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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs199639004

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:72120-72131 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
dupTA / dupTATA / dup(TA)3 / dup(T…

dupTA / dupTATA / dup(TA)3 / dup(TA)4

Variation Type
Indel Insertion and Deletion
Frequency
dupTA=0.00097 (85/87836, GnomAD)
dupTA=0.00000 (0/10826, ALFA)
dupTATA=0.00000 (0/10826, ALFA) (+ 3 more)
dup(TA)3=0.00000 (0/10826, ALFA)
dup(TA)4=0.00000 (0/10826, ALFA)
dupTA=0.0132 (24/1812, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 1 NC_000001.11:g.72120TA[7]
GRCh38.p13 chr 1 NC_000001.11:g.72120TA[8]
GRCh38.p13 chr 1 NC_000001.11:g.72120TA[9]
GRCh38.p13 chr 1 NC_000001.11:g.72120TA[10]
GRCh37.p13 chr 1 NC_000001.10:g.72120TA[7]
GRCh37.p13 chr 1 NC_000001.10:g.72120TA[8]
GRCh37.p13 chr 1 NC_000001.10:g.72120TA[9]
GRCh37.p13 chr 1 NC_000001.10:g.72120TA[10]
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 10826 TATATATATATA=1.00000 TATATATATATATA=0.00000, TATATATATATATATA=0.00000, TATATATATATATATATA=0.00000, TATATATATATATATATATA=0.00000
European Sub 6682 TATATATATATA=1.0000 TATATATATATATA=0.0000, TATATATATATATATA=0.0000, TATATATATATATATATA=0.0000, TATATATATATATATATATA=0.0000
African Sub 2798 TATATATATATA=1.0000 TATATATATATATA=0.0000, TATATATATATATATA=0.0000, TATATATATATATATATA=0.0000, TATATATATATATATATATA=0.0000
African Others Sub 108 TATATATATATA=1.000 TATATATATATATA=0.000, TATATATATATATATA=0.000, TATATATATATATATATA=0.000, TATATATATATATATATATA=0.000
African American Sub 2690 TATATATATATA=1.0000 TATATATATATATA=0.0000, TATATATATATATATA=0.0000, TATATATATATATATATA=0.0000, TATATATATATATATATATA=0.0000
Asian Sub 100 TATATATATATA=1.00 TATATATATATATA=0.00, TATATATATATATATA=0.00, TATATATATATATATATA=0.00, TATATATATATATATATATA=0.00
East Asian Sub 76 TATATATATATA=1.00 TATATATATATATA=0.00, TATATATATATATATA=0.00, TATATATATATATATATA=0.00, TATATATATATATATATATA=0.00
Other Asian Sub 24 TATATATATATA=1.00 TATATATATATATA=0.00, TATATATATATATATA=0.00, TATATATATATATATATA=0.00, TATATATATATATATATATA=0.00
Latin American 1 Sub 140 TATATATATATA=1.000 TATATATATATATA=0.000, TATATATATATATATA=0.000, TATATATATATATATATA=0.000, TATATATATATATATATATA=0.000
Latin American 2 Sub 582 TATATATATATA=1.000 TATATATATATATA=0.000, TATATATATATATATA=0.000, TATATATATATATATATA=0.000, TATATATATATATATATATA=0.000
South Asian Sub 82 TATATATATATA=1.00 TATATATATATATA=0.00, TATATATATATATATA=0.00, TATATATATATATATATA=0.00, TATATATATATATATATATA=0.00
Other Sub 442 TATATATATATA=1.000 TATATATATATATA=0.000, TATATATATATATATA=0.000, TATATATATATATATATA=0.000, TATATATATATATATATATA=0.000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 87836 -

No frequency provided

dupTA=0.00097
gnomAD - Genomes European Sub 40598 -

No frequency provided

dupTA=0.00025
gnomAD - Genomes African Sub 32486 -

No frequency provided

dupTA=0.00046
gnomAD - Genomes American Sub 8770 -

No frequency provided

dupTA=0.0007
gnomAD - Genomes East Asian Sub 2990 -

No frequency provided

dupTA=0.0174
gnomAD - Genomes Ashkenazi Jewish Sub 1666 -

No frequency provided

dupTA=0.0000
gnomAD - Genomes Other Sub 1326 -

No frequency provided

dupTA=0.0015
Korean Genome Project KOREAN Study-wide 1812 -

No frequency provided

dupTA=0.0132
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement (TA)6= dupTA dupTATA dup(TA)3 dup(TA)4
GRCh38.p13 chr 1 NC_000001.11:g.72120_72131= NC_000001.11:g.72120TA[7] NC_000001.11:g.72120TA[8] NC_000001.11:g.72120TA[9] NC_000001.11:g.72120TA[10]
GRCh37.p13 chr 1 NC_000001.10:g.72120_72131= NC_000001.10:g.72120TA[7] NC_000001.10:g.72120TA[8] NC_000001.10:g.72120TA[9] NC_000001.10:g.72120TA[10]
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

12 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss498763761 May 04, 2012 (137)
2 SWEGEN ss2986142173 Nov 08, 2017 (151)
3 SWEGEN ss2986142174 Nov 08, 2017 (151)
4 SWEGEN ss2986142175 Nov 08, 2017 (151)
5 TOPMED ss3066324176 Nov 08, 2017 (151)
6 TOPMED ss3066324177 Nov 08, 2017 (151)
7 TOPMED ss3066324178 Nov 08, 2017 (151)
8 TOPMED ss3066324179 Nov 08, 2017 (151)
9 KOGIC ss3943622810 Apr 25, 2020 (154)
10 GNOMAD ss3986892624 Apr 25, 2021 (155)
11 TOMMO_GENOMICS ss5142033532 Apr 25, 2021 (155)
12 TOMMO_GENOMICS ss5142033533 Apr 25, 2021 (155)
13 gnomAD - Genomes NC_000001.11 - 72120 Apr 25, 2021 (155)
14 Korean Genome Project NC_000001.11 - 72120 Apr 25, 2020 (154)
15 8.3KJPN

Submission ignored due to conflicting rows:
Row 2839 (NC_000001.10:72119::TA 90/16494)
Row 2840 (NC_000001.10:72119::TATA 21/16494)

- Apr 25, 2021 (155)
16 8.3KJPN

Submission ignored due to conflicting rows:
Row 2839 (NC_000001.10:72119::TA 90/16494)
Row 2840 (NC_000001.10:72119::TATA 21/16494)

- Apr 25, 2021 (155)
17 ALFA NC_000001.11 - 72120 Apr 25, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss498763761, ss2986142175, ss5142033532 NC_000001.10:72119::TA NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATA

(self)
6799, 811, ss3066324176, ss3943622810, ss3986892624 NC_000001.11:72119::TA NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATA

(self)
9210000063 NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATA

NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATA

ss2986142173, ss5142033533 NC_000001.10:72119::TATA NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATA

(self)
ss3066324177 NC_000001.11:72119::TATA NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATA

(self)
9210000063 NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATA

NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATA

ss2986142174 NC_000001.10:72119::TATATA NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATATA

(self)
ss3066324178 NC_000001.11:72119::TATATA NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATATA

(self)
9210000063 NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATATA

NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATATA

ss3066324179 NC_000001.11:72119::TATATATA NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATATATA

(self)
9210000063 NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATATATA

NC_000001.11:72119:TATATATATATA:TA…

NC_000001.11:72119:TATATATATATA:TATATATATATATATATATA

Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs199639004

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad