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rs233000563 SNP Detail
Summary
  • ID
    rs233000563
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr19:5849042 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                AGTTACACTT ATCTGTCAAC
AGCAGTCTGC TGTTTCCTGC TCCGAGATGG AATGAAGCAA CTCTTCTGCT TATGAAGAGA
AACCTGTCTG AGGCAAACGA AACATTGGCA CACTGCACCG CCTCGCAGCC GCTCGATCCC
ACTCATCTCA ACAAGCTCAG CTTCTTTTTA CTCCAGGCTT AATGCAGCAT TTTCACTTCA
Y
TTCTATTCTG CTTTTGTAAA AGCAGTTTTG AGATGAACAT TTGATCTTCA CTGTTTTTCA
TCAATTCTTT ACTTTTGTGG ATAAAGCTTG GTAGATAAGC CATAACTTTT AAAGGTATTG
CCATAACTTT ATACTGGTTG CTTTCATTTG CTTAAATTTT TGCATATGCA GCTTTTCATC
AGTAGGAACA ATCTCTGGCT                                            

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
ss401662591 MGP_WTSI_19_5799014 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 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
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
rs233000563 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 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
ss401662591 MGP_WTSI_19_5799014 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr19:5849042 () rs orientation: forward
Symbol Name Transcript Protein Function
Class		 Allele Residue Codon
Position		 AA
Position
Cpgi10480 CpG island 10480 1967 bp proximal
Gm55521 predicted gene, 55521 within coordinates
Malat1 metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) within coordinates
Rr543161 regulatory region 543161 649 bp distal
Rr543162 regulatory region 543162 within coordinates
Rr543163 regulatory region 543163 404 bp proximal
Tssr5416 transcription start site region 5416 1699 bp upstream
Tssr5417 transcription start site region 5417 12 bp downstream
Tssr5418 transcription start site region 5418 495 bp downstream
Tssr5419 transcription start site region 5419 1149 bp downstream
Tssr5420 transcription start site region 5420 1166 bp downstream
Tssr154496 transcription start site region 154496 1979 bp upstream
Tssr157652 transcription start site region 157652 1910 bp upstream
Tssr157653 transcription start site region 157653 1826 bp upstream
Tssr157654 transcription start site region 157654 1772 bp upstream
Tssr157655 transcription start site region 157655 1746 bp upstream
Tssr157656 transcription start site region 157656 1713 bp upstream
Tssr157657 transcription start site region 157657 1593 bp upstream
Tssr157658 transcription start site region 157658 1487 bp upstream
Tssr157659 transcription start site region 157659 1383 bp upstream
Tssr157660 transcription start site region 157660 1287 bp upstream
Tssr157661 transcription start site region 157661 1254 bp upstream
Tssr157662 transcription start site region 157662 1161 bp upstream
Tssr157663 transcription start site region 157663 1100 bp upstream
Tssr157664 transcription start site region 157664 986 bp upstream
Tssr157665 transcription start site region 157665 977 bp upstream
Tssr157666 transcription start site region 157666 945 bp upstream
Tssr157667 transcription start site region 157667 691 bp upstream
Tssr157668 transcription start site region 157668 650 bp upstream
Tssr157669 transcription start site region 157669 631 bp upstream
Tssr157670 transcription start site region 157670 615 bp upstream
Tssr157671 transcription start site region 157671 594 bp upstream
Tssr157672 transcription start site region 157672 544 bp upstream
Tssr157673 transcription start site region 157673 510 bp upstream
Tssr157674 transcription start site region 157674 498 bp upstream
Tssr157675 transcription start site region 157675 485 bp upstream
Tssr157676 transcription start site region 157676 470 bp upstream
Tssr157677 transcription start site region 157677 448 bp upstream
Tssr157678 transcription start site region 157678 434 bp upstream
Tssr157679 transcription start site region 157679 366 bp upstream
Tssr157680 transcription start site region 157680 339 bp upstream
Tssr157681 transcription start site region 157681 318 bp upstream
Tssr157682 transcription start site region 157682 305 bp upstream
Tssr157683 transcription start site region 157683 269 bp upstream
Tssr157684 transcription start site region 157684 259 bp upstream
Tssr157685 transcription start site region 157685 244 bp upstream
Tssr157686 transcription start site region 157686 183 bp upstream
Tssr157687 transcription start site region 157687 162 bp upstream
Tssr157688 transcription start site region 157688 115 bp upstream
Tssr157689 transcription start site region 157689 78 bp upstream
Tssr157690 transcription start site region 157690 6 bp upstream
Tssr157691 transcription start site region 157691 35 bp downstream
Tssr157692 transcription start site region 157692 89 bp downstream
Tssr157693 transcription start site region 157693 146 bp downstream
Tssr157694 transcription start site region 157694 204 bp downstream
Tssr157695 transcription start site region 157695 268 bp downstream
Tssr157696 transcription start site region 157696 289 bp downstream
Tssr157697 transcription start site region 157697 338 bp downstream
Tssr157698 transcription start site region 157698 354 bp downstream
Tssr157699 transcription start site region 157699 412 bp downstream
Tssr157700 transcription start site region 157700 461 bp downstream
Tssr157701 transcription start site region 157701 479 bp downstream
Tssr157702 transcription start site region 157702 515 bp downstream
Tssr157703 transcription start site region 157703 566 bp downstream
Tssr157704 transcription start site region 157704 592 bp downstream
Tssr157705 transcription start site region 157705 613 bp downstream
Tssr157706 transcription start site region 157706 661 bp downstream
Tssr157707 transcription start site region 157707 707 bp downstream
Tssr157708 transcription start site region 157708 717 bp downstream
Tssr157709 transcription start site region 157709 729 bp downstream
Tssr157710 transcription start site region 157710 748 bp downstream
Tssr157711 transcription start site region 157711 767 bp downstream
Tssr157712 transcription start site region 157712 804 bp downstream
Tssr157713 transcription start site region 157713 831 bp downstream
Tssr157714 transcription start site region 157714 882 bp downstream
Tssr157715 transcription start site region 157715 899 bp downstream
Tssr157716 transcription start site region 157716 943 bp downstream
Tssr157717 transcription start site region 157717 970 bp downstream
Tssr157718 transcription start site region 157718 1015 bp downstream
Tssr157719 transcription start site region 157719 1069 bp downstream
Tssr157720 transcription start site region 157720 1088 bp downstream
Tssr157721 transcription start site region 157721 1124 bp downstream
Tssr157722 transcription start site region 157722 1141 bp downstream
Tssr157723 transcription start site region 157723 1216 bp downstream
Tssr157724 transcription start site region 157724 1225 bp downstream
Tssr157725 transcription start site region 157725 1271 bp downstream
Tssr157726 transcription start site region 157726 1276 bp downstream
Tssr157727 transcription start site region 157727 1291 bp downstream
Tssr157728 transcription start site region 157728 1388 bp downstream
Tssr157729 transcription start site region 157729 1587 bp downstream
Tssr157730 transcription start site region 157730 1717 bp downstream
Tssr157731 transcription start site region 157731 1740 bp downstream
Tssr157732 transcription start site region 157732 1783 bp downstream
Tssr157733 transcription start site region 157733 1820 bp downstream
Tssr157734 transcription start site region 157734 1837 bp downstream
Tssr157735 transcription start site region 157735 1861 bp downstream
Tssr157736 transcription start site region 157736 1899 bp downstream
Tssr157737 transcription start site region 157737 1955 bp downstream
Tssr157738 transcription start site region 157738 1986 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