Reference SNP(refSNP) Cluster Report: rs236674

Reference SNP(refSNP) Cluster Report: rs236674

refSNP ID: rs236674
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_005935.2:c.1084-395G>A
NT_016354.18:g.12558462G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44538125 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs236674 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
ss305223	KWOK\|OVLP-000621-339727	fwd/B	C/T	cgatgcattctttctccctcagcttcttta	tgcatttcctggaattatttcagttcaaag	06/30/00	10/10/03	79	Genomic	97 %
ss436068	KWOK\|OVLP-000621-341298	fwd/B	C/T	cgatgcattctttctccctcagcttcttta	tgcatttcctggaattatttcagttcaaag	06/30/00	10/10/03	85	Genomic	99 %
ss621371	SC_JCM\|AC021425.3_11173	fwd/B	C/T	cgatgcattctttctccctcagcttcttta	tgcatttcctggaattatttcagttcaaag	07/12/00	05/16/04	80	Genomic	unknown
ss1069357	KWOK\|OVLP-000804-3315	fwd/B	C/T	cgatgcattctttctccctcagcttcttta	tgcatttcctggaattatttcagttcaaag	09/02/00	10/10/03	86	Genomic	99 %
ss1198206	KWOK\|OVLP-000804-2404	fwd/B	C/T	cgatgcattctttctccctcagcttcttta	tgcatttcctggaattatttcagttcaaag	09/02/00	10/10/03	86	Genomic	97 %
ss1570635	KWOK\|OVLP-000925-54071	fwd/B	C/T	cgatgcattctttctccctcagcttcttta	tgcatttcctggaattatttcagttcaaag	10/04/00	10/10/03	87	Genomic	99 %
ss1628807	KWOK\|OVLP-000925-50661	fwd/B	C/T	cgatgcattctttctccctcagcttcttta	tgcatttcctggaattatttcagttcaaag	10/04/00	10/10/03	87	Genomic	97 %
ss11625682	WI_SSAHASNP\|chr4.NT_016354.15_12505446	rev/T	A/G	ctttgaactgaaataattccaggaaatgca	taaagaagctgagggagaaagaatgcatcg	07/03/03	10/10/03	116	Genomic	unknown
ss20198551	CSHL-HAPMAP\|CSHL-HuFF-200402.chr4.NT_016354.16_12505446	rev/T	A/G	ctttgaactgaaataattccaggaaatgca	taaagaagctgagggagaaagaatgcatcg	02/21/04	03/04/04	120	Genomic	unknown
ss22142854	SSAHASNP\|WGSA-200403-chr4.chr4.NT_016354.16_12505446	rev/T	A/G	ctttgaactgaaataattccaggaaatgca	taaagaagctgagggagaaagaatgcatcg	03/20/04	03/21/04	121	Genomic	unknown
ss23948569	PERLEGEN\|afd0643057	rev/T	A/G	ctttgaactgaaataattccaggaaatgca	taaagaagctgagggagaaagaatgcatcg	08/10/04	09/13/04	123	Genomic	unknown
ss44538125	ABI\|hCV812137	rev/T	A/G	ctttgaactgaaataattccaggaaatgca	taaagaagctgagggagaaagaatgcatcg	07/19/05	07/19/05	126	Genomic	unknown
ss77108008	HGSV\|Cor12156_SNV_20070510.chr4_88367920	rev/T	A/G	ctttgaactgaaataattccaggaaatgca	taaagaagctgagggagaaagaatgcatcg	10/09/07	10/11/07	129	Genomic	unknown
ss81025042	HGSV\|Cor18555_SNV_20070510.chr4_88367920	rev/T	A/G	ctttgaactgaaataattccaggaaatgca	taaagaagctgagggagaaagaatgcatcg	11/27/07	11/27/07	130	Genomic	unknown
ss92674776	BCMHGSC_JDW\|JWB-1814397	rev/T	A/G	ctttgaactgaaataattccaggaaatgca	taaagaagctgagggagaaagaatgcatcg	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 CATAAATGGC AAGTACAATC TTAAAAGTTA TTTCATGTAC TTAAAAAAAA CAACTCCTAT
 TTCAGTGGGC TATGTTGAAA AGTTAAAGCT CTCCAACATA AAAAACTAAA AAACGCCAGT
 TTGTAGAAGA CAATCAAGGT ATAGAACGTG AATGAATTTA ACACCCTGAA TATTATCAAG
 CACATAAACT GTACGTAACA GGTACTGCCA GAGCTTGTGG AGCTGTGAAG ACTGTAGGTG
 ACAGGTTGGG CTGGAAAAGC AGTCTCTCCT CGATGCATTC TTTCTCCCTC AGCTTCTTTA
 Y
 TGCATTTCCT GGAATTATTT CAGTTCAAAG GAAGAAGAAC TTTCCTGTTT GACTTAAGCA
 AACAAGTAAT TCAGGTCACT TGTTCCACTT GGGAGAGTTT TAATGGATTT GACCCTTCCC
 TGATACACAC TATTAGCAAG TAAGAACTTT TTTGAAGGAG AGGAGCTTAA AATTACCTTT
 CTTTTCCATT GAGAAGCTTA ATTTTTACAA TTTTCTCAGT TGAAGGAAAG ATTTCTAAAA
 CTTACAATTG ATATATGTAT CTTGACATGA ATTCTTCTAA ACACATTCAC AAATTTTTCT

GeneView

GeneView via analysis of contig annotation: AFF1 AF4/FMR2 family, member 1

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_016354->NM_005935

function

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


reference	NT_016354->NM_005935->NP_005926	12558462	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs236674 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838915.1	12518443	83756893	minus	A	alt_assembly_8	HuRef	HuRef	view	300
4	NW_922162.1	35125064	85300090	minus	A	alt_assembly_1	Celera	Celera	view	300
4	NT_016354.18	12558462	88229765	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016354 AC022886 AC022886.4 AJ238093 AJ238093.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss23948569	AFD_EUR_PANEL	European	48	IG	0.083	0.333	0.583	0.655	0.250		0.750

	AFD_AFR_PANEL	African American	46	IG	0.043	0.304	0.652	1.000	0.196		0.804

	AFD_CHN_PANEL	Asian	46	IG	0.087	0.348	0.565	0.655	0.261		0.739

ss621371	CEPH		184	AF					0.420		0.580

	CHMJ	Asian	74	IG					0.135	0.014	0.851

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.360+/-0.224	71	50	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .