Reference SNP(refSNP) Cluster Report: rs974071

Reference SNP(refSNP) Cluster Report: rs974071

refSNP ID: rs974071
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_130386.1:c.58+1139C>T
NT_010859.14:g.469568G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10914656 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs974071 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss1425022	TSC-CSHL\|TSC0285455	fwd/B	C/T	aaagagtgtgtgtgagtgagtgtgtgtgtg	gtttctgtgtgtgtgtgtgagagagagaga	09/06/00	10/25/06	86	Genomic	95 %
ss10914656	BCM_SSAHASNP\|chr18.NT_010859.12_469568	rev/T	A/G	tctctctctctctcacacacacacagaaac	cacacacacactcactcacacacactcttt	06/30/03	10/25/06	116	Genomic	unknown
ss12446689	WI_SSAHASNP\|chr18.NT_010859.12_469568	rev/T	A/G	tctctctctctctcacacacacacagaaac	cacacacacactcactcacacacactcttt	07/04/03	10/10/03	116	Genomic	unknown
ss17601239	CSHL-HAPMAP\|CSHL-HuCC-200402.chr18.NT_010859.13_469568	rev/T	A/G	tctctctctctctcacacacacacagaaac	cacacacacactcactcacacacactcttt	02/19/04	03/04/04	120	Genomic	unknown
ss20052710	CSHL-HAPMAP\|CSHL-HuFF-200402.chr18.NT_010859.13_469568	rev/T	A/G	tctctctctctctcacacacacacagaaac	cacacacacactcactcacacacactcttt	02/21/04	03/04/04	120	Genomic	unknown
ss21500773	SSAHASNP\|WGSA-200403-chr18.chr18.NT_010859.13_469568	rev/T	A/G	tctctctctctctcacacacacacagaaac	cacacacacactcactcacacacactcttt	03/20/04	03/20/04	121	Genomic	unknown
ss78560371	HGSV\|Cor12878_SNV_20070510.chr18_469568	rev/T	A/G	tctctctctctctcacacacacacagaaac	cacacacacactcactcacacacactcttt	10/17/07	10/20/07	129	Genomic	unknown
ss80371417	HGSV\|Cor18507_SNV_20070510.chr18_469568	rev/T	A/G	tctctctctctctcacacacacacagaaac	cacacacacactcactcacacacactcttt	11/23/07	11/25/07	130	Genomic	unknown
ss90684422	BCMHGSC_JDW\|JWB-1058037	rev/T	A/G	tctctctctctctcacacacacacagaaac	cacacacacactcactcacacacactcttt	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGGACACAGG GGCTCtgtgg caggctgggg aatggccccc aaaggtgaca gcaccctgaa
 tcctgaaacc tgaatgttac cttatgtggc acaaaggact ttgtaggtgt gattaagttg
 aagagcttga gatggggaga tgatcctggg ttacctgggt gggccctgaa agccatcaca
 agcgtccttg taagagagag gcagagggag atgtgactgc agagagaagg tgatgtgagg
 atggaagcag agatttttgt tatgttctct ggtcaaggaa tataggtggc cattagaagc
 taaaaatgca agggcattaa tggattcttc cttcagagcc tcaggaggga gagctgtata
 ctccccatat ttatatttca gctggctgaa ggtgatttta ggccgctggc ccccagaact
 gtaagaggag aaatctgtat tgtttaagcc agcacgttcg tggtaacctt ttacagcagc
 cgcaggaaac tcatacaCAC CCTCTGCCTC CCAGGCTGCT GCACCTGGTG CTCTTCTTTG
 CTTTGACCTT GCTTCTCTTT GACCTTGAAA TGCCAGTGGT CATTGCAGAG TTTCAAAGGC
 AGCTCCAGGG ATTGGAGGAT TTTCCCAACA GCTTGTTTCT GTGCTTGGCC AGAGGAAATG
 GAGAAGGATA GAGGAGAAAA GAgtgtgtgt gagtgagtgt gtgtgtg
 Y
 gtttctgtgt gtgtgtgaga gagagagaga gagagagaga gTATGAAAAT GAATGAATCT
 ACTTCCTGTT GCTTAAAAAA AGTCCTGGCT GGACTTTGAT TAGAATTAAC AACCCCCAGC
 TGCTCTGCCT CCCGCGTTGC TTTAGCATTT TTCCTTCTGG ACACACACGT CTGCATTACT
 TTCTGGGAAA ACATATGACT TTAAAATAGG AATGCAGTGG CACCAAGCTC ATCTCTCCTG
 C

GeneView

GeneView via analysis of contig annotation: COLEC12 collectin sub-family member 12

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_010859->NM_130386

function

HuRef

NW_001838461->NM_130386

function

Celera

NW_926940->NM_130386

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_010859->NM_130386->NP_569057	469568	reverse	intron

HuRef	NW_001838461->NM_130386->NP_569057	427720	reverse	intron

Celera	NW_926940->NM_130386->NP_569057	354692	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs974071 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_926940.1	354692	354692	minus	A	alt_assembly_1	Celera	Celera	view	707
18	NW_001838461.1	427720	439360	minus	A	alt_assembly_8	HuRef	HuRef	view	707
18	NT_010859.14	469568	469568	minus	G	ref_assembly	reference	reference	view	707

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010859

dbSNP Blast Analysis
GenBank HTGS Finished:
AP005240.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss10914656	HapMap-CEU	European	118	IG	0.390	0.424	0.186	0.403	0.602	0.398

ss1425022	TSC_42_AA		83	AF					0.145	0.855

	TSC_42_C		83	AF					0.386	0.614

	TSC_42_A		83	AF					0.687	0.313

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.479+/-0.100	90	60	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .