925457..91061473 [GRCh38]
Chr5:90221274..90357290 [GRCh37]
Chr5:5q14.3		 pathogenic
GRCh38/hg38 5q14.3(chr5:86766959-92148845)x1 copy number loss See cases [RCV000141419] Chr5:86766959..92148845 [GRCh38]
Chr5:86062776..91444662 [GRCh37]
Chr5:86098532..91480418 [NCBI36]
Chr5:5q14.3		 pathogenic
GRCh38/hg38 5q14.3-22.1(chr5:84603580-111435081)x1 copy number loss See cases [RCV000139656] Chr5:84603580..111435081 [GRCh38]
Chr5:83899398..110770779 [GRCh37]
Chr5:83935154..110798678 [NCBI36]
Chr5:5q14.3-22.1		 pathogenic
GRCh38/hg38 5q14.3(chr5:88368289-92363231)x1 copy number loss See cases [RCV000140963] Chr5:88368289..92363231 [GRCh38]
Chr5:87664106..91698938 [GRCh37]
Chr5:87699862..91724694 [NCBI36]
Chr5:5q14.3		 pathogenic
GRCh38/hg38 5q14.3-23.3(chr5:90374606-128076423)x1 copy number loss See cases [RCV000139893] Chr5:90374606..128076423 [GRCh38]
Chr5:89670423..127412115 [GRCh37]
Chr5:89706179..127440014 [NCBI36]
Chr5:5q14.3-23.3		 pathogenic
1 to 10 of 16 rows

The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
597230790GWAS1326864_Hovarian carcinoma QTL GWAS1326864 (human)0.000007ovarian carcinoma59098186490981865Human
RefSeq Transcripts NG_149763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC034215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles



Database
Acc Id
Source(s)
COSMIC LOC128772272 COSMIC
GTEx LOC128772272 GTEx
Human Proteome Map LOC128772272 Human Proteome Map
NCBI Gene LOC128772272 ENTREZGENE