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Reference SNP (refSNP) Cluster Report: rs3752484                 ** With untested allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/T (FWD)
Allele Origin:A:unknown
T:germline
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:With untested allele [ClinVar]
MAF/MinorAlleleCount:T=0.4289/1619 (1000 Genomes)
A=0.4711/59158 (TOPMED)
HGVS Names
  • CM000685.2:g.18620084T>A
  • NC_000023.10:g.18638204T>A
  • NC_000023.11:g.18620084T>A
  • NG_008475.1:g.199480T>A
  • NM_001037343.1:c.2376+118T>A
  • NM_001323289.1:c.2376+118T>A
  • NM_003159.2:c.2376+118T>A
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 ss283705454 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3752484 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
ss4938512YUSUKE|IMS-JST104656fwd/TA/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc08/01/0210/10/03107Genomicunknown
ss8181488SC_SNP|NT_011586.9_1110792byFreqfwd/TA/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc04/16/0308/05/04114Genomicunknown
ss8528159SC_SNP|NT_011757.12_5552671fwd/TA/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc05/23/0310/10/03116Genomicunknown
ss18035986CSHL-HAPMAP|CSHL-HuCC-200402.chrX.NT_011757.13_14604769fwd/TA/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc02/19/0403/04/04120Genomicunknown
ss23823888PERLEGEN|afd3867129byFreqfwd/TA/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc08/10/0409/13/04123Genomicunknown
ss43539822ABI|hCV342496byFreqfwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc07/18/0511/03/06126Genomicunknown
ss61706081SI_EXO|NT_011757.14_14604769fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc07/11/0608/17/06127Genomicunknown
ss65792266ILLUMINA|Human1-rs3752484fwd/TA/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc10/10/0610/10/06127Genomicunknown
ss76820908AFFY|AFFY_6_1M_SNP_A-8682382rev/A/Tgacataatacagtgcaaaatgtcaagtctcaa08/28/0708/30/07129Genomicunknown
ss83522817HGSV|Cor18956_SNV_20070510.chrX_18397861fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc11/30/0712/05/07130Genomicunknown
ss85497982HGSV|Cor19129_SNV_20070510.chrX_18397861fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc12/06/0712/09/07130Genomicunknown
ss85638320HGSV|Cor18517_SNV_20070510.chrX_18397861fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc12/06/0712/09/07130Genomicunknown
ss104887421KRIBB_YJKIM|KHS1279739fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc07/10/0807/10/08130Genomicunknown
ss105717300BGI|BGI_rs3752484fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc09/10/0806/18/09130Genomicunknown
ss115596075ILLUMINA-UK|NA18507_000013480_NCBI36.1_chrX_18548125fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc01/15/0901/15/09130Genomic99 %
ss157371133GMI|GMI_SNP_72930286fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc06/24/0906/25/09131Genomicunknown
ss161780654ENSEMBL|ENSSNP3116097byFreqfwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc09/24/0903/07/10131Genomicunknown
ss163048863COMPLETE_GENOMICS|NA07022_36_chrX_18548125fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc09/29/0909/29/09132Genomicunknown
ss204172495BUSHMAN|BUSHMAN-chrX-18548124fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc02/16/1003/10/10132Genomicunknown
ss208883658BCM-HGSC-SUB|BCM_CMT_1011-3339093fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc03/15/1003/20/10132Genomicunknown
ss283705454GMI|GMI_AK_SNP_8025897fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc12/16/1012/16/10137Genomicunknown
ss294530827PJP|SNP_4037185_chrX_18548125fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc01/21/1101/21/11134Genomicunknown
ss3413409541000GENOMES|20100804_snps_92658_chrX_18638204fwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc03/23/1103/23/11134Genomicunknown
ss538296843CHWRETT|CDKL5: c.2376+118T>Afwd/A/Ttgattgttttcttattgagacttgacattttgcactgtattatgtctctttctgaaattc08/08/1208/08/12137Genomicunknown
ss566785254TISHKOFF|snp_chrX_18638204fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga11/22/1211/23/12138Genomicunknown
ss662716956SSMP|X_18638204fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga12/14/1202/14/15138Genomicunknown
ss1082815236JMKIDD_LAB|HGDP_WGS_chrX_18638204fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga07/10/1407/12/14142Genomicunknown
ss1432011046DDI|DDI_rs3752484fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga11/04/1411/05/14144Genomicunknown
ss15536871961000GENOMES|PHASE3_chrX_461020byFreqfwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga08/16/1408/07/15144Genomicunknown
ss1583339781EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3752484fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga02/19/1502/20/15144Genomicunknown
ss1640416070EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_X_18638204_45113964fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga03/04/1503/04/15144Genomicunknown
ss1683410103EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_X_18638204_45113964fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga03/04/1503/04/15144Genomicunknown
ss1939182691WEILL_CORNELL_DGM|SNV:chrX:18638204fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga10/16/1510/19/15147Genomicunknown
ss1971350029GENOMED|rs3752484fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga02/16/1602/16/16147Genomicunknown
ss2158968666USC_VALOUEV|NC_000023.10:g.18638204T>Afwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga11/17/1611/17/16150Genomicunknown
ss2316005007HUMAN_LONGEVITY|HLI-X-18620084-T-Afwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga11/18/1611/18/16150Genomicunknown
ss2629672795SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV6916365fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga01/06/1701/06/17151Genomicunknown
ss2710097113GRF|rs3752484fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga02/13/1702/13/17151Genomicunknown
ss2976935527GNOMAD|rs3752484fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga05/23/1705/23/17151Genomicunknown
ss3019695015SWEGEN|NC_000023.10:g.18638204T>Afwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga05/30/1705/30/17151Genomicunknown
ss3029014369BIOINF_KMB_FNS_UNIBA|X.18620084T>Afwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga07/05/1707/05/17151Genomicunknown
ss3606387996TOPMED|TOPMed_freeze_5?chrX:18,620,084fwd/A/Tgttttcttattgagacttgacattttgcactgtattatgtctctttctga10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3752484|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=151
 CTGAGGTCTT CAACAGCATG GAAATAGTCT TGCAGCAACA GTTACAGGTC ATATAATGCT
 CAAATTGCTC TTTTGAGTGA GCCTGTGCCA GAGGATAATC ACTAACCATG GTTGATTAAA
 TTTAGTTCCT CCTGTGCTTT TTTAGAGGCT CTTTACCCAA GTGTTTGATT CTTCCCGGCT
 ATAGGAACCT AGTGTCATGC ATTTTCAGTC CTTATTATAT TTGTCACACA ATGGCAAGAA
 AATGATTGAA AAATCAATAT GATAAAAATG TCTTCTCATT TAGGAAAAGT CCTGAAAATA
 TTAGTCATTC AGAGCAACTC AAGGAAAAAG AGAAGCAAGG ATTTTTCAGG TCAATGAAAA
 AGAAAAAGAA GAAATCTCAA ACAGTAAGTA GATGACCAGT TTCTATATAT AATAACATGT
 TTCTGCATTA TTCAATGGAT ACTTTACACT TTGCACTTGG CAATCAAAGT TGATTGTTTT
 CTTATTGAGA CTTGACATTT
 W
 TGCACTGTAT TATGTCTCTT TCTGAAATTC TTTACAACTA TCCTCTCAAC AGAGCCTTTT
 CTACATTCAA CAGAATCTCC AGGAATAGAA GAAATTTAAT TTGGATGACA GAGAACACTT
 TAAGCCTTTC TCAATATACT TCTTATCTAT GTGGGCTTAT ATTAATGTAA AAACTTTGAA
 GACACAGGAT TTGTTTCTCT CTGGGGATTT AAAGATATGC ATAAACTTAG GAAATGGGTT
 TTGGTTTACT TTTAAATGTT GAAATTTGTA AATAACCATC ATTCCTTATT CTCTCCTGGC
 TGGTTACAGA ATTCCTACGT TGCCAGGTGT GTTTCTGAGT TATATAGTCA CAAAGATCGT
 ATCTGGGATT TTAGGGCTTG CGTTAGAAGG AAAATATGTT TGCCTTTTGA TCGCGCTGTG
 GGTTGGAATG CACCTTATCT CCTGGGAGCC CTTTGCCTGA ACAAAGAGCT GGCTCCATGG
 GACCGTTCAC ATCACTTCAC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
Z92542.2
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.
Source0/A
0/T
A
A/A
A/T
T
T/T
HWP0
A
T
ss115596075YRI 2IG 1.00000000 1.00000000
ss1553687196EAS 1008AF 0.517899990.48209998
EUR 1006AF 0.244500000.75550002
AFR 1322AF 0.512899990.48710003
AMR 694AF 0.491399970.50860000
SAS 978AF 0.377299990.62270004
ss161780654ENSEMBL_celera 4IG 0.50000000 0.50000000 0.500000000.50000000
ss163048863CEUEuropean 1IG 1.00000000 1.00000000
ss23823888AFD_EUR_PANELEuropean 46IG0.173913050.34782609 0.086956520.17391305 0.217391300.449329000.260869560.260869560.47826087
AFD_AFR_PANELAfrican American 46IG0.304347810.17391305 0.217391300.13043478 0.173913050.150318000.239130440.434782590.32608697
AFD_CHN_PANELAsian 48IG 0.416666660.29166666 0.291666660.05004300 0.562500000.43750000
ss43539822AoD_African_American 90AF 0.680000010.31999999
AoD_Caucasian 92AF 0.270000010.73000002
AoD_Chinese 90AF 0.680000010.31999999
AoD_Japanese 90AF 0.690000000.31000000
ss8181488HapMap-CEUEuropean 224IG 0.196428570.25892857 0.544642870.00100000 0.325892870.67410713
HapMap-HCBAsian 86IG 0.581395330.23255815 0.186046510.00499800 0.697674390.30232558
HapMap-JPTAsian 172IG 0.546511650.20930232 0.244186040.00100000 0.651162800.34883720
HapMap-YRISub-Saharan African 222IG 0.594594600.21621622 0.189189200.00100000 0.702702700.29729730
CHMJAsian 74IG 0.71621621 0.28378379 0.716216210.28378379
HAPMAP-ASW 98IG 0.448979590.22448979 0.326530610.00100000 0.561224460.43877551
HAPMAP-CHBAsian 82IG 0.634146330.26829270 0.097560970.15022200 0.768292670.23170732
HAPMAP-CHD 170IG 0.658823550.24705882 0.094117650.02002200 0.782352920.21764706
HAPMAP-GIH 176IG 0.295454530.26136363 0.443181810.00100000 0.426136370.57386363
HAPMAP-LWK 178IG 0.730337080.20224719 0.067415730.01002800 0.831460650.16853933
HAPMAP-MEX 100IG 0.680000010.16000000 0.160000000.00100000 0.759999990.23999999
HAPMAP-MKK 284IG 0.507042230.25352111 0.239436630.00100000 0.633802830.36619717
HAPMAP-TSI 172IG 0.220930230.27906978 0.500000000.00100000 0.360465110.63953489

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.490+/-0.0700000

  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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