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rs253546837 SNP Detail
Summary
  • ID
    rs253546837
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr2:30305699 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                GGCCCCGCGG CCACCGGGCC
    CGGCGGGCTG CCGGTGGGGC AGGACTCACG GGGCGGAGCT TTGGTGGCTC GCAGTCCCCG
    GCCGCTCGCC CCGATCTCGG GGTGGGCCCA AGCCGGGGAG TGGCCGCAGA GGGCGGGGCT
    TGCGGAGACG GACCTCTAGC TCAGCTGTTA GCAGCCCGGC GCTGGGCTCC CGTCACGGGG
    Y
    CACAACGGTA GGCGCTGTCC CGCTCGTGCT CTCCGCCTCC GAAAGCCACC TTAGCTGTCG
    AGGCGGTCAC GTGCGTTCAA GTCTGACTGG TGTCCTTGAA CGTCACTCTA GGAATGGCAG
    GAGAACACAA CTGTTGACTG GGGACTGTCT CAGATTGCTT GGGTGGAGGC ATGCACAAAG
    AAGATGACAG GTGGCCTTGC                                            
    
    Y = C/T
    

    Note: Sequence in lower case indicates low-complexity or repetitive sequence
    BLAST SNP flanking sequence against the mouse Genome
SNP Assays
and
SNP Consensus
Strain alleles of submitted assays, and consensus values for this SNP
Legend
Assay ID Submitter
SNP ID
Submitter
Handle
Population
ss orientation
Variation Type
129P2/OlaHsd
129S1/SvImJ
129S5/SvEvBrd
A/J
AKR/J
B10.RIII-H2 H2-T18/(71NS)SnJ
BALB/cByJ
BALB/cJ
BTBR T<+> Itpr3/J
BUB/BnJ
C3H/HeH
C3H/HeJ
C57BL/6J
C57BL/6NJ
C57BL/10J
C57BL/10SnJ
C57BR/cdJ
C57L/J
C58/J
CAST/EiJ
CBA/J
CE/J
CZECHII/EiJ
DBA/1J
DBA/2J
FVB/NJ
I/LnJ
JF1/MsJ
KK/HlJ
LEWES/EiJ
LP/J
MA/MyJ
MOLF/EiJ
NOD/ShiLtJ
NON/ShiLtJ
NZB/BlNJ
NZO/HlLtJ
NZW/LacJ
PL/J
PWK/PhJ
QSi3/Ianm
QSi5/Ianm
RF/J
RIIIS/J
SEA/GnJ
SJL/J
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
ss353515403 MGP_WTSI_2_30271207 EVA_MGPV3 EVA_MGPV3 f SNP T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T
SNP Consensus Information
SNP Consensus Type
129P2/OlaHsd
129S1/SvImJ
129S5/SvEvBrd
A/J
AKR/J
B10.RIII-H2 H2-T18/(71NS)SnJ
BALB/cByJ
BALB/cJ
BTBR T<+> Itpr3/J
BUB/BnJ
C3H/HeH
C3H/HeJ
C57BL/6J
C57BL/6NJ
C57BL/10J
C57BL/10SnJ
C57BR/cdJ
C57L/J
C58/J
CAST/EiJ
CBA/J
CE/J
CZECHII/EiJ
DBA/1J
DBA/2J
FVB/NJ
I/LnJ
JF1/MsJ
KK/HlJ
LEWES/EiJ
LP/J
MA/MyJ
MOLF/EiJ
NOD/ShiLtJ
NON/ShiLtJ
NZB/BlNJ
NZO/HlLtJ
NZW/LacJ
PL/J
PWK/PhJ
QSi3/Ianm
QSi5/Ianm
RF/J
RIIIS/J
SEA/GnJ
SJL/J
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
rs253546837 SNP T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T
Additional submitted assays for this SNP, where the strain of origin for observed alleles is not specified by the submitter
Assay ID Submitter
SNP ID
Submitter
Handle
Population
ss orientation
Variation
Type
Alleles
ss353515403 MGP_WTSI_2_30271207 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr2:30305699 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Cpgi11436 CpG island 11436 within coordinates
Crat carnitine acetyltransferase 97 bp upstream
Gm16323 predicted gene 16323 349 bp downstream
Ptpa protein phosphatase 2 protein activator 363 bp upstream
Rr554310 regulatory region 554310 1961 bp distal
Rr554311 regulatory region 554311 1299 bp distal
Rr554312 regulatory region 554312 174 bp distal
Rr554313 regulatory region 554313 within coordinates
Rr554314 regulatory region 554314 466 bp proximal
Tssr17115 transcription start site region 17115 4 bp downstream
Tssr17116 transcription start site region 17116 344 bp upstream
Tssr17117 transcription start site region 17117 393 bp upstream
Tssr17118 transcription start site region 17118 409 bp upstream
Tssr17119 transcription start site region 17119 500 bp upstream
Tssr23369 transcription start site region 23369 1569 bp upstream
Tssr23370 transcription start site region 23370 1507 bp upstream
Tssr23371 transcription start site region 23371 319 bp upstream
Tssr23372 transcription start site region 23372 277 bp upstream
Tssr23373 transcription start site region 23373 258 bp upstream
Tssr23374 transcription start site region 23374 238 bp upstream
Tssr23375 transcription start site region 23375 182 bp upstream
Tssr23376 transcription start site region 23376 127 bp upstream
Tssr23377 transcription start site region 23377 75 bp upstream
Tssr23378 transcription start site region 23378 63 bp upstream
Tssr23379 transcription start site region 23379 within coordinates
Tssr23380 transcription start site region 23380 80 bp downstream
Tssr23381 transcription start site region 23381 316 bp downstream

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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last database update
12/17/2024
MGI 6.24
The Jackson Laboratory