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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.

rs3131984

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:779968 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000057 (15/264690, TOPMED)
T=0.000086 (12/140280, GnomAD)
T=0.00005 (1/18520, ALFA) (+ 12 more)
T=0.00000 (0/16760, 8.3KJPN)
T=0.0000 (0/5008, 1000G)
T=0.0000 (0/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.0003 (1/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.000 (0/600, NorthernSweden)
T=0.000 (0/558, SGDP_PRJ)
T=0.000 (0/216, Qatari)
T=0.000 (0/214, Vietnamese)
T=0.00 (0/40, GENOME_DK)
T=0.0 (0/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Intron Variant
LOC100288069 : 2KB Upstream 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.779968T>C
GRCh38.p13 chr 1 NC_000001.11:g.779968T>G
GRCh37.p13 chr 1 NC_000001.10:g.715348T>C
GRCh37.p13 chr 1 NC_000001.10:g.715348T>G
Gene: LOC100288069, uncharacterized LOC100288069 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC100288069 transcript NR_168328.1:n. N/A Upstream Transcript Variant
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X1 XR_002958522.1:n. N/A Intron Variant
LINC01409 transcript variant X5 XR_002958525.1:n. N/A Intron Variant
LINC01409 transcript variant X4 XR_946806.3:n. N/A Intron Variant
LINC01409 transcript variant X2 XR_002958523.1:n. N/A Genic Upstream Transcript Variant
LINC01409 transcript variant X3 XR_002958524.1:n. N/A Genic Upstream 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 (New)
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 T=0.00005 G=0.99995
European Sub 14152 T=0.00000 G=1.00000
African Sub 2898 T=0.0003 G=0.9997
African Others Sub 114 T=0.000 G=1.000
African American Sub 2784 T=0.0004 G=0.9996
Asian Sub 112 T=0.000 G=1.000
East Asian Sub 86 T=0.00 G=1.00
Other Asian Sub 26 T=0.00 G=1.00
Latin American 1 Sub 146 T=0.000 G=1.000
Latin American 2 Sub 610 T=0.000 G=1.000
South Asian Sub 98 T=0.00 G=1.00
Other Sub 504 T=0.000 G=1.000


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
TopMed Global Study-wide 264690 T=0.000057 G=0.999943
gnomAD - Genomes Global Study-wide 140280 T=0.000086 G=0.999914
gnomAD - Genomes European Sub 75964 T=0.00000 G=1.00000
gnomAD - Genomes African Sub 42042 T=0.00029 G=0.99971
gnomAD - Genomes American Sub 13664 T=0.00000 G=1.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.0000 G=1.0000
gnomAD - Genomes East Asian Sub 3134 T=0.0000 G=1.0000
gnomAD - Genomes Other Sub 2152 T=0.0000 G=1.0000
8.3KJPN JAPANESE Study-wide 16760 T=0.00000 G=1.00000
1000Genomes Global Study-wide 5008 T=0.0000 G=1.0000
1000Genomes African Sub 1322 T=0.0000 G=1.0000
1000Genomes East Asian Sub 1008 T=0.0000 G=1.0000
1000Genomes Europe Sub 1006 T=0.0000 G=1.0000
1000Genomes South Asian Sub 978 T=0.000 G=1.000
1000Genomes American Sub 694 T=0.000 G=1.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.0000 G=1.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.0000 G=1.0000
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0003 C=0.0000, G=0.9997
Korean Genome Project KOREAN Study-wide 1832 T=0.0000 G=1.0000
Northern Sweden ACPOP Study-wide 600 T=0.000 G=1.000
SGDP_PRJ Global Study-wide 558 T=0.000 G=1.000
Qatari Global Study-wide 216 T=0.000 G=1.000
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.000 G=1.000
The Danish reference pan genome Danish Study-wide 40 T=0.00 G=1.00
Siberian Global Study-wide 4 T=0.0 G=1.0
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 T= C G
GRCh38.p13 chr 1 NC_000001.11:g.779968= NC_000001.11:g.779968T>C NC_000001.11:g.779968T>G
GRCh37.p13 chr 1 NC_000001.10:g.715348= NC_000001.10:g.715348T>C NC_000001.10:g.715348T>G
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#.

49 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4379461 Mar 26, 2002 (103)
2 WI_SSAHASNP ss6851724 Feb 20, 2003 (111)
3 CSHL-HAPMAP ss17347394 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19848499 Feb 27, 2004 (120)
5 HGSV ss85543445 Dec 16, 2007 (130)
6 BCMHGSC_JDW ss87155353 Mar 23, 2008 (129)
7 HUMANGENOME_JCVI ss97913171 Feb 06, 2009 (130)
8 ENSEMBL ss137751608 Dec 01, 2009 (131)
9 ENSEMBL ss138907787 Dec 01, 2009 (131)
10 GMI ss154522234 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss163702642 Jul 04, 2010 (132)
12 BL ss252863999 May 09, 2011 (134)
13 GMI ss275680533 May 04, 2012 (137)
14 GMI ss283987299 Apr 25, 2013 (138)
15 PJP ss290493751 May 09, 2011 (134)
16 1000GENOMES ss328357080 May 09, 2011 (134)
17 SSMP ss647515845 Apr 25, 2013 (138)
18 JMKIDD_LAB ss1067612310 Aug 21, 2014 (142)
19 1000GENOMES ss1289337920 Aug 21, 2014 (142)
20 DDI ss1425684723 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1573851055 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1599378230 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1642372263 Apr 01, 2015 (144)
24 HAMMER_LAB ss1793705471 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1917959717 Feb 12, 2016 (147)
26 JJLAB ss2019498264 Sep 14, 2016 (149)
27 USC_VALOUEV ss2147483825 Dec 20, 2016 (150)
28 TOPMED ss2321500971 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2624264724 Nov 08, 2017 (151)
30 GRF ss2697374012 Nov 08, 2017 (151)
31 GNOMAD ss2750632870 Nov 08, 2017 (151)
32 SWEGEN ss2986147699 Nov 08, 2017 (151)
33 TOPMED ss3066388466 Nov 08, 2017 (151)
34 CSHL ss3343272175 Nov 08, 2017 (151)
35 URBANLAB ss3646581098 Oct 11, 2018 (152)
36 EVA_DECODE ss3685991621 Jul 12, 2019 (153)
37 ACPOP ss3726715975 Jul 12, 2019 (153)
38 PACBIO ss3783302020 Jul 12, 2019 (153)
39 PACBIO ss3788979907 Jul 12, 2019 (153)
40 PACBIO ss3793852444 Jul 12, 2019 (153)
41 KHV_HUMAN_GENOMES ss3798743084 Jul 12, 2019 (153)
42 EVA ss3825981368 Apr 25, 2020 (154)
43 EVA ss3836378314 Apr 25, 2020 (154)
44 EVA ss3841782311 Apr 25, 2020 (154)
45 SGDP_PRJ ss3847993786 Apr 25, 2020 (154)
46 KRGDB ss3892833244 Apr 25, 2020 (154)
47 KOGIC ss3943628339 Apr 25, 2020 (154)
48 TOPMED ss4436421951 Apr 25, 2021 (155)
49 TOMMO_GENOMICS ss5142049382 Apr 25, 2021 (155)
50 1000Genomes NC_000001.10 - 715348 Oct 11, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 715348 Oct 11, 2018 (152)
52 The Danish reference pan genome NC_000001.10 - 715348 Apr 25, 2020 (154)
53 gnomAD - Genomes NC_000001.11 - 779968 Apr 25, 2021 (155)
54 KOREAN population from KRGDB NC_000001.10 - 715348 Apr 25, 2020 (154)
55 Korean Genome Project NC_000001.11 - 779968 Apr 25, 2020 (154)
56 Northern Sweden NC_000001.10 - 715348 Jul 12, 2019 (153)
57 Qatari NC_000001.10 - 715348 Apr 25, 2020 (154)
58 SGDP_PRJ NC_000001.10 - 715348 Apr 25, 2020 (154)
59 Siberian NC_000001.10 - 715348 Apr 25, 2020 (154)
60 8.3KJPN NC_000001.10 - 715348 Apr 25, 2021 (155)
61 TopMed NC_000001.11 - 779968 Apr 25, 2021 (155)
62 UK 10K study - Twins NC_000001.10 - 715348 Oct 11, 2018 (152)
63 A Vietnamese Genetic Variation Database NC_000001.10 - 715348 Jul 12, 2019 (153)
64 ALFA NC_000001.11 - 779968 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)
rs61378250 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10638, ss3892833244 NC_000001.10:715347:T:C NC_000001.11:779967:T:C (self)
ss85543445 NC_000001.8:755210:T:G NC_000001.11:779967:T:G (self)
ss87155353, ss163702642, ss252863999, ss275680533, ss283987299, ss290493751 NC_000001.9:705210:T:G NC_000001.11:779967:T:G (self)
2585, 75, 1358289, 10638, 840, 1647, 10766, 179, 18689, 75, 21, ss328357080, ss647515845, ss1067612310, ss1289337920, ss1425684723, ss1573851055, ss1599378230, ss1642372263, ss1793705471, ss1917959717, ss2019498264, ss2147483825, ss2321500971, ss2624264724, ss2697374012, ss2750632870, ss2986147699, ss3343272175, ss3726715975, ss3783302020, ss3788979907, ss3793852444, ss3825981368, ss3836378314, ss3847993786, ss3892833244, ss5142049382 NC_000001.10:715347:T:G NC_000001.11:779967:T:G (self)
53445, 6340, 10434, 28286, 11995197993, ss3066388466, ss3646581098, ss3685991621, ss3798743084, ss3841782311, ss3943628339, ss4436421951 NC_000001.11:779967:T:G NC_000001.11:779967:T:G (self)
ss4379461, ss6851724, ss97913171, ss137751608, ss138907787, ss154522234 NT_004350.19:193979:T:G NC_000001.11:779967:T:G (self)
ss17347394, ss19848499 NT_034471.3:193979:T:G NC_000001.11:779967:T:G (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 rs3131984

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