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rs233965804 SNP Detail
Summary
  • ID
    rs233965804
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr3:34705885 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                ATCCAAATTA ACGCAAAAAC
    CGTGATGCCG ACTAGAAAAC TTTTATGAGA GATCTTGGGA CTTCTTTTTG GGGGACTATT
    TTTGTACAGA GAAAACCTGA GGGCGGCGGG GAGGGCGGGG GAATCGGACC ATGTATAGAT
    CTGGAGGAAA AAAACTACGC AAAACTTTTT TTTAAAGTTC TAGTGGTACG TTAGGCGCTT
    Y
    GCAGGGAGTT CGCAAAAGTC TTTACCAGTA ATATTTAGAG CTAGACTCCG GGCGATGAAA
    AAAAAGTTTT AATATTTGCA AGCAACTTTT GTACAGTATT TATCGAGATA AACATGGCAA
    TCAAATGTCC ATTGTTTATA AGCTGAGAAT TTGCCAATAT TTTTCGAGGA AAGGGTTCTT
    GCTGGGTTTT GATTCTGCAG                                            
    
    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
ss357517508 MGP_WTSI_3_34550658 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
rs233965804 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
ss357517508 MGP_WTSI_3_34550658 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr3:34705885 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Cpgi13072 CpG island 13072 207 bp distal
Gm54566 predicted gene, 54566 1442 bp upstream
Gm64654 predicted gene, 64654 within coordinates
Gm64662 predicted gene, 64662 1871 bp upstream
Gm64674 predicted gene, 64674 1405 bp downstream
Rr366704 regulatory region 366704 1496 bp upstream
Rr370604 regulatory region 370604 1504 bp downstream
Rr575166 regulatory region 575166 1882 bp distal
Rr575168 regulatory region 575168 1321 bp distal
Rr575169 regulatory region 575169 715 bp proximal
Rr575170 regulatory region 575170 1183 bp proximal
Sox2 SRY (sex determining region Y)-box 2 mRNA-UTR
Sox2ot SOX2 overlapping transcript (non-protein coding) within coordinates
Tssr28821 transcription start site region 28821 1802 bp downstream
Tssr28822 transcription start site region 28822 1731 bp downstream
Tssr28823 transcription start site region 28823 1686 bp downstream
Tssr28824 transcription start site region 28824 1547 bp downstream
Tssr28825 transcription start site region 28825 1503 bp downstream
Tssr28826 transcription start site region 28826 956 bp downstream
Tssr28827 transcription start site region 28827 654 bp downstream
Tssr28828 transcription start site region 28828 1850 bp upstream
Tssr32978 transcription start site region 32978 1967 bp upstream
Tssr32979 transcription start site region 32979 1861 bp upstream
Tssr32980 transcription start site region 32980 1016 bp upstream
Tssr32981 transcription start site region 32981 689 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