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Reference SNP (refSNP) Cluster Report: rs10151259                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:119/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (FWD)
Allele Origin:G:germline
T:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:T=0.2105/24638 (ExAC)
T=0.1673/838 (1000 Genomes)
T=0.2326/2792 (GO-ESP)
T=0.2038/25595 (TOPMED)
HGVS Names
  • CM000676.2:g.21321881G>T
  • NC_000014.8:g.21790040G>T
  • NC_000014.9:g.21321881G>T
  • NG_008933.1:g.38905G>T
  • NM_020366.3:c.1639G>T
  • NP_065099.3:p.Ala547Ser
  • XP_005267935.1:p.Ala192Ser
  • XP_005267936.1:p.Ala189Ser
  • XP_005267937.1:p.Ala189Ser
  • XP_005267938.1:p.Ala5Ser
  • XP_011535280.1:p.Ala189Ser
  • XP_011535281.1:p.Ala189Ser
  • XP_011535282.1:p.Ala189Ser
  • XP_011535283.1:p.Ala189Ser
  • XP_011535284.1:p.Ala189Ser
  • XP_016876962.1:p.Ala189Ser
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 ss286800872 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10151259 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
ss14010994WI_SSAHASNP|chr14.NT_026437.10_1710168fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa11/05/0311/22/03119Genomicunknown
ss23798169PERLEGEN|afd0150922byFreqfwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa08/10/0409/13/04123Genomicunknown
ss48415761APPLERA_GI|hCV25959602byFreqrev/TA/Ctttctttgtgatctctattatcattgtcagttttgtcatcattgcctccagttcctcctg09/28/0511/03/06130Genomicunknown
ss66569281ILLUMINA|HumanHap300v1.1_rs10151259fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa11/09/0611/09/06130Genomicunknown
ss66872892ILLUMINA|HumanHap550v1.1_rs10151259fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa11/14/0611/14/06130Genomicunknown
ss66952785ILLUMINA|HumanHap650Yv1.0_rs10151259fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa11/14/0611/14/06130Genomicunknown
ss69150279PERLEGEN|PGP00150922byFreqfwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa01/30/0703/31/08130Genomicunknown
ss74820540AFFY|SNP_M-323561fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa08/09/0708/09/07130Genomicunknown
ss76496375AFFY|AFFY_6_1M_SNP_A-8357405fwd/BG/Tggcaatgatgacaaaactgacaatgataatag08/28/0708/30/07129Genomicunknown
ss89871837BCMHGSC_JDW|JWB-0745177fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa02/26/0802/28/08129Genomicunknown
ss105106431KRIBB_YJKIM|KHS1498754rev/TA/Ctttctttgtgatctctattatcattgtcagttttgtcatcattgcctccagttcctcctg07/10/0807/11/08130Genomicunknown
ss1153812861000GENOMES|NA19240_2008_12_16_2691687_chr14_20859880fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa12/19/0812/19/08130Genomicunknown
ss133861880ENSEMBL|ENSSNP10847902fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa05/11/0905/15/09131Genomicunknown
ss161049210ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP14-20859880-0_T_R_1588117944rev/TA/Ctttctttgtgatctctattatcattgtcagttttgtcatcattgcctccagttcctcctg08/04/0910/05/09131Genomicunknown
ss168861418COMPLETE_GENOMICS|NA19240_36_chr14_20859880fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa10/01/0910/01/09132Genomicunknown
ss206971746BCM-HGSC-SUB|BCM_CMT_1011-2623878fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa03/15/1003/18/10132Genomicunknown
ss2264517611000GENOMES|pilot_1_YRI_8261444_chr14_20859880fwd/G/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa04/22/1004/22/10132Genomicunknown
ss2364550031000GENOMES|pilot_1_CEU_6059632_chr14_20859880fwd/G/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa05/01/1005/01/10132Genomicunknown
ss244239332OMICIA|2010_April_001_072_RPGRIP1_605446_0006fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa05/27/1005/28/10132Genomicunknown
ss254825674BL|SNP4224_14_20859880fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa08/19/1008/19/10134Genomicunknown
ss286800872GMI|GMI_NA10851_SNP_2813663fwd/G/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa12/17/1012/17/10138Genomicunknown
ss291680030PJP|SNP_1186388_chr14_20859880fwd/G/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa01/21/1101/21/11134Genomicunknown
ss295469658OMIM-CURATED-RECORDS|13189fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa01/24/1101/24/11133Genomicunknown
ss479434396ILLUMINA|HumanOmni1-Quad_v1-0_C_kgp7308110-0_T_R_1822056824fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa01/30/1208/28/15146Genomicunknown
ss483265685ILLUMINA|HumanOmni2.5-4v1_B_SNP14-20859880-0_T_R_1627607130fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa01/30/1210/28/16137Genomicunknown
ss483884966ILLUMINA|HumanOmni2.5-4v1_D_kgp7308110-0_T_R_1822056824fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa01/30/1210/27/16137Genomicunknown
ss4910648891000GENOMES|20110521_exome_572687_chr14_21790040fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa02/10/1202/22/12137Genomicunknown
ss491482366EXOME_CHIP|nonsyn_198592_chr_14_21790040fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa03/05/1203/05/12137Genomicunknown
ss491683994CLINSEQ_SNP|SNV-chr14-20859880byFreqfwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa03/06/1209/05/14137Genomicunknown
ss536079909ILLUMINA|HumanOmni5-4v1_B_kgp7308110-0_T_R_1822056824fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa06/22/1208/29/15146Genomicunknown
ss562045232RISN-LSDB|RISN-RPGRIP:c.1639G>Tfwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa11/23/1212/21/12137Genomicunknown
ss563959334TISHKOFF|snp_chr14_21790040fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa11/22/1211/23/12138Genomicunknown
ss659618739SSMP|14_21790040fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa12/14/1202/13/15138Genomicunknown
ss713165658NHLBI-ESP|ESP6500SI-chr14-21790040fwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa02/20/1302/20/13138Genomicunknown
ss779519468ILLUMINA|HumanOmni25Exome-8v1_A_kgp7308110-0_T_R_1822056824fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/30/1307/10/15146Genomicunknown
ss780699214ILLUMINA|HumanOmni25Exome-8v1_A_exm1086401-0_T_R_1922711176fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/30/1307/10/15146Genomicunknown
ss782386103ILLUMINA|HumanOmni2.5-4v1_H_kgp7308110-0_T_R_1822056824fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/30/1307/29/15146Genomicunknown
ss783373351ILLUMINA|HumanOmniExpressExome-8v1_A_exm1086401-0_T_R_1922711176fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/31/1306/18/15146Genomicunknown
ss794276704GENEREVIEWS|NM_020366.3:c.1639G>Tfwd/BG/Tcaggaggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaaagaaa06/07/1306/07/13137Genomicunknown
ss834989928ILLUMINA|HumanOmni2.5-8v1_A_kgp7308110-0_T_R_1822056824fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa09/18/1307/29/15146Genomicunknown
ss974487786JMKIDD_LAB|KhoeSan_Exomes_chr14_21790040fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa03/06/1403/06/14142Genomicunknown
ss990910039EVA-GONL|EVA-GONL_rs10151259fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa04/23/1404/25/14142Genomicunknown
ss1067543697JMKIDD_LAB|HGDP_exomes_chr14_21790040fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa07/09/1407/09/14142Genomicunknown
ss1079477261JMKIDD_LAB|HGDP_WGS_chr14_21790040fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa07/10/1407/12/14142Genomicunknown
ss13501263191000GENOMES|PHASE3_V1_63314790fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa08/16/1408/16/14142Genomicunknown
ss1397673402HAMMER_LAB|HAMMER_LAB_rs10151259fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa09/30/1409/30/14146Genomicunknown
ss1427351442DDI|DDI_rs10151259fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa11/04/1411/04/14144Genomicunknown
ss1577111035EVA_GENOME_DK|EVA_GENOME_DK_snv_rs10151259fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa02/19/1502/19/15144Genomicunknown
ss1584088482EVA_FINRISK|EVA_FINRISK_rs10151259fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa02/27/1502/27/15144Genomicunknown
ss1631275567EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_14_21790040_35037107fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa03/04/1503/04/15144Genomicunknown
ss1674269600EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_14_21790040_35037107fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa03/04/1503/04/15144Genomicunknown
ss1691389598EVA_EXAC|EVA_EXAC_6656394fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa03/04/1503/04/15144Genomicunknown
ss1694900088EVA_DECODE|EVA_DECODE_14_20859880_15203_rs10151259fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa03/02/1503/04/15144Genomicunknown
ss1711366188EVA_MGP|EVA_XIMO_481948fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa03/09/1503/09/15144Genomicunknown
ss1713428213EVA_SVP|EVA_SVP_1122580fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa03/12/1503/12/15144Genomicunknown
ss1934286539WEILL_CORNELL_DGM|SNV:chr14:21790040fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa10/16/1510/17/15147Genomicunknown
ss1959537205ILLUMINA|exm1086401-0_T_R_1922711176fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa11/13/1511/13/15147Genomicunknown
ss2027917241JJLAB|SNP8419796fwd/BG/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa08/29/1608/31/16149Genomicunknown
ss2156288219USC_VALOUEV|NC_000014.8:g.21790040G>Tfwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa11/17/1611/17/16150Genomicunknown
ss2200181264HUMAN_LONGEVITY|HLI-14-21321881-G-Tfwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa11/18/1611/18/16150Genomicunknown
ss2364454409TOPMED|14_21790040_G/Tfwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa11/19/1611/19/16150Genomicunknown
ss2633123502ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp7308110-0_T_R_182205682fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa02/02/1702/02/17151Genomicunknown
ss2740567790GNOMAD|exomes_rs10151259fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/17/1705/17/17151Genomicunknown
ss2749094377GNOMAD|coding_rs10151259fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/17/1705/17/17151Genomicunknown
ss2925194921GNOMAD|rs10151259fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/23/1705/23/17151Genomicunknown
ss2985014196AFFY|Axiom_PsorMich_Affx-10242209fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/24/1705/24/17151Genomicunknown
ss3011841114SWEGEN|NC_000014.8:g.21790040G>Tfwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa05/30/1705/30/17151Genomicunknown
ss3027780657BIOINF_KMB_FNS_UNIBA|14.21321881G>Tfwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa07/05/1707/05/17151Genomicunknown
ss3205446419TOPMED|TOPMed_freeze_5?chr14:21,321,881fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa10/01/1710/01/17151Genomicunknown
ss3350701383CSHL|rs10151259fwd/G/Tggaactggaggcaatgatgacaaaactgacaatgataatagagatcacaa10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs10151259|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 CAAAATCAAC GTGTGTTATC AGGTGCAAGG AAAGATGGTA CAGGAAGGGG ATGGATAACA
 GGAACGTGGG AACCACTCAC AGGACTGGGA ATGAAGCAAG ACCTAAGTTT CCAGGGCTGA
 TACCAGGTGA TGTGCTATCC TGAGCAAACA CACAATGGCT GTCCTTTGAA GAACTTGAGG
 ACTCACACAT GCCCACGGCA CCTTGGCACT AGGAGCCAGT GATGGGGCCA GCCCATGCCA
 ATGGCAAGCG TAAGGCTTCT GGGTTCAAAT TTTGCCAGTC CTAGGAACCA CCCTACCTCA
 ATGATAGCAC AACTAGTCTT GGAGGGGTCT GCAAGGAAAT CAAACCTTCT TCTAGTGGGT
 GAACCTGCCC AGCTAAGGAT AGCAGTCTTC TTGACCTAGC CAGTGCCACA TTTTTTATGC
 TCTTTGGTTT TAGGCCACTG AGATAGAAAA GTTCAGACAT TATTTTGTTT CAGGAGGAAC
 TGGAGGCAAT GATGACAAAA
 K
 CTGACAATGA TAATAGAGAT CACAAAGAAA AGCTGGAGAG GTTGACTCGA CTACTAGACC
 TCAAGAATAA CCGTATCAAG CAGCTGGAAG GTATTTTAAG AAGCCATGAC CTTCCAACAT
 CTGGCAAGTC TTAGTCCTTT GTTCTCCTCA CTTCGGGACC CTTCCACAGC TAACGCCTGT
 GTTCCACTCT GTGTACTTGT CAAGAAGGGT GCCTCTCATA CCCTTAGCAT ATGACTTATC
 CTTCTTGTTC TTTATCCTAT CATTTTTGTT GTTTTTTTTT GCTTGTTTGC TTTTGAGATG
 GAGTCTTGCT CTGTCACTCA GGCTGGAGTG CAGTGGTGCG ATCTTGGCTC ACTGCAACCT
 CTGCCTTCCA GGTTCAAGCG ATTCTCCTGC CTCAGCCTCC CAAGTAGCTG GGATGACAGT
 TGTCCACCAC CATGCCTGGC TAATTTTTTG TATTTTTAGT AGAGATGGGG TTTCACCATG
 TTGGCCAGGT TGGTCTGGAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_026437
dbSNP Blast Analysis
UniGene Cluster ID
126035
OMIM
605446.0006

  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/C
C/C
G/G
G/T
T/T
HWPA
C
G
T
ss133861880ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss1350126319EAS 1008AF 0.995999990.00400000
EUR 1006AF 0.763400020.23660001
AFR 1322AF 0.768499970.23150000
AMR 694AF 0.858799990.14119999
SAS 978AF 0.803700030.19630000
ss168861418YRISub-Saharan African 2IG 1.00000000 1.00000000
ss1691389598ExAc_Aggregated_Populations120830AF 0.794132230.20586775
ss226451761pilot_1_YRI_low_coverage_panel 118AF 0.703389820.29661018
ss236455003pilot_1_CEU_low_coverage_panel 120AF 0.824999990.17500000
ss48415761HapMap-CEUEuropean 226IG0.044247790.336283180.61946905 1.000000000.212389380.78761059
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 226IG0.061946900.407079640.53097343 0.654721000.265486720.73451328
AGI_ASP populationmultiple 74IG 0.567567590.43243244 0.31731000 0.783783790.21621622
HAPMAP-ASW 98IG0.081632650.346938790.57142860 0.583882000.255102040.74489796
HAPMAP-CHD 170IG 0.011764710.98823529 1.000000000.005882350.99411762
HAPMAP-GIH 176IG0.022727270.295454530.68181819 0.751830000.170454550.82954544
HAPMAP-LWK 180IG0.033333340.388888900.57777780 0.317310000.227777780.77222222
HAPMAP-MEX 100IG0.040000000.160000000.80000001 0.099721000.120000000.88000000
HAPMAP-MKK 286IG0.034965030.244755240.72027969 0.371093000.157342660.84265733
HAPMAP-TSI 176IG0.045454550.340909090.61363637 1.000000000.215909090.78409094
ss491683994CSAgilent 593GF 0.572000030.347000000.081000000.15022200 0.745500030.25450000
ss69150279HapMap-CEUEuropean 120IG 0.600000020.366666670.033333340.58388200 0.783333360.21666667
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 0.500000000.400000010.100000000.75183000 0.699999990.30000001

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.332+/-0.2360000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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