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rs223493970 SNP Detail
Summary
  • ID
    rs223493970
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr3:52949797 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                TTTGGGTAGA ATCCAGAACA
    GAGGGCGAGC AAAGTGTAGG AGACTGGAGT TTGGAAGCAG TTTGCAGATG GAACCCGACG
    GGGTGGGGGT GTTCTTCTGT GTTCTTTGTG GAGAGTGTAG CCAGGTGTGC AAGCCAGCCC
    ACCTCATCGA ACCCTTTTGA ATAGCTGACT TGACATTAGG TATTGGAAAA GAGTGAGTGC
    Y
    TGGTCTGAAA TGGCCAGCAG GTGAAAGCAC TGAAGCCAAG GAGTCAAAAT AGGAGGCGTG
    AACACATTTG CCCCGGAAAA TTAAGACAGA AGGCGTTTTT AGTGTTATCG AGTACTGGGG
    GTGTGTAACT ATATATCACC CGATATATAC ACCCGAGTGG TGAATACTGT TAGTTAAATT
    TACAGTAACT GGGGGTGTGT                                            
    
    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
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
ss357971155 MGP_WTSI_3_52846298 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 C T T C T T T T C T T T T T C T T T T T T C 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
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
rs223493970 SNP T T T T T T T T T T T T T T T T T T T C T T C T T T T C T T T T T C T T T T T T C 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
ss357971155 MGP_WTSI_3_52846298 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr3:52949797 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Cpgi13160 CpG island 13160 281 bp distal
Gm42901 predicted gene 42901 228 bp upstream
Lhfpl6 LHFPL tetraspan subfamily member 6 Intron
Noncoding-Transcript-Variant
Rr576626 regulatory region 576626 938 bp distal
Rr576627 regulatory region 576627 783 bp distal
Rr576628 regulatory region 576628 239 bp distal
Rr576629 regulatory region 576629 within coordinates
Rr576630 regulatory region 576630 202 bp distal
Rr576631 regulatory region 576631 79 bp proximal
Rr576632 regulatory region 576632 1856 bp proximal
Tssr29102 transcription start site region 29102 797 bp downstream
Tssr29103 transcription start site region 29103 741 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