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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.

rs2022015

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83062557 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.200922 (53182/264690, TOPMED)
G=0.172154 (42078/244420, ALFA)
G=0.215324 (30138/139966, GnomAD) (+ 16 more)
G=0.19809 (15590/78700, PAGE_STUDY)
G=0.1643 (823/5008, 1000G)
G=0.2511 (1125/4480, Estonian)
G=0.1772 (683/3854, ALSPAC)
G=0.1766 (655/3708, TWINSUK)
G=0.0007 (2/2922, KOREAN)
G=0.149 (149/998, GoNL)
G=0.006 (5/790, PRJEB37584)
G=0.183 (110/600, NorthernSweden)
G=0.213 (66/310, HapMap)
G=0.134 (29/216, Qatari)
G=0.014 (3/214, Vietnamese)
A=0.422 (54/128, SGDP_PRJ)
G=0.17 (7/40, GENOME_DK)
A=0.50 (9/18, Siberian)
G=0.50 (9/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01362 : Intron Variant
LOC107985037 : 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.83062557A>G
GRCh37.p13 chr 1 NC_000001.10:g.83528240A>G
Gene: LINC01362, long intergenic non-protein coding RNA 1362 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01362 transcript NR_147074.1:n. N/A Intron Variant
Gene: LOC107985037, uncharacterized LOC107985037 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985037 transcript XR_001738121.1: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 244420 A=0.827846 G=0.172154
European Sub 217268 A=0.827167 G=0.172833
African Sub 6822 A=0.7074 G=0.2926
African Others Sub 260 A=0.696 G=0.304
African American Sub 6562 A=0.7079 G=0.2921
Asian Sub 3860 A=0.9824 G=0.0176
East Asian Sub 3128 A=0.9984 G=0.0016
Other Asian Sub 732 A=0.914 G=0.086
Latin American 1 Sub 1028 A=0.8210 G=0.1790
Latin American 2 Sub 6580 A=0.8565 G=0.1435
South Asian Sub 366 A=0.915 G=0.085
Other Sub 8496 A=0.8465 G=0.1535


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=0.799078 G=0.200922
gnomAD - Genomes Global Study-wide 139966 A=0.784676 G=0.215324
gnomAD - Genomes European Sub 75844 A=0.80704 G=0.19296
gnomAD - Genomes African Sub 41916 A=0.70248 G=0.29752
gnomAD - Genomes American Sub 13622 A=0.84804 G=0.15196
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.8469 G=0.1531
gnomAD - Genomes East Asian Sub 3112 A=0.9894 G=0.0106
gnomAD - Genomes Other Sub 2148 A=0.8045 G=0.1955
The PAGE Study Global Study-wide 78700 A=0.80191 G=0.19809
The PAGE Study AfricanAmerican Sub 32514 A=0.70976 G=0.29024
The PAGE Study Mexican Sub 10810 A=0.85976 G=0.14024
The PAGE Study Asian Sub 8318 A=0.9950 G=0.0050
The PAGE Study PuertoRican Sub 7918 A=0.7982 G=0.2018
The PAGE Study NativeHawaiian Sub 4534 A=0.9012 G=0.0988
The PAGE Study Cuban Sub 4230 A=0.8187 G=0.1813
The PAGE Study Dominican Sub 3828 A=0.7785 G=0.2215
The PAGE Study CentralAmerican Sub 2450 A=0.8535 G=0.1465
The PAGE Study SouthAmerican Sub 1982 A=0.8749 G=0.1251
The PAGE Study NativeAmerican Sub 1260 A=0.8048 G=0.1952
The PAGE Study SouthAsian Sub 856 A=0.905 G=0.095
1000Genomes Global Study-wide 5008 A=0.8357 G=0.1643
1000Genomes African Sub 1322 A=0.6884 G=0.3116
1000Genomes East Asian Sub 1008 A=0.9891 G=0.0109
1000Genomes Europe Sub 1006 A=0.7932 G=0.2068
1000Genomes South Asian Sub 978 A=0.916 G=0.084
1000Genomes American Sub 694 A=0.841 G=0.159
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7489 G=0.2511
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8228 G=0.1772
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8234 G=0.1766
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9993 G=0.0007
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.851 G=0.149
CNV burdens in cranial meningiomas Global Study-wide 790 A=0.994 G=0.006
CNV burdens in cranial meningiomas CRM Sub 790 A=0.994 G=0.006
Northern Sweden ACPOP Study-wide 600 A=0.817 G=0.183
HapMap Global Study-wide 310 A=0.787 G=0.213
HapMap African Sub 118 A=0.585 G=0.415
HapMap American Sub 104 A=0.837 G=0.163
HapMap Asian Sub 88 A=1.00 G=0.00
Qatari Global Study-wide 216 A=0.866 G=0.134
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.986 G=0.014
SGDP_PRJ Global Study-wide 128 A=0.422 G=0.578
The Danish reference pan genome Danish Study-wide 40 A=0.82 G=0.17
Siberian Global Study-wide 18 A=0.50 G=0.50
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= G
GRCh38.p13 chr 1 NC_000001.11:g.83062557= NC_000001.11:g.83062557A>G
GRCh37.p13 chr 1 NC_000001.10:g.83528240= NC_000001.10:g.83528240A>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#.

78 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2925700 Apr 12, 2001 (94)
2 PERLEGEN ss23145049 Sep 20, 2004 (123)
3 ABI ss44020736 Mar 14, 2006 (126)
4 1000GENOMES ss108366634 Jan 23, 2009 (130)
5 ILLUMINA-UK ss118850578 Feb 14, 2009 (130)
6 ILLUMINA ss160489488 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss164666160 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss166770385 Jul 04, 2010 (132)
9 BUSHMAN ss198701973 Jul 04, 2010 (132)
10 1000GENOMES ss210573055 Jul 14, 2010 (132)
11 1000GENOMES ss218491808 Jul 14, 2010 (132)
12 1000GENOMES ss230612783 Jul 14, 2010 (132)
13 BL ss253232628 May 09, 2011 (134)
14 GMI ss284085121 Apr 25, 2013 (138)
15 ILLUMINA ss480383968 May 04, 2012 (137)
16 ILLUMINA ss480396626 May 04, 2012 (137)
17 ILLUMINA ss481173382 Sep 08, 2015 (146)
18 ILLUMINA ss484989569 May 04, 2012 (137)
19 ILLUMINA ss537023810 Sep 08, 2015 (146)
20 TISHKOFF ss554362110 Apr 25, 2013 (138)
21 SSMP ss648176152 Apr 25, 2013 (138)
22 ILLUMINA ss778850367 Aug 21, 2014 (142)
23 ILLUMINA ss782941098 Aug 21, 2014 (142)
24 ILLUMINA ss783903670 Aug 21, 2014 (142)
25 ILLUMINA ss832196724 Apr 01, 2015 (144)
26 ILLUMINA ss834311017 Aug 21, 2014 (142)
27 EVA-GONL ss975365589 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1068043612 Aug 21, 2014 (142)
29 1000GENOMES ss1291668948 Aug 21, 2014 (142)
30 EVA_GENOME_DK ss1574191738 Apr 01, 2015 (144)
31 EVA_DECODE ss1584739523 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1600582837 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1643576870 Apr 01, 2015 (144)
34 ILLUMINA ss1751935360 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1918568532 Feb 12, 2016 (147)
36 ILLUMINA ss1945999946 Feb 12, 2016 (147)
37 ILLUMINA ss1958288200 Feb 12, 2016 (147)
38 JJLAB ss2019804925 Sep 14, 2016 (149)
39 USC_VALOUEV ss2147822016 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2164129734 Dec 20, 2016 (150)
41 TOPMED ss2326421951 Dec 20, 2016 (150)
42 ILLUMINA ss2632539916 Nov 08, 2017 (151)
43 ILLUMINA ss2710676092 Nov 08, 2017 (151)
44 GNOMAD ss2757361780 Nov 08, 2017 (151)
45 SWEGEN ss2987125417 Nov 08, 2017 (151)
46 ILLUMINA ss3021104359 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3023665251 Nov 08, 2017 (151)
48 TOPMED ss3081730247 Nov 08, 2017 (151)
49 CSHL ss3343543762 Nov 08, 2017 (151)
50 ILLUMINA ss3625543791 Oct 11, 2018 (152)
51 ILLUMINA ss3626140289 Oct 11, 2018 (152)
52 ILLUMINA ss3630574773 Oct 11, 2018 (152)
53 ILLUMINA ss3632898731 Oct 11, 2018 (152)
54 ILLUMINA ss3633593562 Oct 11, 2018 (152)
55 ILLUMINA ss3634333477 Oct 11, 2018 (152)
56 ILLUMINA ss3635287275 Oct 11, 2018 (152)
57 ILLUMINA ss3636010664 Oct 11, 2018 (152)
58 ILLUMINA ss3637037720 Oct 11, 2018 (152)
59 ILLUMINA ss3640040838 Oct 11, 2018 (152)
60 ILLUMINA ss3644495897 Oct 11, 2018 (152)
61 ILLUMINA ss3651432791 Oct 11, 2018 (152)
62 EGCUT_WGS ss3655205962 Jul 12, 2019 (153)
63 EVA_DECODE ss3687150968 Jul 12, 2019 (153)
64 ILLUMINA ss3725039753 Jul 12, 2019 (153)
65 ACPOP ss3727217090 Jul 12, 2019 (153)
66 ILLUMINA ss3744049271 Jul 12, 2019 (153)
67 ILLUMINA ss3744634444 Jul 12, 2019 (153)
68 EVA ss3746440455 Jul 12, 2019 (153)
69 PAGE_CC ss3770821298 Jul 12, 2019 (153)
70 ILLUMINA ss3772135744 Jul 12, 2019 (153)
71 KHV_HUMAN_GENOMES ss3799446498 Jul 12, 2019 (153)
72 EVA ss3826271391 Apr 25, 2020 (154)
73 SGDP_PRJ ss3849250359 Apr 25, 2020 (154)
74 KRGDB ss3894301703 Apr 25, 2020 (154)
75 EVA ss3984460041 Apr 25, 2021 (155)
76 EVA ss4016921144 Apr 25, 2021 (155)
77 TOPMED ss4456688674 Apr 25, 2021 (155)
78 EVA ss5237268959 Apr 25, 2021 (155)
79 1000Genomes NC_000001.10 - 83528240 Oct 11, 2018 (152)
80 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 83528240 Oct 11, 2018 (152)
81 Genetic variation in the Estonian population NC_000001.10 - 83528240 Oct 11, 2018 (152)
82 The Danish reference pan genome NC_000001.10 - 83528240 Apr 25, 2020 (154)
83 gnomAD - Genomes NC_000001.11 - 83062557 Apr 25, 2021 (155)
84 Genome of the Netherlands Release 5 NC_000001.10 - 83528240 Apr 25, 2020 (154)
85 HapMap NC_000001.11 - 83062557 Apr 25, 2020 (154)
86 KOREAN population from KRGDB NC_000001.10 - 83528240 Apr 25, 2020 (154)
87 Northern Sweden NC_000001.10 - 83528240 Jul 12, 2019 (153)
88 The PAGE Study NC_000001.11 - 83062557 Jul 12, 2019 (153)
89 CNV burdens in cranial meningiomas NC_000001.10 - 83528240 Apr 25, 2021 (155)
90 Qatari NC_000001.10 - 83528240 Apr 25, 2020 (154)
91 SGDP_PRJ NC_000001.10 - 83528240 Apr 25, 2020 (154)
92 Siberian NC_000001.10 - 83528240 Apr 25, 2020 (154)
93 TopMed NC_000001.11 - 83062557 Apr 25, 2021 (155)
94 UK 10K study - Twins NC_000001.10 - 83528240 Oct 11, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000001.10 - 83528240 Jul 12, 2019 (153)
96 ALFA NC_000001.11 - 83062557 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
ss108366634, ss118850578, ss160489488, ss164666160, ss166770385, ss198701973, ss210573055, ss253232628, ss284085121, ss480383968, ss1584739523 NC_000001.9:83300827:A:G NC_000001.11:83062556:A:G (self)
2416140, 1326106, 944210, 1583120, 572589, 1479097, 501955, 9351, 610462, 1267339, 338370, 1326106, 284435, ss218491808, ss230612783, ss480396626, ss481173382, ss484989569, ss537023810, ss554362110, ss648176152, ss778850367, ss782941098, ss783903670, ss832196724, ss834311017, ss975365589, ss1068043612, ss1291668948, ss1574191738, ss1600582837, ss1643576870, ss1751935360, ss1918568532, ss1945999946, ss1958288200, ss2019804925, ss2147822016, ss2326421951, ss2632539916, ss2710676092, ss2757361780, ss2987125417, ss3021104359, ss3343543762, ss3625543791, ss3626140289, ss3630574773, ss3632898731, ss3633593562, ss3634333477, ss3635287275, ss3636010664, ss3637037720, ss3640040838, ss3644495897, ss3651432791, ss3655205962, ss3727217090, ss3744049271, ss3744634444, ss3746440455, ss3772135744, ss3826271391, ss3849250359, ss3894301703, ss3984460041, ss4016921144, ss5237268959 NC_000001.10:83528239:A:G NC_000001.11:83062556:A:G (self)
17051520, 112939, 42767, 12783345, 20295009, 12160683704, ss2164129734, ss3023665251, ss3081730247, ss3687150968, ss3725039753, ss3770821298, ss3799446498, ss4456688674 NC_000001.11:83062556:A:G NC_000001.11:83062556:A:G (self)
ss2925700, ss23145049, ss44020736 NT_032977.9:53500157:A:G NC_000001.11:83062556:A: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 rs2022015

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