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rs27045539 SNP Detail
Summary
  • ID
    rs27045539
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr11:96193310 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                TTTTCTCTTT ACTGCCACCC
    ACACCCGAGC AGCAAGCTTC AGGCCCCGTT TTCTTTTCTT CCTTCTCCCT CTCCCCCCTC
    CTTTTTTTAT TTTTAAAGAA AATAGCCGTC TGGCAGAAGG GGCCCAGCTG CGGAGATCTC
    TGGCCGCCCA GCGAGCTCAG CAAGGGGCCG CCGGTCTTCC GAACACCTTC CCAGGGAAGG
    Y
    GGTAAGGCCA TGAGCAAATT CTCCAATTAT TGGCCACCAG CAACACAAGG CTTTGGATTT
    GGTCTCTGAA TGAGATAGCT GGCATCTGGC GAGCTTGTTA AAGGGGATCT GTTTAAACCC
    CAAACTCCCG CAGAAGAGTT ACCACCAAAC CTTAACCGCT CAGACGGTTG TCTCTCTAGT
    CTTTGGCCGA CCGACCATCT                                            
    
    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
BTBR T<+> Itpr3/J
C3H/HeJ
FVB/NJ
KK/HlJ
PWD/PhJ
ss37295458 NES08567233 PERLEGEN MM_PANEL2 f SNP C C C C C C C T
SNP Consensus Information
SNP Consensus Type
129S1/SvImJ
A/J
AKR/J
BTBR T<+> Itpr3/J
C3H/HeJ
FVB/NJ
KK/HlJ
PWD/PhJ
rs27045539 SNP C C C C C C C 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
ss37295458 NES08567233 PERLEGEN MM_PANEL f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr11:96193310 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Cpgi3642 CpG island 3642 1350 bp distal
Cpgi3643 CpG island 3643 601 bp proximal
Hoxb5 homeobox B5 1028 bp upstream
Hoxb5os homeobox B5 and homeobox B6, opposite strand within coordinates
Hoxb6 homeobox B6 915 bp downstream
Rr238046 regulatory region 238046 491 bp proximal
Rr247589 regulatory region 247589 within coordinates
Tssr104489 transcription start site region 104489 1023 bp upstream
Tssr104490 transcription start site region 104490 1070 bp upstream
Tssr104491 transcription start site region 104491 1089 bp upstream
Tssr104492 transcription start site region 104492 1107 bp upstream
Tssr104493 transcription start site region 104493 1130 bp upstream
Tssr104494 transcription start site region 104494 1166 bp upstream
Tssr104495 transcription start site region 104495 1241 bp upstream
Tssr104496 transcription start site region 104496 1413 bp upstream
Tssr104497 transcription start site region 104497 1540 bp upstream
Tssr104498 transcription start site region 104498 1571 bp upstream
Tssr104499 transcription start site region 104499 1596 bp upstream
Tssr104500 transcription start site region 104500 1638 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
12/10/2024
MGI 6.24
The Jackson Laboratory