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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.

rs3039191

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:855379-855381 (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
delAT / dupAT
Variation Type
Indel Insertion and Deletion
Frequency
TAT=0.435494 (115271/264690, TOPMED)
TAT=0.343514 (48081/139968, GnomAD)
TAT=0.33170 (6143/18520, ALFA) (+ 4 more)
TAT=0.38449 (6444/16760, 8.3KJPN)
TAT=0.1443 (535/3708, TWINSUK)
TAT=0.135 (81/600, NorthernSweden)
TAT=0.293 (61/208, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01128 : Non Coding Transcript Variant
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.855380_855381del
GRCh38.p13 chr 1 NC_000001.11:g.855380_855381dup
GRCh37.p13 chr 1 NC_000001.10:g.790760_790761del
GRCh37.p13 chr 1 NC_000001.10:g.790760_790761dup
Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01128 transcript variant 1 NR_047519.1:n.2710_2711del N/A Non Coding Transcript Variant
LINC01128 transcript variant 1 NR_047519.1:n.2710_2711dup N/A Non Coding Transcript Variant
LINC01128 transcript variant 3 NR_047521.1:n.2557_2558del N/A Non Coding Transcript Variant
LINC01128 transcript variant 3 NR_047521.1:n.2557_2558dup N/A Non Coding Transcript Variant
LINC01128 transcript variant 5 NR_047523.1:n.2461_2462del N/A Non Coding Transcript Variant
LINC01128 transcript variant 5 NR_047523.1:n.2461_2462dup N/A Non Coding Transcript Variant
LINC01128 transcript variant 7 NR_047524.1:n.2373_2374del N/A Non Coding Transcript Variant
LINC01128 transcript variant 7 NR_047524.1:n.2373_2374dup N/A Non Coding Transcript Variant
LINC01128 transcript variant 8 NR_047525.1:n.2424_2425del N/A Non Coding Transcript Variant
LINC01128 transcript variant 8 NR_047525.1:n.2424_2425dup N/A Non Coding Transcript Variant
LINC01128 transcript variant 9 NR_047526.1:n. N/A Genic Downstream Transcript Variant
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 18520 TAT=0.33170 T=0.66830
European Sub 14152 TAT=0.23961 T=0.76039
African Sub 2898 TAT=0.7591 T=0.2409
African Others Sub 114 TAT=0.851 T=0.149
African American Sub 2784 TAT=0.7554 T=0.2446
Asian Sub 112 TAT=0.304 T=0.696
East Asian Sub 86 TAT=0.34 T=0.66
Other Asian Sub 26 TAT=0.19 T=0.81
Latin American 1 Sub 146 TAT=0.479 T=0.521
Latin American 2 Sub 610 TAT=0.377 T=0.623
South Asian Sub 98 TAT=0.19 T=0.81
Other Sub 504 TAT=0.395 T=0.605


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
TopMed Global Study-wide 264690 TAT=0.435494 delAT=0.564506
gnomAD - Genomes Global Study-wide 139968 TAT=0.343514 delAT=0.656486
gnomAD - Genomes European Sub 75828 TAT=0.15285 delAT=0.84715
gnomAD - Genomes African Sub 41908 TAT=0.73447 delAT=0.26553
gnomAD - Genomes American Sub 13640 TAT=0.27287 delAT=0.72713
gnomAD - Genomes Ashkenazi Jewish Sub 3322 TAT=0.1613 delAT=0.8387
gnomAD - Genomes East Asian Sub 3128 TAT=0.2554 delAT=0.7446
gnomAD - Genomes Other Sub 2142 TAT=0.3053 delAT=0.6947
8.3KJPN JAPANESE Study-wide 16760 TAT=0.38449 delAT=0.61551
UK 10K study - Twins TWIN COHORT Study-wide 3708 TAT=0.1443 delAT=0.8557
Northern Sweden ACPOP Study-wide 600 TAT=0.135 delAT=0.865
A Vietnamese Genetic Variation Database Global Study-wide 208 TAT=0.293 delAT=0.707
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 TAT= delAT dupAT
GRCh38.p13 chr 1 NC_000001.11:g.855379_855381= NC_000001.11:g.855380_855381del NC_000001.11:g.855380_855381dup
GRCh37.p13 chr 1 NC_000001.10:g.790759_790761= NC_000001.10:g.790760_790761del NC_000001.10:g.790760_790761dup
LINC01128 transcript variant 6 NR_015368.2:n.2415_2417= NR_015368.2:n.2416_2417del NR_015368.2:n.2416_2417dup
LINC01128 transcript variant 1 NR_047519.1:n.2709_2711= NR_047519.1:n.2710_2711del NR_047519.1:n.2710_2711dup
LINC01128 transcript variant 2 NR_047520.1:n.2660_2662= NR_047520.1:n.2661_2662del NR_047520.1:n.2661_2662dup
LINC01128 transcript variant 3 NR_047521.1:n.2556_2558= NR_047521.1:n.2557_2558del NR_047521.1:n.2557_2558dup
LINC01128 transcript variant 4 NR_047522.1:n.2507_2509= NR_047522.1:n.2508_2509del NR_047522.1:n.2508_2509dup
LINC01128 transcript variant 5 NR_047523.1:n.2460_2462= NR_047523.1:n.2461_2462del NR_047523.1:n.2461_2462dup
LINC01128 transcript variant 8 NR_047525.1:n.2423_2425= NR_047525.1:n.2424_2425del NR_047525.1:n.2424_2425dup
LINC01128 transcript variant 7 NR_047524.1:n.2372_2374= NR_047524.1:n.2373_2374del NR_047524.1:n.2373_2374dup
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#.

48 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss4270295 Jan 05, 2002 (102)
2 ABI ss41194687 Mar 14, 2006 (126)
3 HGSV ss77875463 Dec 07, 2007 (129)
4 HGSV ss77927566 Dec 07, 2007 (129)
5 HGSV ss79750671 Dec 16, 2007 (130)
6 HUMANGENOME_JCVI ss95218893 Feb 06, 2009 (130)
7 BCMHGSC_JDW ss103475665 Dec 01, 2009 (131)
8 BGI ss105442307 Mar 15, 2016 (147)
9 GMI ss229263652 May 09, 2011 (134)
10 BL ss255892577 May 09, 2011 (138)
11 GMI ss287939323 May 04, 2012 (138)
12 PJP ss294562324 May 09, 2011 (138)
13 PJP ss294562325 May 09, 2011 (135)
14 1000GENOMES ss325997463 May 09, 2011 (138)
15 1000GENOMES ss498763845 May 04, 2012 (138)
16 LUNTER ss550903127 Apr 25, 2013 (138)
17 TISHKOFF ss553708529 Apr 25, 2013 (138)
18 SSMP ss663206419 Apr 01, 2015 (144)
19 BILGI_BIOE ss666079989 Apr 25, 2013 (138)
20 DDI ss1536213892 Apr 01, 2015 (144)
21 EVA_DECODE ss1584129587 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1709905383 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1709907313 Apr 01, 2015 (144)
24 GENOMED ss1966667350 Jul 19, 2016 (147)
25 JJLAB ss2030297738 Sep 14, 2016 (149)
26 SYSTEMSBIOZJU ss2624264812 Nov 08, 2017 (151)
27 GNOMAD ss2750640712 Nov 08, 2017 (151)
28 SWEGEN ss2986149339 Nov 08, 2017 (151)
29 MCHAISSO ss3063573514 Nov 08, 2017 (151)
30 MCHAISSO ss3063573515 Nov 08, 2017 (151)
31 MCHAISSO ss3064386015 Nov 08, 2017 (151)
32 MCHAISSO ss3065282497 Nov 08, 2017 (151)
33 MCHAISSO ss3065282498 Nov 08, 2017 (151)
34 TOPMED ss3066404074 Nov 08, 2017 (151)
35 BEROUKHIMLAB ss3644051491 Oct 11, 2018 (152)
36 BIOINF_KMB_FNS_UNIBA ss3645022412 Oct 11, 2018 (152)
37 URBANLAB ss3646581258 Oct 11, 2018 (152)
38 EVA_DECODE ss3685992370 Jul 12, 2019 (153)
39 ACPOP ss3726716477 Jul 12, 2019 (153)
40 PACBIO ss3783302184 Jul 12, 2019 (153)
41 PACBIO ss3788980057 Jul 12, 2019 (153)
42 PACBIO ss3793852594 Jul 12, 2019 (153)
43 KHV_HUMAN_GENOMES ss3798743791 Jul 12, 2019 (153)
44 EVA ss3825981500 Apr 25, 2020 (154)
45 EVA ss3836378456 Apr 25, 2020 (154)
46 EVA ss3841782458 Apr 25, 2020 (154)
47 TOPMED ss4436437996 Apr 25, 2021 (155)
48 TOMMO_GENOMICS ss5142052896 Apr 25, 2021 (155)
49 gnomAD - Genomes NC_000001.11 - 855379 Apr 25, 2021 (155)
50 Northern Sweden NC_000001.10 - 790759 Jul 12, 2019 (153)
51 8.3KJPN NC_000001.10 - 790759 Apr 25, 2021 (155)
52 TopMed NC_000001.11 - 855379 Apr 25, 2021 (155)
53 UK 10K study - Twins NC_000001.10 - 790760 Apr 25, 2020 (154)
54 A Vietnamese Genetic Variation Database NC_000001.10 - 790759 Jul 12, 2019 (153)
55 ALFA NC_000001.11 - 855379 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).

Associated ID History Updated (Build)
rs61627478 May 27, 2008 (130)
rs144200903 Sep 17, 2011 (135)
rs137938478 Apr 25, 2013 (138)
rs140340715 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77875463, ss77927566, ss79750671 NC_000001.8:830622:AT: NC_000001.11:855378:TAT:T (self)
ss255892577, ss287939323, ss294562324, ss325997463, ss550903127, ss1584129587 NC_000001.9:780621:TA: NC_000001.11:855378:TAT:T (self)
ss294562325 NC_000001.9:780622:AT: NC_000001.11:855378:TAT:T (self)
1342, 22203, 95, ss498763845, ss663206419, ss666079989, ss1966667350, ss2030297738, ss2624264812, ss2750640712, ss2986149339, ss3644051491, ss3726716477, ss3783302184, ss3788980057, ss3793852594, ss3825981500, ss3836378456, ss5142052896 NC_000001.10:790758:TA: NC_000001.11:855378:TAT:T (self)
457, ss553708529, ss1709905383, ss1709907313 NC_000001.10:790759:AT: NC_000001.11:855378:TAT:T (self)
69363, 20089, 44331, ss3063573514, ss3063573515, ss3064386015, ss3065282497, ss3065282498, ss3066404074, ss3645022412, ss3646581258, ss3685992370, ss3798743791, ss3841782458, ss4436437996 NC_000001.11:855378:TA: NC_000001.11:855378:TAT:T (self)
5654796912 NC_000001.11:855378:TAT:T NC_000001.11:855378:TAT:T (self)
ss105442307, ss229263652 NT_004350.19:269390:TA: NC_000001.11:855378:TAT:T (self)
ss4270295, ss41194687, ss95218893, ss103475665 NT_004350.19:269391:AT: NC_000001.11:855378:TAT:T (self)
ss1536213892 NC_000001.10:790758::TA NC_000001.11:855378:TAT:TATAT (self)
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 rs3039191

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