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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs2314130

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:63033777 (GRCh38.p14) 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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.357214 (94551/264690, TOPMED)
G=0.372374 (52014/139682, GnomAD)
G=0.26170 (7395/28258, 14KJPN) (+ 16 more)
G=0.36755 (6943/18890, ALFA)
G=0.26444 (4432/16760, 8.3KJPN)
G=0.3090 (1979/6404, 1000G_30x)
G=0.3075 (1540/5008, 1000G)
G=0.3808 (1706/4480, Estonian)
G=0.3254 (1254/3854, ALSPAC)
G=0.3490 (1294/3708, TWINSUK)
G=0.2551 (747/2928, KOREAN)
G=0.2691 (493/1832, Korea1K)
G=0.383 (230/600, NorthernSweden)
G=0.241 (121/502, SGDP_PRJ)
G=0.259 (56/216, Qatari)
G=0.227 (49/216, Vietnamese)
G=0.42 (40/96, Ancient Sardinia)
G=0.30 (16/54, Siberian)
G=0.35 (14/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01749 : Intron Variant
LINC00029 : 500B Downstream Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 G=0.36755 T=0.63245
European Sub 14286 G=0.36476 T=0.63524
African Sub 2946 G=0.4233 T=0.5767
African Others Sub 114 G=0.421 T=0.579
African American Sub 2832 G=0.4234 T=0.5766
Asian Sub 112 G=0.125 T=0.875
East Asian Sub 86 G=0.12 T=0.88
Other Asian Sub 26 G=0.15 T=0.85
Latin American 1 Sub 146 G=0.301 T=0.699
Latin American 2 Sub 610 G=0.259 T=0.741
South Asian Sub 98 G=0.33 T=0.67
Other Sub 692 G=0.342 T=0.658


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 G=0.357214 T=0.642786
gnomAD - Genomes Global Study-wide 139682 G=0.372374 T=0.627626
gnomAD - Genomes European Sub 75714 G=0.36157 T=0.63843
gnomAD - Genomes African Sub 41770 G=0.41587 T=0.58413
gnomAD - Genomes American Sub 13618 G=0.31958 T=0.68042
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.4412 T=0.5588
gnomAD - Genomes East Asian Sub 3116 G=0.2291 T=0.7709
gnomAD - Genomes Other Sub 2146 G=0.3434 T=0.6566
14KJPN JAPANESE Study-wide 28258 G=0.26170 T=0.73830
Allele Frequency Aggregator Total Global 18890 G=0.36755 T=0.63245
Allele Frequency Aggregator European Sub 14286 G=0.36476 T=0.63524
Allele Frequency Aggregator African Sub 2946 G=0.4233 T=0.5767
Allele Frequency Aggregator Other Sub 692 G=0.342 T=0.658
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.259 T=0.741
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.301 T=0.699
Allele Frequency Aggregator Asian Sub 112 G=0.125 T=0.875
Allele Frequency Aggregator South Asian Sub 98 G=0.33 T=0.67
8.3KJPN JAPANESE Study-wide 16760 G=0.26444 T=0.73556
1000Genomes_30x Global Study-wide 6404 G=0.3090 T=0.6910
1000Genomes_30x African Sub 1786 G=0.4110 T=0.5890
1000Genomes_30x Europe Sub 1266 G=0.3294 T=0.6706
1000Genomes_30x South Asian Sub 1202 G=0.2180 T=0.7820
1000Genomes_30x East Asian Sub 1170 G=0.2205 T=0.7795
1000Genomes_30x American Sub 980 G=0.314 T=0.686
1000Genomes Global Study-wide 5008 G=0.3075 T=0.6925
1000Genomes African Sub 1322 G=0.4107 T=0.5893
1000Genomes East Asian Sub 1008 G=0.2252 T=0.7748
1000Genomes Europe Sub 1006 G=0.3340 T=0.6660
1000Genomes South Asian Sub 978 G=0.220 T=0.780
1000Genomes American Sub 694 G=0.316 T=0.684
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.3808 T=0.6192
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.3254 T=0.6746
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.3490 T=0.6510
KOREAN population from KRGDB KOREAN Study-wide 2928 G=0.2551 C=0.0000, T=0.7449
Korean Genome Project KOREAN Study-wide 1832 G=0.2691 T=0.7309
Northern Sweden ACPOP Study-wide 600 G=0.383 T=0.617
SGDP_PRJ Global Study-wide 502 G=0.241 T=0.759
Qatari Global Study-wide 216 G=0.259 T=0.741
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.227 T=0.773
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 96 G=0.42 T=0.58
Siberian Global Study-wide 54 G=0.30 T=0.70
The Danish reference pan genome Danish Study-wide 40 G=0.35 T=0.65
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.p14 chr 20 NC_000020.11:g.63033777G>C
GRCh38.p14 chr 20 NC_000020.11:g.63033777G>T
GRCh37.p13 chr 20 NC_000020.10:g.61665129G>C
GRCh37.p13 chr 20 NC_000020.10:g.61665129G>T
Gene: LINC01749, long intergenic non-protein coding RNA 1749 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01749 transcript NR_033370.1:n. N/A Intron Variant
Gene: LINC00029, long intergenic non-protein coding RNA 29 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
LINC00029 transcript NR_028295.1:n. N/A 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
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= C T
GRCh38.p14 chr 20 NC_000020.11:g.63033777= NC_000020.11:g.63033777G>C NC_000020.11:g.63033777G>T
GRCh37.p13 chr 20 NC_000020.10:g.61665129= NC_000020.10:g.61665129G>C NC_000020.10:g.61665129G>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#.

73 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3262614 Sep 28, 2001 (100)
2 SC_SNP ss8310667 Apr 21, 2003 (114)
3 BCM_SSAHASNP ss14304435 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss19479942 Feb 27, 2004 (120)
5 SSAHASNP ss21759902 Apr 05, 2004 (121)
6 HGSV ss77676587 Dec 06, 2007 (129)
7 HGSV ss78561178 Dec 06, 2007 (129)
8 HGSV ss84608702 Dec 15, 2007 (130)
9 BGI ss106199104 Feb 06, 2009 (130)
10 1000GENOMES ss112240247 Jan 25, 2009 (130)
11 IGMI-SNU ss115485281 Feb 06, 2009 (130)
12 ENSEMBL ss138271643 Dec 01, 2009 (131)
13 ENSEMBL ss143643000 Dec 01, 2009 (131)
14 GMI ss156617266 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss168421131 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss170094106 Jul 04, 2010 (132)
17 BUSHMAN ss203944789 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss208684982 Jul 04, 2010 (132)
19 1000GENOMES ss228449630 Jul 14, 2010 (132)
20 1000GENOMES ss237899871 Jul 15, 2010 (132)
21 1000GENOMES ss244056041 Jul 15, 2010 (132)
22 GMI ss283444465 May 04, 2012 (137)
23 GMI ss287485481 Apr 25, 2013 (138)
24 PJP ss292598411 May 09, 2011 (134)
25 SSMP ss662245544 Apr 25, 2013 (138)
26 EVA-GONL ss994904112 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1082336441 Aug 21, 2014 (142)
28 1000GENOMES ss1365472992 Aug 21, 2014 (142)
29 DDI ss1429104994 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1579576064 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1639156843 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1682150876 Apr 01, 2015 (144)
33 HAMMER_LAB ss1809583687 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1938426325 Feb 12, 2016 (147)
35 GENOMED ss1969171293 Jul 19, 2016 (147)
36 JJLAB ss2029993678 Sep 14, 2016 (149)
37 USC_VALOUEV ss2158564948 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2244200993 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2629489525 Nov 08, 2017 (151)
40 GRF ss2704262487 Nov 08, 2017 (151)
41 GNOMAD ss2969381579 Nov 08, 2017 (151)
42 SWEGEN ss3018468179 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3028830082 Nov 08, 2017 (151)
44 CSHL ss3352593805 Nov 08, 2017 (151)
45 URBANLAB ss3651054908 Oct 12, 2018 (152)
46 EGCUT_WGS ss3685153830 Jul 13, 2019 (153)
47 EVA_DECODE ss3707304546 Jul 13, 2019 (153)
48 ACPOP ss3743548445 Jul 13, 2019 (153)
49 EVA ss3758863569 Jul 13, 2019 (153)
50 PACBIO ss3788694378 Jul 13, 2019 (153)
51 PACBIO ss3793578282 Jul 13, 2019 (153)
52 PACBIO ss3798465697 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3822017794 Jul 13, 2019 (153)
54 EVA ss3835762946 Apr 27, 2020 (154)
55 EVA ss3841506295 Apr 27, 2020 (154)
56 EVA ss3847020080 Apr 27, 2020 (154)
57 SGDP_PRJ ss3889476984 Apr 27, 2020 (154)
58 KRGDB ss3939801598 Apr 27, 2020 (154)
59 KOGIC ss3982634519 Apr 27, 2020 (154)
60 EVA ss3985891684 Apr 27, 2021 (155)
61 TOPMED ss5094572387 Apr 27, 2021 (155)
62 TOMMO_GENOMICS ss5230447075 Apr 27, 2021 (155)
63 1000G_HIGH_COVERAGE ss5309422529 Oct 16, 2022 (156)
64 EVA ss5438546432 Oct 16, 2022 (156)
65 HUGCELL_USP ss5501640682 Oct 16, 2022 (156)
66 1000G_HIGH_COVERAGE ss5616172705 Oct 16, 2022 (156)
67 SANFORD_IMAGENETICS ss5663561149 Oct 16, 2022 (156)
68 TOMMO_GENOMICS ss5790502853 Oct 16, 2022 (156)
69 YY_MCH ss5818196025 Oct 16, 2022 (156)
70 EVA ss5845938508 Oct 16, 2022 (156)
71 EVA ss5853215458 Oct 16, 2022 (156)
72 EVA ss5924144646 Oct 16, 2022 (156)
73 EVA ss5958494929 Oct 16, 2022 (156)
74 1000Genomes NC_000020.10 - 61665129 Oct 12, 2018 (152)
75 1000Genomes_30x NC_000020.11 - 63033777 Oct 16, 2022 (156)
76 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 61665129 Oct 12, 2018 (152)
77 Genetic variation in the Estonian population NC_000020.10 - 61665129 Oct 12, 2018 (152)
78 The Danish reference pan genome NC_000020.10 - 61665129 Apr 27, 2020 (154)
79 gnomAD - Genomes NC_000020.11 - 63033777 Apr 27, 2021 (155)
80 KOREAN population from KRGDB NC_000020.10 - 61665129 Apr 27, 2020 (154)
81 Korean Genome Project NC_000020.11 - 63033777 Apr 27, 2020 (154)
82 Northern Sweden NC_000020.10 - 61665129 Jul 13, 2019 (153)
83 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000020.10 - 61665129 Apr 27, 2021 (155)
84 Qatari NC_000020.10 - 61665129 Apr 27, 2020 (154)
85 SGDP_PRJ NC_000020.10 - 61665129 Apr 27, 2020 (154)
86 Siberian NC_000020.10 - 61665129 Apr 27, 2020 (154)
87 8.3KJPN NC_000020.10 - 61665129 Apr 27, 2021 (155)
88 14KJPN NC_000020.11 - 63033777 Oct 16, 2022 (156)
89 TopMed NC_000020.11 - 63033777 Apr 27, 2021 (155)
90 UK 10K study - Twins NC_000020.10 - 61665129 Oct 12, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000020.10 - 61665129 Jul 13, 2019 (153)
92 ALFA NC_000020.11 - 63033777 Apr 27, 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)
rs60182439 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
46978992, ss3939801598 NC_000020.10:61665128:G:C NC_000020.11:63033776:G:C (self)
ss77676587, ss78561178, ss84608702, ss112240247, ss168421131, ss170094106, ss203944789, ss208684982, ss283444465, ss287485481, ss292598411 NC_000020.9:61135573:G:T NC_000020.11:63033776:G:T (self)
78960602, 43721396, 30892078, 5741003, 46978992, 16833310, 1117611, 20468247, 41493964, 11081302, 88416382, 43721396, 9640755, ss228449630, ss237899871, ss244056041, ss662245544, ss994904112, ss1082336441, ss1365472992, ss1429104994, ss1579576064, ss1639156843, ss1682150876, ss1809583687, ss1938426325, ss1969171293, ss2029993678, ss2158564948, ss2629489525, ss2704262487, ss2969381579, ss3018468179, ss3352593805, ss3685153830, ss3743548445, ss3758863569, ss3788694378, ss3793578282, ss3798465697, ss3835762946, ss3841506295, ss3889476984, ss3939801598, ss3985891684, ss5230447075, ss5438546432, ss5663561149, ss5845938508, ss5958494929 NC_000020.10:61665128:G:T NC_000020.11:63033776:G:T (self)
103698640, 556847544, 39012520, 124339957, 369681332, 13837827216, ss2244200993, ss3028830082, ss3651054908, ss3707304546, ss3822017794, ss3847020080, ss3982634519, ss5094572387, ss5309422529, ss5501640682, ss5616172705, ss5790502853, ss5818196025, ss5853215458, ss5924144646 NC_000020.11:63033776:G:T NC_000020.11:63033776:G:T (self)
ss8310667, ss14304435, ss19479942, ss21759902 NT_011333.5:401759:G:T NC_000020.11:63033776:G:T (self)
ss3262614, ss106199104, ss115485281, ss138271643, ss143643000, ss156617266 NT_011333.6:401759:G:T NC_000020.11:63033776: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 rs2314130

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.post761+d5e8e07