LOC130056553 (ATAC-STARR-seq lymphoblastoid silent region 6135) - Rat Genome Database

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Gene: LOC130056553 (ATAC-STARR-seq lymphoblastoid silent region 6135) Homo sapiens
Analyze
Symbol: LOC130056553
Name: ATAC-STARR-seq lymphoblastoid silent region 6135
RGD ID: 329844792
Description: This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 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
GRCh3814102,928,299 - 102,928,488 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714103,394,636 - 103,394,825 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.01497,164,544 - 97,164,733 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130056553
21 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 14q32.2-32.33(chr14:100309382-106855263)x1 copy number loss See cases [RCV000050938] Chr14:100309382..106855263 [GRCh38]
Chr14:100775719..107263478 [GRCh37]
Chr14:99845472..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:99831655-106855263)x1 copy number loss See cases [RCV000133831] Chr14:99831655..106855263 [GRCh38]
Chr14:100297992..107263478 [GRCh37]
Chr14:99367745..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:97938637-106855263)x1 copy number loss See cases [RCV000050696] Chr14:97938637..106855263 [GRCh38]
Chr14:98404974..107263478 [GRCh37]
Chr14:97474727..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100309382-105987610)x3 copy number gain See cases [RCV000135410] Chr14:100309382..105987610 [GRCh38]
Chr14:100775719..106453697 [GRCh37]
Chr14:99845472..105524742 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q24.3-32.33(chr14:73655772-106879298)x3 copy number gain See cases [RCV000134000] Chr14:73655772..106879298 [GRCh38]
Chr14:74122475..107287505 [GRCh37]
Chr14:73192228..106358550 [NCBI36]
Chr14:14q24.3-32.33		 pathogenic
GRCh38/hg38 14q32.31-32.33(chr14:102584963-104898605)x1 copy number loss See cases [RCV000051580] Chr14:102584963..104898605 [GRCh38]
Chr14:103051300..105364942 [GRCh37]
Chr14:102121053..104435987 [NCBI36]
Chr14:14q32.31-32.33		 pathogenic
GRCh38/hg38 14q32.13-32.33(chr14:95524407-106879501)x1 copy number loss See cases [RCV000136032] Chr14:95524407..106879501 [GRCh38]
Chr14:95990744..107287708 [GRCh37]
Chr14:95060497..106358753 [NCBI36]
Chr14:14q32.13-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100808300-106855263)x1 copy number loss See cases [RCV000051113] Chr14:100808300..106855263 [GRCh38]
Chr14:101274637..107263478 [GRCh37]
Chr14:100344390..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q32.12-32.33(chr14:92540983-104863658)x3 copy number gain See cases [RCV000135896] Chr14:92540983..104863658 [GRCh38]
Chr14:93007328..105329995 [GRCh37]
Chr14:92077081..104401040 [NCBI36]
Chr14:14q32.12-32.33		 pathogenic
NM_030943.4(AMN):c.208-2A>G single nucleotide variant Imerslund-Grasbeck syndrome [RCV000050164]|Imerslund-Grasbeck syndrome type 1 [RCV001280864]|Imerslund-Grasbeck syndrome type 2 [RCV000005037]|not provided [RCV001815177] Chr14:102928424 [GRCh38]
Chr14:103394761 [GRCh37]
Chr14:14q32.32		 pathogenic|likely pathogenic
NM_030943.4(AMN):c.208-1G>C single nucleotide variant Imerslund-Grasbeck syndrome [RCV000050163]|Imerslund-Grasbeck syndrome type 2 [RCV003338400] Chr14:102928425 [GRCh38]
Chr14:103394762 [GRCh37]
Chr14:14q32.32		 pathogenic|likely pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:99448012-106850609)x3 copy number gain See cases [RCV000135875] Chr14:99448012..106850609 [GRCh38]
Chr14:99914349..107258824 [GRCh37]
Chr14:98984102..106329869 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
NM_030943.4(AMN):c.208-15C>G single nucleotide variant Imerslund-Grasbeck syndrome [RCV002755847] Chr14:102928411 [GRCh38]
Chr14:103394748 [GRCh37]
Chr14:14q32.32		 likely benign
GRCh38/hg38 14q32.31-32.33(chr14:102210395-104449321)x1 copy number loss See cases [RCV000051579] Chr14:102210395..104449321 [GRCh38]
Chr14:102676732..104926965 [GRCh37]
Chr14:101746485..103998010 [NCBI36]
Chr14:14q32.31-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:97638520-106855263)x3 copy number gain See cases [RCV000135400] Chr14:97638520..106855263 [GRCh38]
Chr14:98104857..107263478 [GRCh37]
Chr14:97174610..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
NM_030943.4(AMN):c.250G>A (p.Gly84Arg) single nucleotide variant Imerslund-Grasbeck syndrome [RCV002690962] Chr14:102928468 [GRCh38]
Chr14:103394805 [GRCh37]
Chr14:14q32.32		 uncertain significance
NM_030943.4(AMN):c.208-16C>T single nucleotide variant Imerslund-Grasbeck syndrome [RCV002128936]|not provided [RCV004716881] Chr14:102928410 [GRCh38]
Chr14:103394747 [GRCh37]
Chr14:14q32.32		 benign
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q32.31-32.33(chr14:102605096-106879298)x1 copy number loss See cases [RCV000143154] Chr14:102605096..106879298 [GRCh38]
Chr14:103071433..107287505 [GRCh37]
Chr14:102141186..106358550 [NCBI36]
Chr14:14q32.31-32.33		 pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
NC_000014.9:g.102573453_103575949del deletion Mitochondrial complex 4 deficiency, nuclear type 17 [RCV003123350] Chr14:102573453..103575949 [GRCh38]
Chr14:14q32.31-32.33		 pathogenic
GRCh38/hg38 14q32.31-32.33(chr14:101925670-106876323)x1 copy number loss See cases [RCV000139633] Chr14:101925670..106876323 [GRCh38]
Chr14:102392007..107284531 [GRCh37]
Chr14:101461760..106355576 [NCBI36]
Chr14:14q32.31-32.33		 pathogenic
NM_030943.4(AMN):c.268G>A (p.Val90Met) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003085722] Chr14:102928486 [GRCh38]
Chr14:103394823 [GRCh37]
Chr14:14q32.32		 uncertain significance
GRCh38/hg38 14q32.31-32.33(chr14:102263440-106874929)x1 copy number loss Neurodevelopmental disorder [RCV003327606] Chr14:102263440..106874929 [GRCh38]
Chr14:14q32.31-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100582059-106877229)x1 copy number loss See cases [RCV000143662] Chr14:100582059..106877229 [GRCh38]
Chr14:101048396..107285437 [GRCh37]
Chr14:100118149..106356482 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q31.3-32.33(chr14:86094030-106832642)x3 copy number gain See cases [RCV000052295] Chr14:86094030..106832642 [GRCh38]
Chr14:86560374..107240869 [GRCh37]
Chr14:85630127..106311914 [NCBI36]
Chr14:14q31.3-32.33		 pathogenic
NM_030943.4(AMN):c.208-10T>C single nucleotide variant Imerslund-Grasbeck syndrome [RCV000861901]|Imerslund-Grasbeck syndrome type 2 [RCV002501205]|not provided [RCV004715339] Chr14:102928416 [GRCh38]
Chr14:103394753 [GRCh37]
Chr14:14q32.32		 benign|likely benign
GRCh38/hg38 14q32.12-32.33(chr14:91455861-106832642)x3 copy number gain See cases [RCV000052296] Chr14:91455861..106832642 [GRCh38]
Chr14:91922205..107240869 [GRCh37]
Chr14:90991958..106311914 [NCBI36]
Chr14:14q32.12-32.33		 pathogenic
GRCh38/hg38 14q32.31-32.33(chr14:101665602-106855263)x1 copy number loss See cases [RCV000142453] Chr14:101665602..106855263 [GRCh38]
Chr14:102131939..107263478 [GRCh37]
Chr14:101201692..106334523 [NCBI36]
Chr14:14q32.31-32.33		 pathogenic
NM_030943.4(AMN):c.231C>T (p.Leu77=) single nucleotide variant not provided [RCV000933498] Chr14:102928449 [GRCh38]
Chr14:103394786 [GRCh37]
Chr14:14q32.32		 likely benign
GRCh38/hg38 14q32.31-32.33(chr14:102239422-106877229)x1 copy number loss See cases [RCV000141932] Chr14:102239422..106877229 [GRCh38]
Chr14:102705759..107285437 [GRCh37]
Chr14:101775512..106356482 [NCBI36]
Chr14:14q32.31-32.33		 pathogenic
NM_030943.4(AMN):c.249C>G (p.Ala83=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003502556] Chr14:102928467 [GRCh38]
Chr14:103394804 [GRCh37]
Chr14:14q32.32		 likely benign
NC_000014.8:g.(?_103355877)_(103395332_?)dup duplication Herpes simplex encephalitis, susceptibility to, 3 [RCV000803917] Chr14:102889540..102928995 [GRCh38]
Chr14:103355877..103395332 [GRCh37]
Chr14:14q32.32		 uncertain significance
GRCh38/hg38 14q24.3-32.33(chr14:77222795-106879298)x3 copy number gain See cases [RCV000138230] Chr14:77222795..106879298 [GRCh38]
Chr14:77689138..107287505 [GRCh37]
Chr14:76758891..106358550 [NCBI36]
Chr14:14q24.3-32.33		 pathogenic
NC_000014.9:g.(?_102870182)_(102930700_?)del deletion Imerslund-Grasbeck syndrome [RCV000638880] Chr14:102870182..102930700 [GRCh38]
Chr14:103336519..103397037 [GRCh37]
Chr14:14q32.32		 pathogenic
NC_000014.8:g.(?_103336519)_(103397037_?)dup duplication Herpes simplex encephalitis, susceptibility to, 3 [RCV000650557] Chr14:102870182..102930700 [GRCh38]
Chr14:103336519..103397037 [GRCh37]
Chr14:14q32.32		 uncertain significance
NM_030943.4(AMN):c.246A>G (p.Gly82=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV002615696] Chr14:102928464 [GRCh38]
Chr14:103394801 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.258C>T (p.Gly86=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003505468] Chr14:102928476 [GRCh38]
Chr14:103394813 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.208-20T>C single nucleotide variant Imerslund-Grasbeck syndrome [RCV003504915] Chr14:102928406 [GRCh38]
Chr14:103394743 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.208-14C>T single nucleotide variant Imerslund-Grasbeck syndrome [RCV003506233] Chr14:102928412 [GRCh38]
Chr14:103394749 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.213G>A (p.Leu71=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003505995] Chr14:102928431 [GRCh38]
Chr14:103394768 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.264A>G (p.Ser88=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003506052] Chr14:102928482 [GRCh38]
Chr14:103394819 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.219G>A (p.Leu73=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003612972] Chr14:102928437 [GRCh38]
Chr14:103394774 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.235C>T (p.Leu79=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003612302] Chr14:102928453 [GRCh38]
Chr14:103394790 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.249C>A (p.Ala83=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003839835] Chr14:102928467 [GRCh38]
Chr14:103394804 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.249C>T (p.Ala83=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003832201] Chr14:102928467 [GRCh38]
Chr14:103394804 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.240T>C (p.Ala80=) single nucleotide variant Imerslund-Grasbeck syndrome [RCV003611898] Chr14:102928458 [GRCh38]
Chr14:103394795 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.208-18dup duplication Imerslund-Grasbeck syndrome [RCV003613020] Chr14:102928407..102928408 [GRCh38]
Chr14:103394744..103394745 [GRCh37]
Chr14:14q32.32		 likely benign
NM_030943.4(AMN):c.208-17G>T single nucleotide variant Imerslund-Grasbeck syndrome [RCV003823320] Chr14:102928409 [GRCh38]
Chr14:103394746 [GRCh37]
Chr14:14q32.32		 likely benign

Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130056553 COSMIC
GTEx LOC130056553 GTEx
Human Proteome Map LOC130056553 Human Proteome Map
NCBI Gene LOC130056553 ENTREZGENE