About   Help   FAQ
rs239904877 SNP Detail
Summary
  • ID
    rs239904877
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr3:16235654 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                ATTTGGGAAA GAGTTTTACA
    CACAGGTCAT TACTTATTAT GTCTCTGTTG TCATCTATTA TTCTTCCTGG GTGGTAACAT
    TCTTGATCCT CAGTTGAACA TATATTTCAC AATACATGTT TCAGTTCCCT TGCAACCAAG
    AATTTTCAGA GAACAATGTT GTAGTTAGTA GGAGGTAGAC AGGTGTGGGA AATAAAATTG
    Y
    TATGAAATAT CCGGAGAGAG CACTCTGCTC TCCCTGCCTG CCCCGCTCTT TTCTCTTTCC
    TTTTAGTGTG GTGGGGTTGT GATGATGGCT GGAAGGAGAA CAGCCACCTC TGCGGCACTG
    ATGGAGTGTT CTAGAGGTGA TCCCAGGGGC ACACACACGG GGATCGGAAA AACATTTTCA
    GGAGTGGTTC TCTCCTATCA                                            
    
    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
ss357083982 MGP_WTSI_3_16081490 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
rs239904877 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
ss357083982 MGP_WTSI_3_16081490 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr3:16235654 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Cpgi12993 CpG island 12993 1391 bp proximal
Gm64384 predicted gene, 64384 1032 bp downstream
Rr397612 regulatory region 397612 1494 bp upstream
Rr573789 regulatory region 573789 1104 bp distal
Rr573790 regulatory region 573790 1232 bp proximal
Rr573791 regulatory region 573791 1757 bp proximal
Tssr28473 transcription start site region 28473 1687 bp upstream
Tssr28474 transcription start site region 28474 1718 bp upstream
Tssr28475 transcription start site region 28475 1807 bp upstream
Ythdf3 YTH N6-methyladenosine RNA binding protein 3 1722 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)
Citing These Resources
Funding Information
Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
Send questions and comments to User Support.
last database update
03/18/2025
MGI 6.24
The Jackson Laboratory

Building initial tooltip...