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rs239999841 SNP Detail
Summary
  • ID
    rs239999841
  • Variation Type
    SNP
  • Alleles
    A/T
Genome Location and Flanking Sequence
  • Location
    Chr6:116111907 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                GAAGGATACT AAGGGGCCAT
    CTTGGAATAG ACTCCCTATT AGCAGTAGGC AGGACAACTA GCCACTGCTT AGAAAACCAA
    GAGAACAGAT CATGTATGTT TAGTCATTCT AAGGCAATTA AATTCTGTTG TTTTTTTTTT
    TTTTATAATC ATGACTGAGT ATCAACATGC TGAAACTCAG CAAATTCAGA GGAGAGTGAG
    W
    GATAAATATC CCAATCTACA TGGATTTTAG TAAAAATTCG AAACCTTTTG CTACCATCCA
    TCTATATTCA TCAAGCTCAA TGGTAATTAG AGGTGACGAG TATGTTCTTT TGGGAGGCCA
    AAGCAAAGAA AAATCTTGTA AATTAAATTC TTGCTGAAGG AAAAAAAAAA AAAAAAACCA
    GGGCTGGAGA GATGGCTCAG                                            
    
    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
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
ss369766695 MGP_WTSI_6_116084964 EVA_MGPV3 EVA_MGPV3 f SNP A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A
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
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
rs239999841 SNP A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A
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
ss369766695 MGP_WTSI_6_116084964 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP A/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr6:116111907 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Rr637158 regulatory region 637158 1051 bp proximal
Rr637159 regulatory region 637159 1178 bp proximal
Rr637160 regulatory region 637160 1468 bp proximal
Tmcc1 transmembrane and coiled coil domains 1 Intron
Tssr62558 transcription start site region 62558 1053 bp upstream
Tssr62559 transcription start site region 62559 1038 bp upstream

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