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rs257504486 SNP Detail
Summary
  • ID
    rs257504486
  • Variation Type
    SNP
  • Alleles
    A/T
Genome Location and Flanking Sequence
  • Location
    Chr3:34703059 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                TTACGTCTGG ACAATGGGAG
    ATCGGCTAAA ATTACCCTCT CGGGTCCTGG GCAGGCAAGA TTCTTGAACC CCTACCCCCG
    CCCCCAGCCC ATTCTCCCAC AGCCTGGGCT TGCTTGGTGC CGGCTCCTCG GGTTCGGCGG
    GCCTTCTCTC CGCCTGCACC TGCACCTCTG GACCCCGCGC GCTTCCCAGG CCCCGGCGCC
    W
    CTCGGCCGGG CCTTCGTGAC TACCACCGTG CCTGTCAGCA GGGGCAATGC CGGCTGCGCT
    GCCCCATCCT GAGAACGCTG CGTGGGAGGG AGTTTGTGAG CGCAGCCCAA ATGCCACCTC
    CGCGCCTCGC GGTGGGATGC CAGGAAGTTG CGTGACCCTC CCCCCATCCC CTGCACTCGG
    GAGCTTCTTT CCGTTGATGC                                            
    
    W = A/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
LG/J
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
SM/J
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
ss357517484 MGP_WTSI_3_34547832 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 A 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
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
LG/J
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
SM/J
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
rs257504486 SNP T T T T T T T T T T T T T T T T T T T A 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
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
ss357517484 MGP_WTSI_3_34547832 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP A/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr3:34703059 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Cpgi13072 CpG island 13072 within coordinates
Gm64654 predicted gene, 64654 1089 bp downstream
Gm64662 predicted gene, 64662 within coordinates
Gm64674 predicted gene, 64674 1083 bp upstream
Rr370604 regulatory region 370604 within coordinates
Rr575165 regulatory region 575165 1933 bp distal
Rr575166 regulatory region 575166 within coordinates
Rr575167 regulatory region 575167 1006 bp distal
Rr575168 regulatory region 575168 945 bp proximal
Sox2 SRY (sex determining region Y)-box 2 1495 bp upstream
Sox2ot SOX2 overlapping transcript (non-protein coding) within coordinates
Tssr28821 transcription start site region 28821 1013 bp upstream
Tssr28822 transcription start site region 28822 1077 bp upstream
Tssr28823 transcription start site region 28823 1114 bp upstream
Tssr28824 transcription start site region 28824 1264 bp upstream
Tssr28825 transcription start site region 28825 1312 bp upstream
Tssr28826 transcription start site region 28826 1856 bp upstream
Tssr32975 transcription start site region 32975 421 bp upstream
Tssr32976 transcription start site region 32976 42 bp downstream
Tssr32977 transcription start site region 32977 814 bp downstream
Tssr32978 transcription start site region 32978 846 bp downstream
Tssr32979 transcription start site region 32979 937 bp downstream
Tssr32980 transcription start site region 32980 1804 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
03/18/2025
MGI 6.24
The Jackson Laboratory