rs239898542 SNP Detail

Summary

• ID
  rs239898542
• Variation Type
  SNP
• Alleles
  A/G

• Created in dbSNP Build
  137
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr3:132796592 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CTCTTTAAAA TGATTGAGTC
  ACAATTTCAG CAGCGTCAAT GGCAGTGTAT GCTCCTCAAA GTGCAGTTTA ACACTCATAT
  AGCTTAAAGT TTGATCTACT AAATATGACA GCAAATCAGT TGTATTGTAA CAGTTTATTC
  TCATGGCATT TCAAGACCAT ATTTACATGT TTAAAGTCAC TTCCAGTTCT TGCTTTTTAA
  R
  TTGTGGGACA GCACGAGGGA AACTTGACAA ATGCCACCAT CTTTAGCAAT AATGTGGTAC
  GAGATACACT CGTTTATTTT TTCTGACCTT AAGGAATTTA TGACAAAGGA TTTGGTGGTG
  AGTATGGCGG GGGATGGAGA TGGGGTGGTG TAATTCCCCA GTCAAAGTTA GAGAGGTATG
  TATTAGGGTA TTCTTTTTTT                                            
  
  R = A/G
  

  
  Note: Sequence in lower case indicates low-complexity or repetitive sequence

  ---

SNP Assays
and
SNP Consensus

Strain alleles of submitted assays, and consensus values for this SNP

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
ss359780781	MGP_WTSI_3_132753795	EVA_MGPV3	EVA_MGPV3	f	SNP	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	G	A	A	A	A
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
rs239898542					SNP	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	G	A	A	A	A

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
ss359780781	MGP_WTSI_3_132753795	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:132796592 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13847	CpG island 13847			349 bp proximal
Gstcd	glutathione S-transferase, C-terminal domain containing			Intron
				Noncoding-Transcript-Variant
Ints12	integrator complex subunit 12			1024 bp upstream
Rr398028	regulatory region 398028			64 bp upstream
Rr398029	regulatory region 398029			926 bp upstream
Rr585500	regulatory region 585500			within coordinates
Rr585501	regulatory region 585501			984 bp proximal
Rr585502	regulatory region 585502			1020 bp proximal
Rr585503	regulatory region 585503			1192 bp proximal
Tssr31768	transcription start site region 31768			996 bp upstream
Tssr31769	transcription start site region 31769			1013 bp upstream
Tssr31770	transcription start site region 31770			1055 bp upstream
Tssr31771	transcription start site region 31771			1092 bp upstream
Tssr31772	transcription start site region 31772			1739 bp upstream
Tssr35744	transcription start site region 35744			905 bp downstream
Tssr35745	transcription start site region 35745			933 bp downstream
Tssr35746	transcription start site region 35746			967 bp downstream
Tssr35747	transcription start site region 35747			1198 bp downstream
Tssr35748	transcription start site region 35748			1214 bp downstream
Tssr35749	transcription start site region 35749			1547 bp downstream