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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs180749          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:79/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_031900.1:c.635C>T
NP_114106.1:p.Thr212Ile
NT_006576.15:g.35006362G>A
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss44674512 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs180749 during BLAST analysis for the current build.

NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss240047KWOK|OVLP-000621-345285rev/BC/Tcttacacacttggcttgacaaacgtagggactacaagatggaactccctggtgggacagg06/30/0010/10/0379Genomic94 %
ss240061KWOK|OVLP-000621-346495rev/BC/Tcttacacacttggcttgacaaacgtagggactacaagatggaactccctggtgggacagg06/30/0010/10/0385Genomic94 %
ss626437SC_JCM|AC025447.3_50285byFreqfwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag07/12/0010/25/0680Genomicunknown
ss1055303KWOK|OVLP-000804-233581rev/BC/Tcttacacacttggcttgacaaacgtagggactacaagatggaactccctggtgggacagg09/02/0010/10/0386Genomic94 %
ss1750239KWOK|OVLP-000925-416762fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag10/05/0010/10/0387Genomic94 %
ss3234086YUSUKE|IMS-JST044171byFreqfwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag09/05/0110/10/03100Genomicunknown
ss10260303BCM_SSAHASNP|chr5.NT_006576.13_17459798fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag06/27/0310/10/03116Genomicunknown
ss11761158WI_SSAHASNP|chr5.NT_006576.13_17459798fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag07/04/0310/10/03116Genomicunknown
ss22327302SSAHASNP|WGSA-200403-chr5.chr5.NT_006576.14_17485711fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag03/21/0403/21/04121Genomicunknown
ss23986266PERLEGEN|afd4232761byFreqfwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag08/10/0409/13/04123Genomicunknown
ss44674512ABI|hCV1018735byFreqfwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag07/19/0511/03/06126Genomicunknown
ss48411729APPLERA_GI|hCV1018735byFreqfwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag09/28/0511/03/06126Genomicunknown
ss65725927ILLUMINA|Human1-rs180749fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag10/10/0610/10/06127Genomicunknown
ss66088529AFFY|SNP_A-1938057byFreqrev/BC/Tttgacaaacgtagggactacaagatggaactc10/27/0608/14/07127Genomicunknown
ss68932145PERLEGEN|PGP04232761byFreqfwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag01/30/0708/14/07127Genomicunknown
ss74868905ILLUMINA|ILMN_Human_1M_rs180749fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag08/28/0708/29/07129Genomicunknown
ss76039385AFFY|AFFY_6_1M_SNP_A-1938057rev/BC/Tttgacaaacgtagggactacaagatggaactc08/28/0708/29/07130Genomicunknown
ss81408540KRIBB_YJKIM|KHS34725fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag11/30/0711/30/07130Genomicunknown
ss85155961HGSV|Cor19129_SNV_20070510.chr5_35069362fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag12/06/0712/08/07130Genomicunknown
ss93058438BCMHGSC_JDW|JWB-1962543fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag02/26/0803/03/08129Genomicunknown
ss98611240HUMANGENOME_JCVI|1103654073881fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag04/01/0804/01/08130Genomicunknown
ss1089538631000GENOMES|CEU.trio.12.15.2008_1243034_chr5_35069362fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag12/15/0812/16/08130Genomicunknown
ss1116847331000GENOMES|NA19240_2008_12_16_1113652_chr5_35069362fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag12/16/0812/17/08130Genomicunknown
ss116564737ILLUMINA-UK|NA18507_000053678_NCBI36.1_chr5_35069362fwd/TA/Gcctgtcccaccagggagttccatcttgtagtccctacgtttgtcaagccaagtgtgtaag01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs180749|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 ATTCTCAGAG CCTTGCAGTT TACTTGATTT TATTTAAAAG CAAAATACAT TTTAAAACTC
 TGTCATTAAT TATTACTCAG ACTCGGAAGG CCTTTCTAAT GGTGTCCTCA AGTGGTCTCC
 AATTCAATTA GGTCAAATTG AGCCCCTGAT TAATGACAGG CTTTATATTA GTTTCTAATC
 CTTATACCAG GAAAACCTGA TCAACTACTT CACATACCCA GTAGTCTTTA AAGAAACAAG
 AGAAAAATCT CCAAACTCAC TGGTTGGCAA CCTGTCCCAC CAGGGAGTTC CATCTTGTAG
 R
 TCCCTACGTT TGTCAAGCCA AGTGTGTAAG GACTGCATCC ATGGTAGGCT CCTCTGCAGA
 GAAGAAACAA CAGGAGGATG GGGTCAAGTT CCTGGTCCAC TGAGTAGGAC AAAAGAGAAA
 ACCCAGGAAG GCTATGAAGA TGAAATAGAA CATCATTCGC ATTCACCTCT GATTTCTAAG
 AACGCATCTA AGCTTATGTC GGATCAATGT ACTTAATAGT CTTTTCTAAC TGTTGTTAGA
 AAACATAGAT TTGAAACTGT GAAAGGAATT TTGGAGAACA TTTGTCCAAG AACTCCAATC

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_006576 ABBA01039261 AC010368 AC011145 AC011145.3 AC025447.3
dbSNP Blast Analysis
UniGene Cluster ID
34494

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss23986266 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.783 0.174 0.043 0.273 0.870 0.130
AFD_CHN_PANEL Asian 48 IG 0.583 0.417 0.200 0.792 0.208
ss3234086 JBIC-allele 1478 AF 0.801 0.200
ss44674512 HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 90 IG 0.667 0.289 0.044 1.000 0.811 0.189
HapMap-JPT Asian 88 IG 0.682 0.318 0.251 0.841 0.159
HapMap-YRI Sub-Saharan African 118 IG 0.593 0.373 0.034 0.439 0.780 0.220
AoD_African_American 90 AF 0.860 0.140
ss48411729 AGI_ASP population multiple 78 IG 0.769 0.205 0.026 0.655 0.872 0.128
ss626437 CEPH 184 AF 0.990 0.010
EURAME 30 GF 1.000 1.000
AFRAME 30 GF 0.133 0.200 0.667 0.233 0.767
ss66088529 HapMap-CEU European 118 GF 1.000 1.000
HapMap-HCB Asian 90 GF 0.667 0.289 0.044 0.811 0.189
HapMap-JPT Asian 90 GF 0.689 0.311 0.844 0.156
HapMap-YRI Sub-Saharan African 120 GF 0.583 0.383 0.033 0.775 0.225
ss68932145 HapMap-CEU European 120 GF 1.000 1.000
HapMap-HCB Asian 90 GF 0.667 0.289 0.044 0.811 0.189
HapMap-JPT Asian 90 GF 0.689 0.311 0.844 0.156
HapMap-YRI Sub-Saharan African 120 GF 0.583 0.383 0.033 0.775 0.225
ss76039385 ICMHP 6 IG 1.000 1.000

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.274+/-0.249 1219 1003 276 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .