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rs239948838 SNP Detail
Summary
  • ID
    rs239948838
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr5:87840684 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                TATGCCTAAA GGATTATTTT
ATTGAAATGA CTGGAAAGGA AATAGGTTCT CAAAGAAAAA AAATAGAAAA TCCAATTTTT
CACAAACTAT TTTGTATACA TTATTGACTT GCATTTTCAA CTCCATATTG AACACTTATA
AAATTCCTGT AATATAACTG AGAAGCATAT AGAGTCCATG GGTCGAATTC AAATGAATGC
Y
ATATAATACA TAGAATAAAT AAAAGAATAC ATTTTCTTTT CTTCCATGTA GATTAATTCA
GAAATATATC ATTTTTGTAG CATGATCCAA AGGTGAAAAG ATTTGTACAT TTCCAGTTTC
AGTCAGTTCT GTGAAAGAAA GATGTATAAT CATTTCTGTT GTGTTAAATC AGTGATTCCC
AACATTCCCT TTAATACTGC                                            

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
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
ss365777249 MGP_WTSI_5_88121850 EVA_MGPV3 EVA_MGPV3 f SNP C C C C C C C C C C C C C C C C C C T 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
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
rs239948838 SNP C C C C C C C C C C C C C C C C C C T 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
ss365777249 MGP_WTSI_5_88121850 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr5:87840684 () rs orientation: forward
Symbol Name Transcript Protein Function
Class		 Allele Residue Codon
Position		 AA
Position
Csn2 casein beta within coordinates
D5Mit12 DNA segment, Chr 5, Massachusetts Institute of Technology 12 1037 bp proximal
D5Mit16 DNA segment, Chr 5, Massachusetts Institute of Technology 16 1043 bp proximal
D5Mit16.1 DNA segment, Chr 5, Massachusetts Institute of Technology 16.1 1143 bp proximal
D5Mit16.2 DNA segment, Chr 5, Massachusetts Institute of Technology 16.2 841 bp proximal
Tssr1529 transcription start site region 1529 1729 bp upstream
Tssr46883 transcription start site region 46883 1676 bp upstream
Tssr46884 transcription start site region 46884 1689 bp upstream
Tssr46885 transcription start site region 46885 1717 bp upstream
Tssr46886 transcription start site region 46886 1745 bp upstream
Tssr46887 transcription start site region 46887 1762 bp upstream
Tssr46888 transcription start site region 46888 1831 bp upstream
Tssr46889 transcription start site region 46889 1880 bp upstream
Tssr46890 transcription start site region 46890 1895 bp upstream
Tssr46891 transcription start site region 46891 1939 bp upstream
Tssr46892 transcription start site region 46892 1943 bp upstream
Tssr46893 transcription start site region 46893 1971 bp upstream
Tssr51613 transcription start site region 51613 146 bp upstream
Tssr51614 transcription start site region 51614 83 bp upstream
Tssr51615 transcription start site region 51615 27 bp upstream
Tssr51616 transcription start site region 51616 within coordinates
Tssr51617 transcription start site region 51617 8 bp downstream
Tssr51618 transcription start site region 51618 1705 bp downstream
Tssr51619 transcription start site region 51619 1743 bp downstream
Tssr51620 transcription start site region 51620 1752 bp downstream
Tssr51621 transcription start site region 51621 1761 bp downstream
Tssr51622 transcription start site region 51622 1799 bp downstream
Tssr51623 transcription start site region 51623 1824 bp downstream
Tssr51624 transcription start site region 51624 1842 bp downstream
Tssr51625 transcription start site region 51625 1848 bp downstream
Tssr51626 transcription start site region 51626 1858 bp downstream
Tssr51627 transcription start site region 51627 1873 bp downstream
Tssr51628 transcription start site region 51628 1914 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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Send questions and comments to User Support. 		last database update
12/17/2024
MGI 6.24 		The Jackson Laboratory