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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs12529          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:52/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/G
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_003739.4:c.15C>G
NP_003730.4:p.His5Gln
NT_077567.3:g.5076651C>G
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 ss71643788 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12529 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
ss14808CGAP-GAI|59410byFreqfwd/TC/Ggtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc08/23/9904/07/0452cDNA99 %
ss1524960LEE|402003fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc09/13/0010/10/0394cDNAunknown
ss2827711TSC-CSHL|TSC1005569byFreqrev/BC/Ggaagtggccatcatttagctttacacactgtgtttggaatccattccctgtcacttgtct01/03/0104/07/0494Genomicunknown
ss3243083YUSUKE|IMS-JST053168byFreqrev/BC/Ggaagtggccatcatttagctttacacactgtgtttggaatccattccctgtcacttgtct09/05/0110/10/03100Genomicunknown
ss3529113SC_JCM|AB032154.1_3112fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc09/24/0110/10/03100Genomicunknown
ss4415683LEE|e402003fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc04/26/0210/10/03106cDNAunknown
ss6903636SNP500CANCER|AKR1C3-01byFreqfwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc02/14/0304/07/04113Genomicunknown
ss15593589SC_SNP|NT_077567.3_5076651fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc11/17/0311/22/03120Genomicunknown
ss16252230CGAP-GAI|1503805fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc11/18/0311/22/03120cDNAunknown
ss16505559CSHL-HAPMAP|CSHL-HuAA-200402.chr10.NT_077567.3_5076651fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc02/17/0403/04/04120Genomicunknown
ss19186427CSHL-HAPMAP|CSHL-HuDD-200402.chr10.NT_077567.3_5076651fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc02/20/0403/04/04120Genomicunknown
ss19898583CSHL-HAPMAP|CSHL-HuFF-200402.chr10.NT_077567.3_5076651fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc02/21/0403/04/04120Genomicunknown
ss20683672SSAHASNP|WGSA-200403-chr10.chr10.NT_077567.3_5076651fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc03/18/0403/19/04121Genomicunknown
ss35074011KYUGEN|QH07355byFreqfwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc03/04/0511/02/06125Genomicunknown
ss38343012CEPH|G9-SN-E1S2fwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc05/19/0505/19/05125GenomicC100 %
ss38530440ABI|hCV8723970byFreqfwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc07/15/0511/02/06126Genomicunknown
ss65725539ILLUMINA|Human1-rs12529fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc10/10/0610/10/06127Genomicunknown
ss69068306PERLEGEN|PGP04749804byFreqfwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc01/30/0708/14/07127Genomicunknown
ss71643788SI_EXO|NT_077567.3_5076651byFreqfwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc05/07/0703/31/08127Genomicunknown
ss74810369AFFY|SNP_M-183909fwd/TC/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc08/09/0708/09/07128Genomicunknown
ss74874996ILLUMINA|ILMN_Human_1M_rs12529fwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc08/28/0708/29/07129Genomicunknown
ss77657095HGSV|Cor12156_SNV_20070510.chr10_5126651fwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc10/09/0710/14/07129Genomicunknown
ss83674767HGSV|Cor18555_SNV_20070510.chr10_5126651fwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc11/27/0712/05/07130Genomicunknown
ss84521046HGSV|Cor19240_SNV_20070510.chr10_5126651fwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc11/30/0712/07/07130Genomicunknown
ss86272204CORNELL|hCV8723970fwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc01/21/0801/21/08129Genomicunknown
ss1091862931000GENOMES|CEU.trio.12.15.2008_2283481_chr10_5126651fwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc12/15/0812/16/08130Genomicunknown
ss1152901631000GENOMES|NA19240_2008_12_16_2063759_chr10_5126651fwd/C/Gagacaagtgacagggaatggattccaaacacagtgtgtaaagctaaatgatggccacttc12/18/0812/19/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12529|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=130
 TATCACGGCA GAAACGAAAA AAGATATTTG TAGCTGGAGG TTTTTATAGT CTAACATATG
 GTTGCTATTT GTTCTACAAA TCCTTTTGAA TAATTTAATA TAGAGATTTA GAATAGAAAA
 TAATACTTTA GATAGAAATT AATGAGTTTA TTATAACCAT ATATTATAAT AATTTACTTA
 GGAATTCTCT TTGATAAGAA ACAAATGAAC TGAATGCAAT TTTCTCCACA GACCATATAA
 GACTGCCTAT GTACCTCCTC CTACATGCCA TTGGTTAACC ATCAGTCAGT TTGCAGGGGT
 GGGGGGAGGG GTTTCCTGCC CATTGTTTTT GTAATCTCTG AGGAGAAGCA GCAGCAAACA
 TTTGCTAGTC AGACAAGTGA CAGGGAATGG ATTCCAAACA
 S
 CAGTGTGTAA AGCTAAATGA TGGCCACTTC ATGCCTGTAT TGGGATTTGG CACCTATGCA
 CCTCCAGAGG TAAGAATAAT TCCTTTTAGT TTTCGGATTT CAAAAGAATA AACCTAGTAG
 AAGTGAAACC CGTATTGGGT TGTAAGGTTC GTGTTCCTAC CTTACTCTGG ATGACTCACT
 GGTCTAGGTT TCCTAGGCTA GGAGAAAAAA GTAGGCAATC CTTGTTCTGC ATTGAGGTCC
 ATTCCTATGG TCACGTACTG CTTATTTTTC GTTTGTGCAC TGTTTCTTTC TTCTGTTCAT
 GTCTAGTTCC CAGCTTGGCA GAATATGTAA AACTCAGTAT TGAAGAACAC TGTTGGTCAT
 CTCCCTCTGG TGGAGATTAA TTGCAATAGG AGTGATTTCT

  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
S68288 AH004942 AL391427 BI828901 D17793 Hs.78183 L43831 S68288
dbSNP Blast Analysis
UniGene Cluster ID
78183

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/G
 G/G
 HWP C
 G
ss14808 POOLED_CEPH 188 AF 0.395 0.605
ss2827711 TSC_42_AA 83 AF 0.434 0.566
TSC_42_C 84 AF 0.500 0.500
TSC_42_A 83 AF 0.952 0.048
CEPH 93 AF 0.604 0.396
COHORT_CONSORTIUM_B 76 AF 0.569 0.431
COHORT_CONSORTIUM_C 76 AF 0.632 0.368
COHORT_CONSORTIUM_H 76 AF 0.149 0.851
COHORT_CONSORTIUM_J 76 AF 0.171 0.829
COHORT_CONSORTIUM_L 76 AF 0.347 0.653
CEPH-TRIOS 606 AF 0.600 0.400
ss3243083 JBIC-allele 1484 AF 0.106 0.894
ss35074011 CAU200 400 AF 0.410 0.590
JSA426 852 AF 0.260 0.740
ss38530440 HapMap-CEU European 120 IG 0.333 0.533 0.133 0.403 0.600 0.400
HapMap-HCB Asian 90 IG 0.022 0.311 0.667 0.752 0.178 0.822
HapMap-JPT Asian 88 IG 0.114 0.886 0.752 0.057 0.943
HapMap-YRI Sub-Saharan African 120 IG 0.283 0.467 0.250 0.655 0.517 0.483
AoD_African_American 90 AF 0.630 0.370
AoD_Caucasian 92 AF 0.540 0.460
AoD_Chinese 90 AF 0.230 0.770
AoD_Japanese 90 AF 0.070 0.930
ss6903636 P1 204 GF 0.245 0.402 0.353 0.100 0.446 0.554
CAUC1 62 GF 0.387 0.452 0.161 1.000 0.613 0.387
AFR1 48 GF 0.250 0.583 0.167 0.403 0.541 0.458
HISP1 46 GF 0.261 0.435 0.304 0.584 0.478 0.521
PAC1 48 GF 0.042 0.125 0.833 0.150 0.104 0.896
ss69068306 HapMap-CEU European 120 GF 0.333 0.533 0.133 0.600 0.400
HapMap-HCB Asian 90 GF 0.022 0.311 0.667 0.178 0.822
HapMap-JPT Asian 90 GF 0.133 0.867 0.067 0.933
HapMap-YRI Sub-Saharan African 120 GF 0.283 0.467 0.250 0.517 0.483
ss71643788 HapMap-CEU European 120 IG 0.333 0.533 0.133 0.600 0.400
HapMap-HCB Asian 90 IG 0.022 0.311 0.667 0.178 0.822
HapMap-JPT Asian 88 IG 0.114 0.886 0.057 0.943
HapMap-YRI Sub-Saharan African 120 IG 0.283 0.467 0.250 0.517 0.483

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.476+/-0.108 525 409 270 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
 YES YES YES

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Revised: May 25, 2006 1:38 PM .