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Reference SNP (refSNP) Cluster Report: rs2414739                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/149
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMed
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.3209/1607 (1000 Genomes)
HGVS Names
  • NC_000015.10:g.61701935G>A
  • NC_000015.9:g.61994134G>A
  • XR_001751569.1:n.77+13180C>T
Links , Linkout
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 ss282286589 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2414739 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
ss3381940TSC-CSHL|TSC1664685byFreqfwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg09/20/0104/07/04100Genomicunknown
ss21246596SSAHASNP|WGSA-200403-chr15.chr15.NT_010194.16_32784691fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg03/19/0403/19/04121Genomicunknown
ss23812432PERLEGEN|afd3078086byFreqfwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg08/10/0409/13/04123Genomicunknown
ss43770986ABI|hCV15800064fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg07/18/0507/18/05126Genomicunknown
ss65996768AFFY|SNP_A-1733999rev/BC/Taaagaccttctccgtgtccctagtaatgccaactgattcccactcgaggg10/26/0610/26/06127Genomicunknown
ss66743331ILLUMINA|HumanHap300v1.1_rs2414739fwd/BA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg11/09/0611/09/06127Genomicunknown
ss67252902ILLUMINA|HumanHap550v1.1_rs2414739fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg11/14/0611/14/06127Genomicunknown
ss67650838ILLUMINA|HumanHap650Yv1.0_rs2414739fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg11/14/0611/14/06127Genomicunknown
ss69178862PERLEGEN|PGP03078086byFreqfwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg01/30/0708/14/07127Genomicunknown
ss70731246ILLUMINA|HumanHap550v3.0__rs2414739rev/BC/Tcaaataaagaccttctccgtgtccctagtaatgccaactgattcccactcgaggggcttt04/20/0703/30/08130Genomicunknown
ss71300757ILLUMINA|HumanHap650Yv3.0_rs2414739fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg04/23/0704/23/07127Genomicunknown
ss75727268ILLUMINA|ILMN_Human_1M_rs2414739fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg08/28/0708/29/07129Genomicunknown
ss79134174ILLUMINA|HumanHap300v2.0_rs2414739fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg04/18/0711/18/07130Genomicunknown
ss84047092KRIBB_YJKIM|KHS613964fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg12/04/0712/06/07130Genomicunknown
ss84827229HGSV|Cor18517_SNV_20070510.chr15_59781426fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg12/06/0712/08/07130Genomicunknown
ss90183034BCMHGSC_JDW|JWB-0866667fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg02/26/0802/29/08129Genomicunknown
ss96764673HUMANGENOME_JCVI|1103645630691fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg03/27/0803/27/08130Genomicunknown
ss106435113BGI|BGI_rs2414739fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg09/15/0806/18/09130Genomicunknown
ss1088790531000GENOMES|CEU.trio.12.15.2008_3179373_chr15_59781426fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg12/16/0812/16/08130Genomicunknown
ss1142842751000GENOMES|NA19240_2008_12_16_2853166_chr15_59781426fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg12/18/0812/18/08130Genomicunknown
ss118256259ILLUMINA-UK|NA18507_000051398_NCBI36.1_chr15_59781426fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg01/20/0901/21/09130Genomic99 %
ss122030245ILLUMINA|HumanCNV370v1_C_rs2414739fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg04/14/0904/15/09131Genomicunknown
ss136384573ENSEMBL|ENSSNP7033747fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg05/11/0905/15/09131Genomicunknown
ss136881876ENSEMBL|ENSSNP1121862fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg12/08/0810/15/09131Genomicunknown
ss153910805ILLUMINA|Human610_Quadv1_B_rs2414739-127_B_R_1501717057rev/BC/Tcaaataaagaccttctccgtgtccctagtaatgccaactgattcccactcgaggggcttt06/18/0906/20/09131Genomicunknown
ss156632797GMI|GMI_SNP_35560194fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg06/24/0906/25/09131Genomicunknown
ss159388636ILLUMINA|Human660W-Quad_v1_A_rs2414739-128_B_R_1501717057rev/BC/Tcaaataaagaccttctccgtgtccctagtaatgccaactgattcccactcgaggggcttt07/06/0907/07/09131Genomicunknown
ss160545537ILLUMINA|HumanOmni1-Quad_v1-0_B_rs2414739-128_B_R_1501717057rev/BC/Tcaaataaagaccttctccgtgtccctagtaatgccaactgattcccactcgaggggcttt08/04/0910/03/09131Genomicunknown
ss168163921COMPLETE_GENOMICS|NA07022_36_chr15_59781426fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg09/30/0909/30/09132Genomicunknown
ss169693806COMPLETE_GENOMICS|NA19240_36_chr15_59781426fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg10/01/0910/01/09132Genomicunknown
ss171216647COMPLETE_GENOMICS|NA20431_36_chr15_59781426fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg10/01/0910/01/09132Genomicunknown
ss171248276ILLUMINA|HumanCNV370-Quadv3_C_rs2414739-127_B_R_1501717057rev/BC/Tcaaataaagaccttctccgtgtccctagtaatgccaactgattcccactcgaggggcttt10/01/0910/03/09132Genomicunknown
ss173334539ILLUMINA|Human1M-Duov3_B_rs2414739-127_B_R_1501717057rev/BC/Tcaaataaagaccttctccgtgtccctagtaatgccaactgattcccactcgaggggcttt10/01/0910/03/09132Genomicunknown
ss200935640BUSHMAN|BUSHMAN-chr15-59781425fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg02/16/1003/07/10132Genomicunknown
ss207209511BCM-HGSC-SUB|BCM_CMT_1011-2703006fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg03/15/1003/18/10132Genomicunknown
ss2269325911000GENOMES|pilot_1_YRI_8742274_chr15_59781426fwd/A/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg04/22/1004/22/10132Genomicunknown
ss2368068971000GENOMES|pilot_1_CEU_6411526_chr15_59781426fwd/A/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg05/01/1005/01/10132Genomicunknown
ss2431891131000GENOMES|pilot_1_CHB+JPT_5074190_chr15_59781426fwd/A/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg05/01/1005/01/10132Genomicunknown
ss255043545BL|SNP47982_15_59781426fwd/TA/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg08/19/1008/20/10134Genomicunknown
ss282286589GMI|GMI_AK_SNP_6606988fwd/A/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg12/16/1012/16/10137Genomicunknown
ss286967485GMI|GMI_NA10851_SNP_2980276fwd/A/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg12/17/1012/17/10138Genomicunknown
ss291735851PJP|SNP_1242209_chr15_59781426fwd/A/Gaaagcccctcgagtgggaatcagttggcattactagggacacggagaaggtctttatttg01/21/1101/21/11134Genomicunknown
ss480562555ILLUMINA|HumanOmni2.5-4v1_B_rs2414739-128_B_R_1772573412rev/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt01/30/1210/28/16137Genomicunknown
ss480576946ILLUMINA|HumanOmniExpress-12v1_C_rs2414739-131_B_R_1857227136rev/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt01/30/1210/27/16137Genomicunknown
ss481396415ILLUMINA|HumanOmni1-Quad_v1-0_C_rs2414739-131_B_R_1865699669fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt01/30/1208/28/15146Genomicunknown
ss485076865ILLUMINA|HumanOmni2.5-4v1_D_rs2414739-131_B_R_1857227136rev/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt01/30/1210/27/16137Genomicunknown
ss537088444ILLUMINA|HumanOmni5-4v1_B_rs2414739-131_B_R_1894820440fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt06/22/1208/29/15146Genomicunknown
ss564526497TISHKOFF|snp_chr15_61994134fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt11/22/1211/23/12138Genomicunknown
ss660257447SSMP|15_61994134fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt12/14/1202/13/15138Genomicunknown
ss778495485ILLUMINA|HumanOmni25Exome-8v1_A_rs2414739-131_B_R_1865699669fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt05/30/1307/10/15146Genomicunknown
ss782984720ILLUMINA|HumanOmni2.5-4v1_H_rs2414739-131_B_R_1857227136fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt05/30/1307/29/15146Genomicunknown
ss783945662ILLUMINA|HumanOmniExpressExome-8v1_A_rs2414739-131_B_R_1894820440fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt05/31/1306/18/15146Genomicunknown
ss825464692ILLUMINA|HumanCNV370v1_C_rs2414739-126_B_R_IFB1136168629:0fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt06/24/1311/21/14144Genomicunknown
ss832241372ILLUMINA|HumanOmniExpress-12v1_H_rs2414739-131_B_R_1857227136fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt09/17/1306/18/15146Genomicunknown
ss833951537ILLUMINA|HumanOmni2.5-8v1_A_rs2414739-131_B_R_1865699669fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt09/18/1307/29/15146Genomicunknown
ss991863599EVA-GONL|EVA-GONL_rs2414739fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt04/23/1404/30/14142Genomicunknown
ss1080186503JMKIDD_LAB|HGDP_WGS_chr15_61994134fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt07/10/1407/12/14142Genomicunknown
ss13537665031000GENOMES|PHASE3_V1_67110982fwd/A/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt08/16/1408/16/14142Genomicunknown
ss1427649981DDI|DDI_rs2414739fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt11/04/1411/04/14144Genomicunknown
ss1577661747EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2414739fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt02/19/1502/19/15144Genomicunknown
ss1633160246EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_15_61994134_37114382fwd/A/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt03/04/1503/04/15144Genomicunknown
ss1676154279EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_15_61994134_37114382fwd/A/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt03/04/1503/04/15144Genomicunknown
ss1695885015EVA_DECODE|EVA_DECODE_15_59781426_299594_rs2414739fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt03/02/1503/04/15144Genomicunknown
ss1713495993EVA_SVP|EVA_SVP_1190360fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt03/12/1503/12/15144Genomicunknown
ss1752166759ILLUMINA|OmniExpressExome-8v1-1_B_rs2414739-131_B_R_1894820440fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt05/27/1506/09/15146Genomicunknown
ss1808238455HAMMER_LAB|Hsieh_7263613fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt07/15/1507/16/15146Genomicunknown
ss1935270898WEILL_CORNELL_DGM|SNV:chr15:61994134fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt10/16/1510/18/15147Genomicunknown
ss1946395755ILLUMINA|HumanCoreExome-12v1-0_C_rs2414739-131_B_R_1894820440fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt10/29/1510/29/15147Genomicunknown
ss1959618480ILLUMINA|rs2414739-131_B_R_1894820440fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt11/13/1511/13/15147Genomicunknown
ss1968127408GENOMED|rs2414739fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt02/16/1602/16/16147Genomicunknown
ss2028415348JJLAB|SNP8917903fwd/TA/Gccctcgagtgggaatcagttggcattactagggacacggagaaggtcttt08/29/1608/31/16149Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2414739|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=149
 CTGTAAAAAT TACAGAAAAT CATTTAAATC TAAACATTCC AAAGTAGGAG AAGGTTAAGT
 AAACTCTGGG ACATACAGTC TATGTATATG GCCATTTACA TGATGTTTAC AAAGAGCATT
 TAACCAATTT TTTAAAATTG TTGAATTCTG GCCTAGCGTT TCCCGGTGAA GGTCAAAGTC
 CAAAATTAAT GCCAGAAAAA CAAGTGAAGG AAGCTTACCT ACTGTAAAAT TACATCACAC
 ATTCCAGGCA CTGGGGAGAT GAAATAGGTT TCAATAATAC ATGTCTATCT CTTCTCTCTA
 AAAGGGGTGC CCAGGAGTCC GTGCAATTGG CATTACCGGA AAAACATCAG CCAAGAAGGA
 AAAGACAATG GGGAACAGAT TTTGCCCTAA CCTTAACCCT AATTCTAAAA AATTTAGACA
 TTTCTAATAG TCATAACTGA CCAAAAGTCT TCAAATAGAA CAGTGAGGGC AAAGCCCCTC
 GAGTGGGAAT CAGTTGGCAT
 R
 TACTAGGGAC ACGGAGAAGG TCTTTATTTG TAAGGAGAAA AGTCCTGACT CCAACTTTTC
 ATAAACTAAC AATTTCAGTC CAAGACACTA AATTTTTAGT AACTTTTAGT AGAGTACTTT
 TTAAGATTCT ACTAAGTAAG CCTTAGTTCT ATACAGAAAC AGAAATGAAA AAAAGGGAAA
 ATAAAATCTT TCTACAGACA CAACATTTGT CAATAAGAAC CAAAGAAAAG GAATGGAATT
 TAAAATCAAA TCAGGAAGTT GAACACAAAT CAAGCTTTAA GAACCACTAG ATAAAACCAG
 GATCTTTTCC TTTTCTTCTC AGTTAGCATA GCAGGGGTTG GCTGTAGCTG GGAGCCTATG
 TCATCAATGC TGCTCTGCTG CTCTCCCTAA GATATCTAGG GATTCCAGGG AAGACACAAT
 CTGCGATGTC AGCATCAGCT GTCTCCTGTG ATGCAGCAGA CAGAAGGCAG ACAGGCAGAG
 ACAGCCATCC AAATAACACT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010194 ABBA01038931
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/G
G/G
HWPA
G
ss118256259YRI 2IG 1.00000000 0.500000000.50000000
ss1353766503EAS 1008AF 0.806500020.19350000
EUR 1006AF 0.720699970.27930000
AFR 1322AF 0.481799990.51820004
AMR 694AF 0.780999960.21899998
SAS 978AF 0.699400010.30059999
ss136384573ENSEMBL_Watson 2IG1.00000000 1.00000000
ss136881876ENSEMBL_Venter 2IG1.00000000 1.00000000
ss168163921CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss169693806YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss171216647PGP 2IG 1.00000000 0.500000000.50000000
ss226932591pilot_1_YRI_low_coverage_panel 118AF 0.550847470.44915253
ss236806897pilot_1_CEU_low_coverage_panel 120AF 0.716666640.28333333
ss23812432AFD_EUR_PANELEuropean 46IG0.434782590.521739130.043478260.273322000.695652190.30434781
AFD_AFR_PANELAfrican American 42IG0.285714300.571428600.142857150.479500000.571428600.42857143
AFD_CHN_PANELAsian 46IG0.739130440.26086956 0.751830000.869565190.13043478
ss243189113pilot_1_CHB+JPT_low_coverage_panel 120AF 0.816666660.18333334
ss3381940AfAmAfrican American 12IG0.166666670.666666690.16666667 0.500000000.50000000
CaucasianEuropean 24IG0.583333310.333333340.083333340.751830000.750000000.25000000
AsianAsian 12IG0.666666690.33333334 0.833333310.16666667
CEPHEuropean 10IG0.800000010.20000000 0.899999980.10000000
PDpanelGlobal 48IG0.291666660.458333340.250000000.751830000.520833310.47916666
HapMap-CEUEuropean 226IG0.539823000.398230080.061946900.751830000.738938030.26106194
HapMap-HCBAsian 86IG0.790697690.162790700.046511630.099721000.872093020.12790698
HapMap-JPTAsian 172IG0.616279070.337209310.046511631.000000000.784883740.21511628
HapMap-YRISub-Saharan African 226IG0.212389380.522123870.265486720.654721000.473451320.52654868
HAPMAP-ASW 98IG0.204081640.673469360.122448980.020022000.540816310.45918366
HAPMAP-CHBAsian 82IG0.609756110.39024389 0.371093000.804878060.19512194
HAPMAP-CHD 170IG0.647058840.282352950.070588240.200325000.788235310.21176471
HAPMAP-GIH 176IG0.443181810.420454530.136363640.527089000.653409060.34659091
HAPMAP-LWK 180IG0.322222230.455555560.222222220.479500000.550000010.44999999
HAPMAP-MEX 100IG0.620000000.38000000 0.342782000.810000000.19000000
HAPMAP-MKK 286IG0.601398590.363636370.034965030.402784000.783216770.21678321
HAPMAP-TSI 176IG0.534090940.397727280.068181821.000000000.732954560.26704547
ss69178862HapMap-CEUEuropean 120IG0.483333320.466666670.050000000.250592000.716666640.28333333
HapMap-HCBAsian 90IG0.800000010.155555560.044444450.099721000.877777760.12222222
HapMap-JPTAsian 90IG0.644444470.311111120.044444451.000000000.800000010.20000000
HapMap-YRISub-Saharan African 120IG0.250000000.550000010.200000000.438578000.524999980.47499999
ss96764673J. Craig Venter 2IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.436+/-0.167131811062820ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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