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dbSNP
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Reference SNP (refSNP) Cluster Report: rs138950                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:78/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
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:A=0.0409/205 (1000 Genomes)
A=0.0773/9705 (TOPMED)
HGVS Names
  • CM000684.2:g.43182780G>A
  • NC_000022.10:g.43578786G>A
  • NC_000022.11:g.43182780G>A
  • NM_015140.3:c.347+200C>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 ss8290624 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs138950 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
ss147341SC|dJ526I14_37230fwd/TA/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga06/12/0010/10/0378Genomicunknown
ss8290624SC_SNP|NT_011520.8_22781473fwd/TA/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga04/17/0310/10/03114Genomicunknown
ss80750555KRIBB_YJKIM|KHS1000282fwd/TA/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga11/26/0711/26/07130Genomicunknown
ss91933625BCMHGSC_JDW|JWB-1531697fwd/TA/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga02/26/0803/02/08129Genomicunknown
ss1126785461000GENOMES|CEU.trio.12.15.2008_3816688_chr22_41908730fwd/TA/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga12/17/0812/17/08130Genomicunknown
ss117420180ILLUMINA-UK|NA18507_000032572_NCBI36.1_chr22_41908730fwd/TA/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga01/19/0901/19/09130Genomic99 %
ss138361805ENSEMBL|ENSSNP11933911fwd/TA/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga05/15/0905/17/09131Genomicunknown
ss208839839BCM-HGSC-SUB|BCM_CMT_1011-3295274fwd/TA/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga03/15/1003/20/10132Genomicunknown
ss2380849251000GENOMES|pilot_1_CEU_7689554_chr22_41908730fwd/A/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga05/01/1005/01/10132Genomicunknown
ss292769791PJP|SNP_2276149_chr22_41908730fwd/A/Gtgggagaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgccacgga01/21/1101/21/11134Genomicunknown
ss566672737TISHKOFF|snp_chr22_43578786fwd/TA/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc11/22/1211/23/12138Genomicunknown
ss662602068SSMP|22_43578786fwd/TA/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc12/14/1202/14/15138Genomicunknown
ss995402565EVA-GONL|EVA-GONL_rs138950fwd/TA/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc04/23/1405/01/14142Genomicunknown
ss13673705371000GENOMES|PHASE3_V1_81271027fwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc08/16/1408/16/14142Genomicunknown
ss1579770382EVA_GENOME_DK|EVA_GENOME_DK_snv_rs138950fwd/TA/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc02/19/1502/20/15144Genomicunknown
ss1640100670EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_22_43578786_44766494fwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc03/04/1503/04/15144Genomicunknown
ss1683094703EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_22_43578786_44766494fwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc03/04/1503/04/15144Genomicunknown
ss1699473988EVA_DECODE|EVA_DECODE_22_41908730_206282_rs138950fwd/TA/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc03/02/1503/05/15144Genomicunknown
ss1809810695HAMMER_LAB|Hsieh_8842812fwd/TA/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc07/15/1507/16/15146Genomicunknown
ss1938970703WEILL_CORNELL_DGM|SNV:chr22:43578786fwd/TA/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc10/16/1510/19/15147Genomicunknown
ss2030258033JJLAB|SNP10760588fwd/TA/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc08/29/1608/31/16149Genomicunknown
ss2158879064USC_VALOUEV|NC_000022.10:g.43578786G>Afwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc11/17/1611/17/16150Genomicunknown
ss2247752436HUMAN_LONGEVITY|HLI-22-43182780-G-Afwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc11/18/1611/18/16150Genomicunknown
ss2974994226GNOMAD|rs138950fwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc05/23/1705/23/17151Genomicunknown
ss2985240888AFFY|Axiom_PsorMich_Affx-19697837fwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc05/24/1705/24/17151Genomicunknown
ss2985858628AFFY|Axiom_Smokesc1_Affx-19697837fwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc05/24/1705/24/17151Genomicunknown
ss3019390380SWEGEN|NC_000022.10:g.43578786G>Afwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc05/30/1705/30/17151Genomicunknown
ss3028964885BIOINF_KMB_FNS_UNIBA|22.43182780G>Afwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc07/05/1707/05/17151Genomicunknown
ss3352859580CSHL|rs138950fwd/A/Ggaggctctcaggccgcggtccatccgtcaccccaggaacgctgtgttgcc10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs138950|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CTGCCCAAAG AGCTGTGCGT GGACACAGGG GCCCAGCAAG TTTCTCTGAG GGTCCACAAA
 ACCTTTGGCA GATGGGCCTG CAGGCCTGAC CTAGGGATAG CCACTCTTGG TCCctggggg
 caggaagcct ggggtacagt ctcagctctg ccctaactac accgtggtcc ttggcaaggc
 caggcctgct ctgggtctca ggtcctcaGG TGTTCCAGGG CCCACCCCAG ATTCCAATTT
 AGCAGGACCA GAGAGGGGCT GTGACTGGGG AGGAGTAAGG CTGACCTGCA CCCTTAACCT
 GGAGGGTGAC CTCGAGCAAA ACTGGAACTT CTAATCCCCT GTAGCAGGAC CACTGTGACA
 ATGAGACCGC TGGGAGAGGC TCTCAGGCCG CGGTCCATCC
 R
 GTCACCCCAG GAACGCTGTG TTGCCACGGA CAGTACTCTG AAGCCCTGAT GGACACACCG
 CTGGCCACAC GTGCTTGCCA CAAAGCTGTC CTAAGGAAGA TGTCCAGCGG CGGTGCAGGG
 CCCAGGAGAA TCTGCATTAC TGCATCTCCC ACCTTTCACC AAGTGAAGGT TGTGGTGGTG
 TCTCTGGCCA GGCTCCTACC TGTTGGGGTG GGCTGCCTGG AGCCCGCTCT CCCTGGTCAC
 GATGACCTTG TAGCACAGCT CGTTCCCCGG GTTGGGCTGC TGCTTCCGCA CCTCCCGGGC
 TGCCTCGTCC TCCTCCTCTT CTACCTCCTC CACTTGCATG ATCCCAAACA CTTCCCCAGC
 GTCGAAAACC TGGGGGCCAG AGTTCCCGTC AGCAGGGGTG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
Z82214
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/G
G/G
HWPA
G
ss117420180YRI 2IG1.00000000 0.500000000.50000000
ss1367370537EAS 1008AF 0.001000000.99900001
EUR 1006AF 0.131200000.86880004
AFR 1322AF 0.018200000.98179996
AMR 694AF 0.040300000.95969999
SAS 978AF 0.020400000.97960001
ss138361805ENSEMBL_Watson 2IG1.00000000 0.500000000.50000000
ss238084925pilot_1_CEU_low_coverage_panel 120AF 0.200000000.80000001
ss80750555KHP1 176AF 1.00000000 1.00000000
KHP_Korean 176IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.079+/-0.1820000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN