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rs249440296 SNP Detail
Summary
  • ID
    rs249440296
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr1:40123218 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                TGGGGGGCAG GGGATGAGAT
    TTGCATTTGT TCTTATTCCT ACATCATTCT GGAGGTCGGA GGTCTGCATG GGCCTCAGTG
    GGCTAGAATG AATTGTAGTC CATACAGGGT CCCTGGAGCC ACAAGGGCAG CATCCATGTC
    TTGGGTTTTT GTCCAGCCTC TGGCTCTCTG GCTCATGGAC TGCAGCACTA CACACACCAT
    Y
    CTCTTCCTCC TTTGGCTGTC TTACCACTTT TTCCTGAAGC ACCAAACCCG AGCCTGTCTC
    CGGACCTGGA AATCCTTAAC TTACATTAGC AGTCACTTTC TCTACATTAA GCAGCATGTT
    CCCAGCTTCC AAAGACTCAG ACAAAAAGTT AAAAACAAAA CCAACCAAAC AAACAAACAA
    ACAAAAAGCC AAACAAAGGC                                            
    
    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
ss349341392 MGP_WTSI_1_40140903 EVA_MGPV3 EVA_MGPV3 f SNP C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C
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
rs249440296 SNP C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C
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
ss349341392 MGP_WTSI_1_40140903 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr1:40123218 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Cpgi194 CpG island 194 1703 bp proximal
Gm16894 predicted gene, 16894 within coordinates
Il1r2 interleukin 1 receptor, type II 654 bp upstream
Rr29353 regulatory region 29353 1182 bp proximal
Rr396010 regulatory region 396010 1678 bp upstream
Tssr62 transcription start site region 62 652 bp upstream
Tssr6411 transcription start site region 6411 675 bp upstream
Tssr6412 transcription start site region 6412 706 bp upstream
Tssr6413 transcription start site region 6413 717 bp upstream
Tssr6414 transcription start site region 6414 1140 bp upstream
Tssr11414 transcription start site region 11414 1765 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
12/10/2024
MGI 6.24
The Jackson Laboratory