LOC129929206 (ATAC-STARR-seq lymphoblastoid silent region 127) - Rat Genome Database

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Gene: LOC129929206 (ATAC-STARR-seq lymphoblastoid silent region 127) Homo sapiens
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Symbol: LOC129929206
Name: ATAC-STARR-seq lymphoblastoid silent region 127
RGD ID: 329409443
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
GRCh3813,858,308 - 3,858,357 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713,774,872 - 3,774,921 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.013,369,906 - 3,369,955 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p36.33-36.32(chr1:1118636-4179080)x1 copy number loss See cases [RCV000134211] Chr1:1118636..4179080 [GRCh38]
Chr1:1054016..4239140 [GRCh37]
Chr1:1043879..4139000 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:844347-6916587)x1 copy number loss See cases [RCV000133943] Chr1:844347..6916587 [GRCh38]
Chr1:779727..6976647 [GRCh37]
Chr1:769590..6899234 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.32(chr1:3712088-4027367)x4 copy number gain See cases [RCV000133657] Chr1:3712088..4027367 [GRCh38]
Chr1:3628652..4087427 [GRCh37]
Chr1:3618512..3987287 [NCBI36]
Chr1:1p36.32		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:844347-5682587)x1 copy number loss See cases [RCV000050642] Chr1:844347..5682587 [GRCh38]
Chr1:779727..5742647 [GRCh37]
Chr1:769590..5665234 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:844347-4398122)x1 copy number loss See cases [RCV000134137] Chr1:844347..4398122 [GRCh38]
Chr1:779727..4458182 [GRCh37]
Chr1:769590..4358042 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:792758-5006311)x3 copy number gain See cases [RCV000051779] Chr1:792758..5006311 [GRCh38]
Chr1:728138..5066371 [GRCh37]
Chr1:718001..4966231 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.23(chr1:844347-8171914)x1 copy number loss See cases [RCV000136554] Chr1:844347..8171914 [GRCh38]
Chr1:779727..8231974 [GRCh37]
Chr1:769590..8154561 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:844347-6477436)x1 copy number loss See cases [RCV000051143] Chr1:844347..6477436 [GRCh38]
Chr1:779727..6537496 [GRCh37]
Chr1:769590..6460083 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:844353-5827192)x3 copy number gain See cases [RCV000134750] Chr1:844353..5827192 [GRCh38]
Chr1:779733..5887252 [GRCh37]
Chr1:769596..5809839 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:826553-4719105)x3 copy number gain See cases [RCV000051780] Chr1:826553..4719105 [GRCh38]
Chr1:761933..4779165 [GRCh37]
Chr1:751796..4679025 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:870177-4426613)x1 copy number loss See cases [RCV000052063] Chr1:870177..4426613 [GRCh38]
Chr1:805557..4486673 [GRCh37]
Chr1:795420..4386533 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:821713-7000838)x1 copy number loss See cases [RCV000138896] Chr1:821713..7000838 [GRCh38]
Chr1:757093..7060898 [GRCh37]
Chr1:746956..6983485 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.32-36.23(chr1:2844760-8007940)x1 copy number loss See cases [RCV000051086] Chr1:2844760..8007940 [GRCh38]
Chr1:2761325..8068000 [GRCh37]
Chr1:2751185..7990587 [NCBI36]
Chr1:1p36.32-36.23		 pathogenic
GRCh38/hg38 1p36.33-36.23(chr1:859215-8747647)x1 copy number loss See cases [RCV000052045] Chr1:859215..8747647 [GRCh38]
Chr1:794595..8807706 [GRCh37]
Chr1:784458..8730293 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:874379-4973261)x1 copy number loss See cases [RCV000136715] Chr1:874379..4973261 [GRCh38]
Chr1:809759..5033321 [GRCh37]
Chr1:799622..4933181 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:1022094-4665295)x1 copy number loss See cases [RCV000137380] Chr1:1022094..4665295 [GRCh38]
Chr1:957474..4725355 [GRCh37]
Chr1:947337..4625215 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:872305-4133409)x1 copy number loss See cases [RCV000052066] Chr1:872305..4133409 [GRCh38]
Chr1:807685..4193469 [GRCh37]
Chr1:797548..4093329 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.32(chr1:2683403-4729121)x1 copy number loss See cases [RCV000052073] Chr1:2683403..4729121 [GRCh38]
Chr1:2614842..4789181 [GRCh37]
Chr1:2604702..4689041 [NCBI36]
Chr1:1p36.32		 pathogenic
GRCh38/hg38 1p36.33-36.22(chr1:844347-12470133)x1 copy number loss See cases [RCV000136695] Chr1:844347..12470133 [GRCh38]
Chr1:779727..12530188 [GRCh37]
Chr1:769590..12452775 [NCBI36]
Chr1:1p36.33-36.22		 pathogenic|likely pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:629044-7008678)x1 copy number loss See cases [RCV000051995] Chr1:629044..7008678 [GRCh38]
Chr1:564424..7068738 [GRCh37]
Chr1:554287..6991325 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:1181847-5507243)x1 copy number loss See cases [RCV000052070] Chr1:1181847..5507243 [GRCh38]
Chr1:1117227..5567303 [GRCh37]
Chr1:1107090..5489890 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:821713-4155674)x1 copy number loss See cases [RCV000051996] Chr1:821713..4155674 [GRCh38]
Chr1:757093..4215734 [GRCh37]
Chr1:746956..4115594 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.23(chr1:629025-8537745)x1 copy number loss See cases [RCV000051993] Chr1:629025..8537745 [GRCh38]
Chr1:564405..8597804 [GRCh37]
Chr1:554268..8520391 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.32-36.31(chr1:2906020-5336116)x1 copy number loss See cases [RCV000137587] Chr1:2906020..5336116 [GRCh38]
Chr1:2822585..5396176 [GRCh37]
Chr1:2812445..5296036 [NCBI36]
Chr1:1p36.32-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:844347-4665295)x1 copy number loss See cases [RCV000052040] Chr1:844347..4665295 [GRCh38]
Chr1:779727..4725355 [GRCh37]
Chr1:769590..4625215 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:778698-4898439)x1 copy number loss See cases [RCV000140164] Chr1:778698..4898439 [GRCh38]
Chr1:714078..4958499 [GRCh37]
Chr1:703941..4858359 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:821713-5239643)x1 copy number loss See cases [RCV000137978] Chr1:821713..5239643 [GRCh38]
Chr1:757093..5299703 [GRCh37]
Chr1:746956..5199563 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.32(chr1:3695587-4084682)x3 copy number gain See cases [RCV000137798] Chr1:3695587..4084682 [GRCh38]
Chr1:3612151..4144742 [GRCh37]
Chr1:3602011..4044602 [NCBI36]
Chr1:1p36.32		 uncertain significance
GRCh38/hg38 1p36.33-36.22(chr1:914086-9567122)x1 copy number loss See cases [RCV000141970] Chr1:914086..9567122 [GRCh38]
Chr1:849466..9627180 [GRCh37]
Chr1:839329..9549767 [NCBI36]
Chr1:1p36.33-36.22		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:821713-5480263)x1 copy number loss See cases [RCV000140709] Chr1:821713..5480263 [GRCh38]
Chr1:757093..5540323 [GRCh37]
Chr1:746956..5462910 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:844353-6477474)x1 copy number loss See cases [RCV000139404] Chr1:844353..6477474 [GRCh38]
Chr1:779733..6537534 [GRCh37]
Chr1:769596..6460121 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:821713-5099990)x1 copy number loss See cases [RCV000141318] Chr1:821713..5099990 [GRCh38]
Chr1:757093..5160050 [GRCh37]
Chr1:746956..5059910 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.32-36.23(chr1:2868477-7332569)x1 copy number loss See cases [RCV000141437] Chr1:2868477..7332569 [GRCh38]
Chr1:2785042..7392629 [GRCh37]
Chr1:2774902..7315216 [NCBI36]
Chr1:1p36.32-36.23		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:821713-4225085)x1 copy number loss See cases [RCV000141356] Chr1:821713..4225085 [GRCh38]
Chr1:757093..4285145 [GRCh37]
Chr1:746956..4185005 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.32-36.13(chr1:3006193-17688934)x1 copy number loss See cases [RCV000053714] Chr1:3006193..17688934 [GRCh38]
Chr1:2922757..18015429 [GRCh37]
Chr1:2912617..17888016 [NCBI36]
Chr1:1p36.32-36.13		 pathogenic
GRCh38/hg38 1p36.33-36.22(chr1:911300-9329925)x1 copy number loss See cases [RCV000142615] Chr1:911300..9329925 [GRCh38]
Chr1:846680..9389984 [GRCh37]
Chr1:836543..9312571 [NCBI36]
Chr1:1p36.33-36.22		 pathogenic
GRCh38/hg38 1p36.32-36.23(chr1:3472163-7842947)x1 copy number loss See cases [RCV000053720] Chr1:3472163..7842947 [GRCh38]
Chr1:3388727..7903007 [GRCh37]
Chr1:3378587..7825594 [NCBI36]
Chr1:1p36.32-36.23		 pathogenic
GRCh38/hg38 1p36.32(chr1:2518272-4413203) copy number gain Anomalous pulmonary venous return [RCV003223566] Chr1:2518272..4413203 [GRCh38]
Chr1:1p36.32		 uncertain significance
GRCh38/hg38 1p36.33-36.23(chr1:898721-7811306)x1 copy number loss See cases [RCV000142651] Chr1:898721..7811306 [GRCh38]
Chr1:834101..7871366 [GRCh37]
Chr1:823964..7793953 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:821713-3928354)x3 copy number gain See cases [RCV000138165] Chr1:821713..3928354 [GRCh38]
Chr1:757093..3823583 [GRCh37]
Chr1:746956..3834778 [NCBI36]
Chr1:1p36.33-36.32		 likely pathogenic
GRCh38/hg38 1p36.33-36.22(chr1:902111-9556305)x1 copy number loss See cases [RCV000141577] Chr1:902111..9556305 [GRCh38]
Chr1:837491..9616363 [GRCh37]
Chr1:827354..9538950 [NCBI36]
Chr1:1p36.33-36.22		 pathogenic
GRCh38/hg38 1p36.33-36.23(chr1:844347-7870545)x1 copy number loss See cases [RCV000142709] Chr1:844347..7870545 [GRCh38]
Chr1:779727..7930605 [GRCh37]
Chr1:769590..7853192 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.33-35.1(chr1:99125-34026935)x3 copy number gain Trisomy 12p [RCV003447845] Chr1:99125..34026935 [GRCh38]
Chr1:1p36.33-35.1		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298451OSTEAR17_HOsteoarthritis QTL 17 (human)2.40.0004Joint/bone inflammationosteoarthritis11125188105Human
1298463BP9_HBlood pressure QTL 9 (human)3.9Blood pressurehypertension susceptibility1125188105Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129929206 COSMIC
GTEx LOC129929206 GTEx
Human Proteome Map LOC129929206 Human Proteome Map
NCBI Gene LOC129929206 ENTREZGENE