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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.

rs2977670

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:788511 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.26301 (4408/16760, 8.3KJPN)
G=0.1669 (903/5412, ALFA)
G=0.2200 (1102/5008, 1000G) (+ 10 more)
G=0.0400 (154/3854, ALSPAC)
G=0.0440 (163/3708, TWINSUK)
G=0.2020 (592/2930, KOREAN)
G=0.034 (34/998, GoNL)
G=0.037 (22/600, NorthernSweden)
G=0.154 (75/488, SGDP_PRJ)
G=0.299 (94/314, HapMap)
G=0.190 (41/216, Qatari)
G=0.03 (1/40, GENOME_DK)
G=0.03 (1/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Intron 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.788511G>A
GRCh38.p13 chr 1 NC_000001.11:g.788511G>C
GRCh38.p13 chr 1 NC_000001.11:g.788511G>T
GRCh37.p13 chr 1 NC_000001.10:g.723891G>A
GRCh37.p13 chr 1 NC_000001.10:g.723891G>C
GRCh37.p13 chr 1 NC_000001.10:g.723891G>T
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 5412 G=0.1669 A=0.0000, C=0.8331, T=0.0000
European Sub 4596 G=0.0668 A=0.0000, C=0.9332, T=0.0000
African Sub 594 G=0.938 A=0.000, C=0.062, T=0.000
African Others Sub 30 G=1.00 A=0.00, C=0.00, T=0.00
African American Sub 564 G=0.934 A=0.000, C=0.066, T=0.000
Asian Sub 2 G=1.0 A=0.0, C=0.0, T=0.0
East Asian Sub 2 G=1.0 A=0.0, C=0.0, T=0.0
Other Asian Sub 0 G=0 A=0, C=0, T=0
Latin American 1 Sub 8 G=1.0 A=0.0, C=0.0, T=0.0
Latin American 2 Sub 2 G=1.0 A=0.0, C=0.0, T=0.0
South Asian Sub 0 G=0 A=0, C=0, T=0
Other Sub 210 G=0.129 A=0.000, C=0.871, T=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
8.3KJPN JAPANESE Study-wide 16760 G=0.26301 C=0.73699
1000Genomes Global Study-wide 5008 G=0.2200 C=0.7800
1000Genomes African Sub 1322 G=0.5151 C=0.4849
1000Genomes East Asian Sub 1008 G=0.2083 C=0.7917
1000Genomes Europe Sub 1006 G=0.0517 C=0.9483
1000Genomes South Asian Sub 978 G=0.070 C=0.930
1000Genomes American Sub 694 G=0.131 C=0.869
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.0400 C=0.9600
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.0440 C=0.9560
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2020 A=0.0000, C=0.7980
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.034 C=0.966
Northern Sweden ACPOP Study-wide 600 G=0.037 C=0.963
SGDP_PRJ Global Study-wide 488 G=0.154 C=0.846
HapMap Global Study-wide 314 G=0.299 C=0.701
HapMap African Sub 118 G=0.492 C=0.508
HapMap American Sub 112 G=0.071 C=0.929
HapMap Asian Sub 84 G=0.33 C=0.67
Qatari Global Study-wide 216 G=0.190 C=0.810
The Danish reference pan genome Danish Study-wide 40 G=0.03 C=0.97
Siberian Global Study-wide 30 G=0.03 C=0.97
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 G= A C T
GRCh38.p13 chr 1 NC_000001.11:g.788511= NC_000001.11:g.788511G>A NC_000001.11:g.788511G>C NC_000001.11:g.788511G>T
GRCh37.p13 chr 1 NC_000001.10:g.723891= NC_000001.10:g.723891G>A NC_000001.10:g.723891G>C NC_000001.10:g.723891G>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#.

57 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4191663 Nov 05, 2001 (101)
2 WI_SSAHASNP ss6851725 Feb 20, 2003 (111)
3 CSHL-HAPMAP ss16399802 Feb 27, 2004 (120)
4 ILLUMINA ss65798767 Oct 15, 2006 (127)
5 HGSV ss78163595 Dec 06, 2007 (129)
6 HGSV ss78764316 Dec 06, 2007 (129)
7 BCMHGSC_JDW ss87155374 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss97913175 Feb 05, 2009 (130)
9 BGI ss105111637 Dec 01, 2009 (131)
10 ILLUMINA-UK ss118438178 Feb 14, 2009 (130)
11 ENSEMBL ss137751620 Dec 01, 2009 (131)
12 ENSEMBL ss138905911 Dec 01, 2009 (131)
13 GMI ss154522241 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss163702668 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss205287261 Jul 04, 2010 (132)
16 1000GENOMES ss218190347 Jul 14, 2010 (132)
17 1000GENOMES ss230395410 Jul 14, 2010 (132)
18 1000GENOMES ss238114944 Jul 15, 2010 (132)
19 BL ss252864003 May 09, 2011 (134)
20 GMI ss275680560 May 04, 2012 (137)
21 GMI ss283987305 Apr 25, 2013 (138)
22 PJP ss290493755 May 09, 2011 (134)
23 SSMP ss647515880 Apr 25, 2013 (138)
24 EVA-GONL ss974769091 Aug 21, 2014 (142)
25 1000GENOMES ss1289338094 Aug 21, 2014 (142)
26 DDI ss1425684731 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1573851066 Apr 01, 2015 (144)
28 EVA_DECODE ss1584129360 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1599378241 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1642372274 Apr 01, 2015 (144)
31 WEILL_CORNELL_DGM ss1917959781 Feb 12, 2016 (147)
32 GENOMED ss1966667310 Jul 19, 2016 (147)
33 JJLAB ss2019498276 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147483833 Dec 20, 2016 (150)
35 TOPMED ss2321501395 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2624264731 Nov 08, 2017 (151)
37 GRF ss2697374049 Nov 08, 2017 (151)
38 GNOMAD ss2750633525 Nov 08, 2017 (151)
39 SWEGEN ss2986147808 Nov 08, 2017 (151)
40 TOPMED ss3066389903 Nov 08, 2017 (151)
41 TOPMED ss3066389904 Nov 08, 2017 (151)
42 TOPMED ss3066389905 Nov 08, 2017 (151)
43 CSHL ss3343272203 Nov 08, 2017 (151)
44 URBANLAB ss3646581105 Oct 11, 2018 (152)
45 EVA_DECODE ss3685991680 Jul 12, 2019 (153)
46 ACPOP ss3726716018 Jul 12, 2019 (153)
47 EVA ss3745720728 Jul 12, 2019 (153)
48 PACBIO ss3783302035 Jul 12, 2019 (153)
49 PACBIO ss3788979914 Jul 12, 2019 (153)
50 PACBIO ss3793852451 Jul 12, 2019 (153)
51 KHV_HUMAN_GENOMES ss3798743140 Jul 12, 2019 (153)
52 EVA ss3825981376 Apr 25, 2020 (154)
53 EVA ss3836378320 Apr 25, 2020 (154)
54 EVA ss3841782318 Apr 25, 2020 (154)
55 SGDP_PRJ ss3847993911 Apr 25, 2020 (154)
56 KRGDB ss3892833348 Apr 25, 2020 (154)
57 TOMMO_GENOMICS ss5142049614 Apr 25, 2021 (155)
58 1000Genomes NC_000001.10 - 723891 Oct 11, 2018 (152)
59 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 723891 Oct 11, 2018 (152)
60 The Danish reference pan genome NC_000001.10 - 723891 Apr 25, 2020 (154)
61 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 54890 (NC_000001.11:788510:G:C 114790/139970)
Row 54891 (NC_000001.11:788510:G:T 2/140080)

- Apr 25, 2021 (155)
62 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 54890 (NC_000001.11:788510:G:C 114790/139970)
Row 54891 (NC_000001.11:788510:G:T 2/140080)

- Apr 25, 2021 (155)
63 Genome of the Netherlands Release 5 NC_000001.10 - 723891 Apr 25, 2020 (154)
64 HapMap NC_000001.11 - 788511 Apr 25, 2020 (154)
65 KOREAN population from KRGDB NC_000001.10 - 723891 Apr 25, 2020 (154)
66 Northern Sweden NC_000001.10 - 723891 Jul 12, 2019 (153)
67 Qatari NC_000001.10 - 723891 Apr 25, 2020 (154)
68 SGDP_PRJ NC_000001.10 - 723891 Apr 25, 2020 (154)
69 Siberian NC_000001.10 - 723891 Apr 25, 2020 (154)
70 8.3KJPN NC_000001.10 - 723891 Apr 25, 2021 (155)
71 UK 10K study - Twins NC_000001.10 - 723891 Oct 11, 2018 (152)
72 ALFA NC_000001.11 - 788511 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
10742, ss3892833348 NC_000001.10:723890:G:A NC_000001.11:788510:G:A (self)
14464662077, ss3066389903 NC_000001.11:788510:G:A NC_000001.11:788510:G:A (self)
ss78163595, ss78764316 NC_000001.8:763753:G:C NC_000001.11:788510:G:C (self)
ss87155374, ss118438178, ss163702668, ss205287261, ss252864003, ss275680560, ss283987305, ss290493755, ss1584129360 NC_000001.9:713753:G:C NC_000001.11:788510:G:C (self)
2770, 97, 1358300, 203, 10742, 883, 1711, 10891, 187, 18921, 97, ss218190347, ss230395410, ss238114944, ss647515880, ss974769091, ss1289338094, ss1425684731, ss1573851066, ss1599378241, ss1642372274, ss1917959781, ss1966667310, ss2019498276, ss2147483833, ss2321501395, ss2624264731, ss2697374049, ss2750633525, ss2986147808, ss3343272203, ss3726716018, ss3745720728, ss3783302035, ss3788979914, ss3793852451, ss3825981376, ss3836378320, ss3847993911, ss3892833348, ss5142049614 NC_000001.10:723890:G:C NC_000001.11:788510:G:C (self)
30, 14464662077, ss3066389904, ss3646581105, ss3685991680, ss3798743140, ss3841782318 NC_000001.11:788510:G:C NC_000001.11:788510:G:C (self)
ss4191663, ss6851725, ss65798767, ss97913175, ss105111637, ss137751620, ss138905911, ss154522241 NT_004350.19:202522:G:C NC_000001.11:788510:G:C (self)
ss16399802 NT_034471.3:202522:G:C NC_000001.11:788510:G:C (self)
14464662077, ss3066389905 NC_000001.11:788510:G:T NC_000001.11:788510:G: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 rs2977670

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