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Reference SNP (refSNP) Cluster Report: rs12502572                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.4760/2384 (1000 Genomes)
A=0.4549/57118 (TOPMED)
HGVS Names
  • CM000666.2:g.140563980G>A
  • CM000666.2:g.140563980G>C
  • NC_000004.11:g.141485134G>A
  • NC_000004.12:g.140563980G>A
  • NC_000004.12:g.140563980G>C
  • NG_012139.1:g.9826C>G
  • NG_012139.1:g.9826C>T
  • NM_021833.4:c.326-462C>G
  • NM_021833.4:c.326-462C>T
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

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


  Submitter records for this RefSNP Cluster back to top
The submission ss277963846 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12502572 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
ss19570061CSHL-HAPMAP|CSHL-HuDD-200402.chr4.NT_016606.16_3033190byFreqfwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag02/20/0410/26/06120Genomicunknown
ss23995099PERLEGEN|afd3596093byFreqfwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag08/10/0409/13/04123Genomicunknown
ss44523393ABI|hCV2052384byFreqfwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag07/19/0511/03/06126Genomicunknown
ss66451934AFFY|SNP_A-2219817byFreqrev/BC/Tccttactctgagttgagcacatttagtacatg10/29/0603/31/08127Genomicunknown
ss68913171PERLEGEN|PGP03596093byFreqfwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag01/30/0703/31/08127Genomicunknown
ss76242825AFFY|AFFY_6_1M_SNP_A-2219817byFreqrev/BC/Tccttactctgagttgagcacatttagtacatg08/28/0703/07/10129Genomicunknown
ss82987837KRIBB_YJKIM|KHS369733fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag11/30/0712/04/07130Genomicunknown
ss84468653HGSV|Cor18555_SNV_20070510.chr4_141842739fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag11/27/0712/07/07130Genomicunknown
ss104125264BGI|BGI_rs12502572fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag06/07/0806/18/09131Genomicunknown
ss1084028811000GENOMES|CEU.trio.12.15.2008_1102107_chr4_141704584fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag12/15/0812/15/08130Genomicunknown
ss1107026811000GENOMES|NA19240_2008_12_16_993569_chr4_141704584fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag12/17/0812/17/08130Genomicunknown
ss117214899ILLUMINA-UK|NA18507_000189620_NCBI36.1_chr4_141704584fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag01/18/0901/18/09130Genomic99 %
ss157988402GMI|GMI_SNP_105140121fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag06/24/0906/25/09131Genomicunknown
ss161503308ENSEMBL|ENSSNP2293809fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag09/24/0909/25/09131Genomicunknown
ss164547927COMPLETE_GENOMICS|NA19240_36_chr4_141704584fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag09/29/0909/29/09132Genomicunknown
ss167230662COMPLETE_GENOMICS|NA20431_36_chr4_141704584fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag09/30/0909/30/09132Genomicunknown
ss172945509AFFY|GenomeWideSNP_5_SNP_A-2219817rev/BC/Tccttactctgagttgagcacatttagtacatg10/01/0910/02/09132Genomicunknown
ss199267152BUSHMAN|BUSHMAN-chr4-141704583fwd/TA/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag02/16/1003/06/10132Genomicunknown
ss2212541201000GENOMES|pilot_1_YRI_3063803_chr4_141704584fwd/A/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag04/22/1004/22/10132Genomicunknown
ss2326301431000GENOMES|pilot_1_CEU_2234772_chr4_141704584fwd/A/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag05/01/1005/01/10132Genomicunknown
ss2398705921000GENOMES|pilot_1_CHB+JPT_1755669_chr4_141704584fwd/A/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag05/01/1005/01/10132Genomicunknown
ss244276592ILLUMINA|CVDSNP55v1_A_rs12502572rev/BC/Tctgaagttttctagccttactctgagttgagcacatttagtacatgatcaacacataaac06/10/1006/10/10132Genomicunknown
ss277963846GMI|GMI_AK_SNP_2284079fwd/A/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag12/16/1012/16/10137Genomicunknown
ss293203196PJP|SNP_2709554_chr4_141704584fwd/A/Ggtttatgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaacttcag01/21/1101/21/11134Genomicunknown
ss557902873TISHKOFF|snp_chr4_141485134fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac11/22/1211/23/12138Genomicunknown
ss651721059SSMP|4_141485134fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac12/14/1202/10/15138Genomicunknown
ss980760387EVA-GONL|EVA-GONL_rs12502572fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac04/23/1404/24/14142Genomicunknown
ss1072019619JMKIDD_LAB|HGDP_WGS_chr4_141485134fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac07/10/1407/11/14142Genomicunknown
ss13121186351000GENOMES|PHASE3_V1_23727877fwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac08/16/1408/16/14142Genomicunknown
ss1397391084HAMMER_LAB|HAMMER_LAB_rs12502572fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac09/30/1409/30/14146Genomicunknown
ss1430074454DDI|DDI_rs12502572fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac11/04/1411/05/14144Genomicunknown
ss1580810101EVA_GENOME_DK|EVA_GENOME_DK_snv_rs12502572fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac02/19/1502/20/15144Genomicunknown
ss1590272514EVA_DECODE|EVA_DECODE_4_141704584_1116754_rs12502572fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac03/02/1503/03/15144Genomicunknown
ss1611332025EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_4_141485134_13127794fwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac03/04/1503/04/15144Genomicunknown
ss1654326058EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_4_141485134_13127794fwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac03/04/1503/04/15144Genomicunknown
ss1712711508EVA_SVP|EVA_SVP_405875fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac03/12/1503/12/15144Genomicunknown
ss1802306362HAMMER_LAB|Hsieh_2513293fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac07/15/1507/15/15146Genomicunknown
ss1924001444WEILL_CORNELL_DGM|SNV:chr4:141485134fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac10/16/1510/17/15147Genomicunknown
ss1969889926GENOMED|rs12502572fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac02/16/1602/16/16147Genomicunknown
ss2022588126JJLAB|SNP3090681fwd/TA/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac08/29/1608/30/16149Genomicunknown
ss2150719753USC_VALOUEV|NC_000004.11:g.141485134G>Afwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac11/17/1611/17/16150Genomicunknown
ss2267773734HUMAN_LONGEVITY|HLI-4-140563980-G-Afwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac11/18/1611/18/16150Genomicunknown
ss2435671963TOPMED|4_141485134_G/Afwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac11/20/1611/20/16150Genomicunknown
ss2625790642SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV1970107fwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac01/06/1701/06/17151Genomicunknown
ss2706211229GRF|rs12502572fwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac02/13/1702/13/17151Genomicunknown
ss2816128570GNOMAD|rs12502572fwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac05/18/1705/18/17151Genomicunknown
ss2995681002SWEGEN|NC_000004.11:g.141485134G>Afwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac05/30/1705/30/17151Genomicunknown
ss3025071356BIOINF_KMB_FNS_UNIBA|4.140563980G>Afwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac07/05/1707/05/17151Genomicunknown
ss3345998925CSHL|rs12502572fwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac10/02/1710/02/17151Genomicunknown
ss3444765679TOPMED|TOPMed_freeze_5?chr4:140,563,980-01fwd/A/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac10/04/1710/04/17151Genomicunknown
ss3444765680TOPMED|TOPMed_freeze_5?chr4:140,563,980-02fwd/C/Gtgtgttgatcatgtactaaatgtgctcaactcagagtaaggctagaaaac10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12502572|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/G'|mol=Genomic|build=151
 TTAGACCAGC TAAAATCTTG CTTCCTAAAC TAGGTGCTGC TATCCAGAGA GAAAAAAAAT
 TATTAAGAAA AAAAATTAAA GACCTAGAAT GCATGCATGT CTTTTTAATT TTCAGTGGTT
 CATATTTTTG TATTTTTTTT TTTTTTGAGA TGGAGTCTTG CTCTGTTATC TAGGCTAGAG
 TGCAGTGGTG TGATCTTGGC TCACTGCAAT CTCCGCCTCC CGGGTTCAAG AGATTCTCCT
 GCCTCAGCCT CCCAAGTAGC TGGGATTATA GGCACGTGCC ACCACAGCCT GCTAAGTTTT
 GTATTTTTAG TAGAGACAGG GTTTCACTAT ATTGGCCAGG CTAGTCTTGA ACTCCTGACC
 TCAGGTGATC CGTCTGCCTC GGCCTCCCAA AGTGCTAGGA TTACAGGTAT GAGCCACCCA
 CCTGGCCCAT ATTTTTGTAT TCTTACAGCT TTTCTATTTC TCTAATGCTT GTTTATGTGT
 TGATCATGTA CTAAATGTGC
 V
 TCAACTCAGA GTAAGGCTAG AAAACTTCAG GTGTCTGAAA TTTTTTAAAA ATGAAGACTT
 TCAAGGAACA AGAAAACACA ATGCTTATTT TCACAGTGGC CTGATTCTTT CCTGTGTTCA
 ACTTGGTTCT TTCCCACATT TAGCTCTCTT TTCAGTATTA TCCGACTGTG AGGAGGCACC
 CATCACCAAT GAGGCTTGAT CTTTCTCCCA CGAATGATCA TGTTAATTAT GGGACTTGGT
 GGCCTTAGAT GAAGCCCAGT GGACAAACTG CACCAAAATG GGCCATCAAG TAGTGTTAGG
 CTACAACATG TGAAGGGAAC AAAAATAAGA AGACAGGAGA GAAGAAAGTG ATTTTTGTCT
 TAAAATTTTG AAAAAAATAG CTTATGTTGC TCAAGACAGA TTTCATTAAG TACAAATAGT
 CTTGAAGCCC AATATTCATT TCTATCATTA AGTAAACATA AAATTAAGGT TCAGTAACAT
 TTACTCAGCA GAGACTTTCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_016606
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA
A/A
A/G
G
G/G
HWPA
G
ss117214899YRI 2IG 1.00000000 1.00000000
ss1312118635EAS 1008AF 0.520799990.47920001
EUR 1006AF 0.329000000.67100000
AFR 1322AF 0.751100000.24890001
AMR 694AF 0.433700000.56630003
SAS 978AF 0.484699990.51530004
ss161503308ENSEMBL_celera 4IG 1.00000000 1.00000000
ss164547927YRISub-Saharan African 2IG 1.00000000 1.00000000
ss167230662PGP 2IG 1.00000000 0.500000000.50000000
ss19570061HapMap-CEUEuropean 226IG 0.106194690.46902654 0.424778760.654721000.340707960.65929204
HapMap-HCBAsian 86IG 0.302325580.44186047 0.255813960.479500000.523255830.47674417
HapMap-JPTAsian 172IG 0.186046510.48837209 0.325581401.000000000.430232550.56976742
HapMap-YRISub-Saharan African 226IG 0.548672560.40707964 0.044247790.342782000.752212410.24778761
CHMJAsian 74IG0.36486486 0.63513511 0.364864860.63513511
HAPMAP-ASW 96IG 0.291666660.50000000 0.208333331.000000000.541666690.45833334
HAPMAP-CHBAsian 82IG 0.219512190.53658539 0.243902440.654721000.487804890.51219511
HAPMAP-CHD 168IG 0.214285720.53571427 0.250000000.527089000.482142870.51785713
HAPMAP-GIH 176IG 0.204545450.51136363 0.284090911.000000000.460227280.53977275
HAPMAP-LWK 180IG 0.566666660.37777779 0.055555561.000000000.755555570.24444444
HAPMAP-MEX 98IG 0.163265300.53061223 0.306122450.583882000.428571430.57142860
HAPMAP-MKK 286IG 0.524475510.36363637 0.111888110.150222000.706293700.29370630
HAPMAP-TSI 176IG 0.102272730.48863637 0.409090910.479500000.346590910.65340906
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss221254120pilot_1_YRI_low_coverage_panel 118AF 0.762711880.23728813
ss232630143pilot_1_CEU_low_coverage_panel 120AF 0.366666670.63333333
ss239870592pilot_1_CHB+JPT_low_coverage_panel 120AF 0.441666660.55833334
ss23995099AFD_EUR_PANELEuropean 46IG 0.130434780.39130434 0.478260870.654721000.326086970.67391306
AFD_AFR_PANELAfrican American 44IG 0.363636370.45454547 0.181818191.000000000.590909060.40909091
AFD_CHN_PANELAsian 48IG 0.208333330.54166669 0.250000000.751830000.479166660.52083331
ss44523393AoD_African_American 90AF 0.639999990.36000001
AoD_Caucasian 92AF 0.239999990.75999999
AoD_Chinese 90AF 0.569999990.43000001
AoD_Japanese 90AF 0.440000000.56000000
ss66451934HapMap-CEUEuropean 118IG 0.135593220.42372882 0.440677970.654721000.347457620.65254235
HapMap-HCBAsian 90IG 0.311111120.44444445 0.244444440.479500000.533333360.46666667
HapMap-JPTAsian 90IG 0.133333340.51111114 0.355555560.654721000.388888900.61111110
HapMap-YRISub-Saharan African 120IG 0.466666670.44999999 0.083333340.751830000.691666660.30833334
ss68913171HapMap-CEUEuropean 120IG 0.133333340.43333334 0.433333340.751830000.349999990.64999998
HapMap-HCBAsian 90IG 0.311111120.44444445 0.244444440.479500000.533333360.46666667
HapMap-JPTAsian 90IG 0.066666670.57777780 0.355555560.099721000.355555560.64444447
HapMap-YRISub-Saharan African 120IG 0.466666670.44999999 0.083333340.751830000.691666660.30833334
ss76242825ICMHP 6IG 0.33333334 0.66666669 0.333333340.66666669

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.499+/-0.0240000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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