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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.

rs2980319

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:841742 (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
A>C / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.266538 (70550/264690, TOPMED)
A=0.266090 (37251/139994, GnomAD)
A=0.21419 (4046/18890, ALFA) (+ 14 more)
A=0.14976 (2510/16760, 8.3KJPN)
A=0.2528 (1266/5008, 1000G)
A=0.1238 (477/3854, ALSPAC)
A=0.1284 (476/3708, TWINSUK)
A=0.1519 (445/2930, KOREAN)
A=0.1567 (287/1832, Korea1K)
A=0.3322 (511/1538, HapMap)
A=0.144 (144/998, GoNL)
A=0.135 (81/600, NorthernSweden)
A=0.145 (77/530, SGDP_PRJ)
A=0.208 (45/216, Qatari)
A=0.079 (17/214, Vietnamese)
A=0.03 (1/40, GENOME_DK)
A=0.18 (4/22, Siberian)
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.841742A>C
GRCh38.p13 chr 1 NC_000001.11:g.841742A>T
GRCh37.p13 chr 1 NC_000001.10:g.777122A>C
GRCh37.p13 chr 1 NC_000001.10:g.777122A>T
Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01128 transcript variant 9 NR_047526.1:n.830A>C N/A Non Coding Transcript Variant
LINC01128 transcript variant 9 NR_047526.1:n.830A>T N/A Non Coding Transcript Variant
LINC01128 transcript variant 1 NR_047519.1:n. N/A Intron Variant
LINC01128 transcript variant 3 NR_047521.1:n. N/A Intron Variant
LINC01128 transcript variant 5 NR_047523.1:n. N/A Intron Variant
LINC01128 transcript variant 7 NR_047524.1:n. N/A Intron Variant
LINC01128 transcript variant 8 NR_047525.1:n. N/A Intron 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 18890 A=0.21419 T=0.78581
European Sub 14286 A=0.15015 T=0.84985
African Sub 2946 A=0.5268 T=0.4732
African Others Sub 114 A=0.623 T=0.377
African American Sub 2832 A=0.5230 T=0.4770
Asian Sub 112 A=0.098 T=0.902
East Asian Sub 86 A=0.09 T=0.91
Other Asian Sub 26 A=0.12 T=0.88
Latin American 1 Sub 146 A=0.329 T=0.671
Latin American 2 Sub 610 A=0.180 T=0.820
South Asian Sub 98 A=0.09 T=0.91
Other Sub 692 A=0.247 T=0.753


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 A=0.266538 T=0.733462
gnomAD - Genomes Global Study-wide 139994 A=0.266090 T=0.733910
gnomAD - Genomes European Sub 75882 A=0.14973 T=0.85027
gnomAD - Genomes African Sub 41886 A=0.52497 T=0.47503
gnomAD - Genomes American Sub 13630 A=0.19068 T=0.80932
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.1530 T=0.8470
gnomAD - Genomes East Asian Sub 3124 A=0.0980 T=0.9020
gnomAD - Genomes Other Sub 2152 A=0.2263 T=0.7737
8.3KJPN JAPANESE Study-wide 16760 A=0.14976 T=0.85024
1000Genomes Global Study-wide 5008 A=0.2528 T=0.7472
1000Genomes African Sub 1322 A=0.5635 T=0.4365
1000Genomes East Asian Sub 1008 A=0.1121 T=0.8879
1000Genomes Europe Sub 1006 A=0.1233 T=0.8767
1000Genomes South Asian Sub 978 A=0.173 T=0.827
1000Genomes American Sub 694 A=0.166 T=0.834
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.1238 T=0.8762
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.1284 T=0.8716
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.1519 C=0.0000, T=0.8481
Korean Genome Project KOREAN Study-wide 1832 A=0.1567 T=0.8433
HapMap Global Study-wide 1538 A=0.3322 T=0.6678
HapMap African Sub 686 A=0.531 T=0.469
HapMap American Sub 590 A=0.205 T=0.795
HapMap Europe Sub 172 A=0.081 T=0.919
HapMap Asian Sub 90 A=0.13 T=0.87
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.144 T=0.856
Northern Sweden ACPOP Study-wide 600 A=0.135 T=0.865
SGDP_PRJ Global Study-wide 530 A=0.145 T=0.855
Qatari Global Study-wide 216 A=0.208 T=0.792
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.079 T=0.921
The Danish reference pan genome Danish Study-wide 40 A=0.03 T=0.97
Siberian Global Study-wide 22 A=0.18 T=0.82
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 A= C T
GRCh38.p13 chr 1 NC_000001.11:g.841742= NC_000001.11:g.841742A>C NC_000001.11:g.841742A>T
GRCh37.p13 chr 1 NC_000001.10:g.777122= NC_000001.10:g.777122A>C NC_000001.10:g.777122A>T
LINC01128 transcript variant 9 NR_047526.1:n.830= NR_047526.1:n.830A>C NR_047526.1:n.830A>T
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#.

64 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4194530 Nov 05, 2001 (101)
2 CSHL-HAPMAP ss16406744 Feb 27, 2004 (120)
3 SSAHASNP ss20457220 Apr 05, 2004 (121)
4 PERLEGEN ss68756305 May 18, 2007 (127)
5 AFFY ss76547819 Dec 08, 2007 (130)
6 HGSV ss78175206 Dec 07, 2007 (129)
7 HUMANGENOME_JCVI ss97913233 Feb 03, 2009 (130)
8 KRIBB_YJKIM ss104885033 Feb 03, 2009 (130)
9 BGI ss105111697 Dec 01, 2009 (131)
10 1000GENOMES ss107938280 Jan 22, 2009 (130)
11 1000GENOMES ss109937314 Jan 24, 2009 (130)
12 ENSEMBL ss137752273 Dec 01, 2009 (131)
13 ENSEMBL ss138893697 Dec 01, 2009 (131)
14 GMI ss154522383 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss162980864 Jul 04, 2010 (132)
16 BUSHMAN ss197885462 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss205088646 Jul 04, 2010 (132)
18 1000GENOMES ss218190424 Jul 14, 2010 (132)
19 1000GENOMES ss230395477 Jul 14, 2010 (132)
20 1000GENOMES ss238114991 Jul 15, 2010 (132)
21 BL ss252864152 May 09, 2011 (134)
22 GMI ss275680872 May 04, 2012 (137)
23 GMI ss283987400 Apr 25, 2013 (138)
24 PJP ss290493806 May 09, 2011 (134)
25 TISHKOFF ss553710501 Apr 25, 2013 (138)
26 SSMP ss647516272 Apr 25, 2013 (138)
27 EVA-GONL ss974769440 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1067612359 Aug 21, 2014 (142)
29 1000GENOMES ss1289339560 Aug 21, 2014 (142)
30 DDI ss1425684884 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1573851173 Apr 01, 2015 (144)
32 EVA_DECODE ss1584129519 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1599378427 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1642372460 Apr 01, 2015 (144)
35 EVA_SVP ss1712305462 Apr 01, 2015 (144)
36 HAMMER_LAB ss1793705831 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1917960488 Feb 12, 2016 (147)
38 GENOMED ss1966667334 Jul 19, 2016 (147)
39 JJLAB ss2019498431 Sep 14, 2016 (149)
40 USC_VALOUEV ss2147484419 Dec 20, 2016 (150)
41 TOPMED ss2321503901 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2624264790 Nov 08, 2017 (151)
43 GRF ss2697374709 Nov 08, 2017 (151)
44 GNOMAD ss2750639422 Nov 08, 2017 (151)
45 SWEGEN ss2986149158 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023513713 Nov 08, 2017 (151)
47 TOPMED ss3066401363 Nov 08, 2017 (151)
48 CSHL ss3343272611 Nov 08, 2017 (151)
49 URBANLAB ss3646581230 Oct 11, 2018 (152)
50 EVA_DECODE ss3685992214 Jul 12, 2019 (153)
51 ACPOP ss3726716409 Jul 12, 2019 (153)
52 EVA ss3745721041 Jul 12, 2019 (153)
53 PACBIO ss3783302160 Jul 12, 2019 (153)
54 PACBIO ss3788980025 Jul 12, 2019 (153)
55 PACBIO ss3793852561 Jul 12, 2019 (153)
56 KHV_HUMAN_GENOMES ss3798743670 Jul 12, 2019 (153)
57 EVA ss3825981474 Apr 25, 2020 (154)
58 EVA ss3836378427 Apr 25, 2020 (154)
59 EVA ss3841782427 Apr 25, 2020 (154)
60 SGDP_PRJ ss3847995637 Apr 25, 2020 (154)
61 KRGDB ss3892835938 Apr 25, 2020 (154)
62 KOGIC ss3943629720 Apr 25, 2020 (154)
63 TOPMED ss4436434634 Apr 25, 2021 (155)
64 TOMMO_GENOMICS ss5142052411 Apr 25, 2021 (155)
65 1000Genomes NC_000001.10 - 777122 Oct 11, 2018 (152)
66 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 777122 Oct 11, 2018 (152)
67 The Danish reference pan genome NC_000001.10 - 777122 Apr 25, 2020 (154)
68 gnomAD - Genomes NC_000001.11 - 841742 Apr 25, 2021 (155)
69 Genome of the Netherlands Release 5 NC_000001.10 - 777122 Apr 25, 2020 (154)
70 HapMap NC_000001.11 - 841742 Apr 25, 2020 (154)
71 KOREAN population from KRGDB NC_000001.10 - 777122 Apr 25, 2020 (154)
72 Korean Genome Project NC_000001.11 - 841742 Apr 25, 2020 (154)
73 Northern Sweden NC_000001.10 - 777122 Jul 12, 2019 (153)
74 Qatari NC_000001.10 - 777122 Apr 25, 2020 (154)
75 SGDP_PRJ NC_000001.10 - 777122 Apr 25, 2020 (154)
76 Siberian NC_000001.10 - 777122 Apr 25, 2020 (154)
77 8.3KJPN NC_000001.10 - 777122 Apr 25, 2021 (155)
78 TopMed NC_000001.11 - 841742 Apr 25, 2021 (155)
79 UK 10K study - Twins NC_000001.10 - 777122 Oct 11, 2018 (152)
80 A Vietnamese Genetic Variation Database NC_000001.10 - 777122 Jul 12, 2019 (153)
81 ALFA NC_000001.11 - 841742 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)
rs56624891 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
13332, ss3892835938 NC_000001.10:777121:A:C NC_000001.11:841741:A:C (self)
ss78175206 NC_000001.8:816984:A:T NC_000001.11:841741:A:T (self)
ss76547819, ss107938280, ss109937314, ss162980864, ss197885462, ss205088646, ss252864152, ss275680872, ss283987400, ss290493806, ss1584129519, ss1712305462 NC_000001.9:766984:A:T NC_000001.11:841741:A:T (self)
4298, 353, 1358407, 480, 13332, 1274, 2418, 12617, 773, 21718, 353, 72, ss218190424, ss230395477, ss238114991, ss553710501, ss647516272, ss974769440, ss1067612359, ss1289339560, ss1425684884, ss1573851173, ss1599378427, ss1642372460, ss1793705831, ss1917960488, ss1966667334, ss2019498431, ss2147484419, ss2321503901, ss2624264790, ss2697374709, ss2750639422, ss2986149158, ss3343272611, ss3726716409, ss3745721041, ss3783302160, ss3788980025, ss3793852561, ss3825981474, ss3836378427, ss3847995637, ss3892835938, ss5142052411 NC_000001.10:777121:A:T NC_000001.11:841741:A:T (self)
66691, 66, 7721, 17934, 40969, 7257230204, ss3023513713, ss3066401363, ss3646581230, ss3685992214, ss3798743670, ss3841782427, ss3943629720, ss4436434634 NC_000001.11:841741:A:T NC_000001.11:841741:A:T (self)
ss4194530, ss68756305, ss97913233, ss104885033, ss105111697, ss137752273, ss138893697, ss154522383 NT_004350.19:255753:A:T NC_000001.11:841741:A:T (self)
ss16406744, ss20457220 NT_034471.3:255753:A:T NC_000001.11:841741:A:T (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 rs2980319

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