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rs238281635 SNP Detail
Summary
  • ID
    rs238281635
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr11:96242517 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                ATCAATTAAA GCAAATAATG
    CCTGTGTTTT CCACTAGGCC TAGACTAGCG ATTGGCGGAG ACCGGTCCCG TGACCATGAA
    TTCCCTGCAA TTTCGGCGGA GTCCTGGGTT TAATAGAGAG AGTCCCCATA CGCTTGTATT
    TATCAGCAAT ATACAATTAT AAAGGCCTAA ATTTAAAAAA AAAAGAGAGA GAGCGAAATC
    Y
    CCCCCCCCCC GCGAAATTGC TCCATTGCAT AAACCTGGGG GGGGCGGGAG AGGGGGGTCC
    CTCTGATTCT CCCTCCTGAC GCCCCCCCCA GCAGGCCCCC TCCCCCACCA TTGAAAGCCA
    TGAATTTTGA ATTTGAGAGG GAGATTGGGT TTATAAACAG CCAGCCATCG CTCGCCGAGT
    GTCTGACTTC CTTCCCCGCT                                            
    
    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
129S1/SvImJ
A/J
AKR/J
B10.RIII-H2 H2-T18/(71NS)SnJ
BALB/cByJ
BALB/cJ
BTBR T<+> Itpr3/J
BUB/BnJ
C57BL/6J
C57BL/6NJ
C57BL/10J
C57BL/10SnJ
C57BR/cdJ
C57L/J
C58/J
CBA/J
CE/J
CZECHII/EiJ
DBA/2J
FVB/NJ
JF1/MsJ
LP/J
MA/MyJ
MOLF/EiJ
NON/ShiLtJ
NZB/BlNJ
PL/J
QSi3/Ianm
QSi5/Ianm
RF/J
RIIIS/J
SEA/GnJ
SJL/J
SM/J
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
ss384367036 MGP_WTSI_11_96213005 EVA_MGPV3 EVA_MGPV3 f SNP T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T
SNP Consensus Information
SNP Consensus Type
129S1/SvImJ
A/J
AKR/J
B10.RIII-H2 H2-T18/(71NS)SnJ
BALB/cByJ
BALB/cJ
BTBR T<+> Itpr3/J
BUB/BnJ
C57BL/6J
C57BL/6NJ
C57BL/10J
C57BL/10SnJ
C57BR/cdJ
C57L/J
C58/J
CBA/J
CE/J
CZECHII/EiJ
DBA/2J
FVB/NJ
JF1/MsJ
LP/J
MA/MyJ
MOLF/EiJ
NON/ShiLtJ
NZB/BlNJ
PL/J
QSi3/Ianm
QSi5/Ianm
RF/J
RIIIS/J
SEA/GnJ
SJL/J
SM/J
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
rs238281635 SNP T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T
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
ss384367036 MGP_WTSI_11_96213005 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr11:96242517 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Cpgi3656 CpG island 3656 321 bp proximal
Cpgi3657 CpG island 3657 977 bp proximal
Hoxb2 homeobox B2 within coordinates
Hoxb3os homeobox B3 and homeobox B2, opposite strand within coordinates
Rr141 regulatory region 141 1243 bp distal
Rr454 regulatory region 454 1471 bp distal
Rr455383 regulatory region 455383 1616 bp distal
Rr455384 regulatory region 455384 1223 bp distal
Rr455385 regulatory region 455385 50 bp distal
Tssr104519 transcription start site region 104519 56 bp downstream
Tssr104520 transcription start site region 104520 178 bp upstream
Tssr104521 transcription start site region 104521 207 bp upstream
Tssr104522 transcription start site region 104522 259 bp upstream
Tssr104523 transcription start site region 104523 283 bp upstream
Tssr104524 transcription start site region 104524 363 bp upstream
Tssr104525 transcription start site region 104525 429 bp upstream
Tssr104526 transcription start site region 104526 1173 bp upstream
Tssr104527 transcription start site region 104527 1195 bp upstream
Tssr104528 transcription start site region 104528 1384 bp upstream
Tssr104529 transcription start site region 104529 1436 bp upstream
Tssr104530 transcription start site region 104530 1464 bp upstream
Tssr104531 transcription start site region 104531 1633 bp upstream
Tssr110331 transcription start site region 110331 1564 bp upstream
Tssr110332 transcription start site region 110332 1492 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
12/17/2024
MGI 6.24
The Jackson Laboratory