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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.

rs323952

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83131527 (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=0.309902 (82028/264690, TOPMED)
G=0.304701 (42632/139914, GnomAD)
G=0.29049 (6963/23970, ALFA) (+ 16 more)
G=0.31832 (5335/16760, 8.3KJPN)
G=0.2784 (1394/5008, 1000G)
G=0.2085 (934/4480, Estonian)
G=0.3028 (1167/3854, ALSPAC)
G=0.3109 (1153/3708, TWINSUK)
G=0.2874 (842/2930, KOREAN)
G=0.2844 (538/1892, HapMap)
G=0.2806 (514/1832, Korea1K)
G=0.282 (281/998, GoNL)
G=0.310 (194/626, Chileans)
G=0.292 (175/600, NorthernSweden)
G=0.269 (58/216, Qatari)
G=0.204 (44/216, Vietnamese)
A=0.400 (84/210, SGDP_PRJ)
G=0.28 (11/40, GENOME_DK)
A=0.44 (8/18, 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.83131527A>G
GRCh37.p13 chr 1 NC_000001.10:g.83597210A>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 23970 A=0.70951 G=0.29049
European Sub 15668 A=0.71968 G=0.28032
African Sub 3624 A=0.6760 G=0.3240
African Others Sub 126 A=0.611 G=0.389
African American Sub 3498 A=0.6784 G=0.3216
Asian Sub 160 A=0.713 G=0.287
East Asian Sub 102 A=0.755 G=0.245
Other Asian Sub 58 A=0.64 G=0.36
Latin American 1 Sub 292 A=0.682 G=0.318
Latin American 2 Sub 2770 A=0.7166 G=0.2834
South Asian Sub 110 A=0.745 G=0.255
Other Sub 1346 A=0.6694 G=0.3306


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=0.690098 G=0.309902
gnomAD - Genomes Global Study-wide 139914 A=0.695299 G=0.304701
gnomAD - Genomes European Sub 75814 A=0.70413 G=0.29587
gnomAD - Genomes African Sub 41896 A=0.67162 G=0.32838
gnomAD - Genomes American Sub 13602 A=0.71710 G=0.28290
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.6687 G=0.3313
gnomAD - Genomes East Asian Sub 3130 A=0.7371 G=0.2629
gnomAD - Genomes Other Sub 2152 A=0.6877 G=0.3123
8.3KJPN JAPANESE Study-wide 16760 A=0.68168 G=0.31832
1000Genomes Global Study-wide 5008 A=0.7216 G=0.2784
1000Genomes African Sub 1322 A=0.6619 G=0.3381
1000Genomes East Asian Sub 1008 A=0.7520 G=0.2480
1000Genomes Europe Sub 1006 A=0.7038 G=0.2962
1000Genomes South Asian Sub 978 A=0.769 G=0.231
1000Genomes American Sub 694 A=0.751 G=0.249
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7915 G=0.2085
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.6972 G=0.3028
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6891 G=0.3109
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7126 G=0.2874
HapMap Global Study-wide 1892 A=0.7156 G=0.2844
HapMap American Sub 770 A=0.736 G=0.264
HapMap African Sub 692 A=0.697 G=0.303
HapMap Asian Sub 254 A=0.732 G=0.268
HapMap Europe Sub 176 A=0.676 G=0.324
Korean Genome Project KOREAN Study-wide 1832 A=0.7194 G=0.2806
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.718 G=0.282
Chileans Chilean Study-wide 626 A=0.690 G=0.310
Northern Sweden ACPOP Study-wide 600 A=0.708 G=0.292
Qatari Global Study-wide 216 A=0.731 G=0.269
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.796 G=0.204
SGDP_PRJ Global Study-wide 210 A=0.400 G=0.600
The Danish reference pan genome Danish Study-wide 40 A=0.72 G=0.28
Siberian Global Study-wide 18 A=0.44 G=0.56
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.83131527= NC_000001.11:g.83131527A>G
GRCh37.p13 chr 1 NC_000001.10:g.83597210= NC_000001.10:g.83597210A>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#.

64 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss414357 Jul 12, 2000 (79)
2 SC_JCM ss595601 Jul 16, 2000 (80)
3 KWOK ss1023556 Oct 04, 2000 (86)
4 SC_SNP ss13020155 Dec 05, 2003 (119)
5 SC_SNP ss15556856 Feb 27, 2004 (120)
6 PERLEGEN ss23145056 Sep 20, 2004 (123)
7 ABI ss44001633 Mar 14, 2006 (126)
8 AFFY ss76844663 Dec 06, 2007 (129)
9 HGSV ss84200083 Dec 15, 2007 (130)
10 HGSV ss84222749 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss87583964 Mar 23, 2008 (129)
12 KRIBB_YJKIM ss104815088 Feb 06, 2009 (130)
13 1000GENOMES ss108367176 Jan 23, 2009 (130)
14 ILLUMINA-UK ss118850810 Feb 14, 2009 (130)
15 ENSEMBL ss138025314 Dec 01, 2009 (131)
16 GMI ss155265383 Dec 01, 2009 (131)
17 BCM-HGSC-SUB ss205323197 Jul 04, 2010 (132)
18 1000GENOMES ss210573153 Jul 14, 2010 (132)
19 1000GENOMES ss218492058 Jul 14, 2010 (132)
20 1000GENOMES ss230612972 Jul 14, 2010 (132)
21 1000GENOMES ss238291045 Jul 15, 2010 (132)
22 GMI ss275903168 May 04, 2012 (137)
23 PJP ss290550957 May 09, 2011 (134)
24 TISHKOFF ss554362554 Apr 25, 2013 (138)
25 SSMP ss648176425 Apr 25, 2013 (138)
26 EVA-GONL ss975366067 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1068043933 Aug 21, 2014 (142)
28 1000GENOMES ss1291670594 Aug 21, 2014 (142)
29 DDI ss1425876317 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1574191947 Apr 01, 2015 (144)
31 EVA_DECODE ss1584740012 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1600583807 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1643577840 Apr 01, 2015 (144)
34 EVA_SVP ss1712348381 Apr 01, 2015 (144)
35 HAMMER_LAB ss1794652618 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1918568947 Feb 12, 2016 (147)
37 GENOMED ss1966794197 Jul 19, 2016 (147)
38 JJLAB ss2019805147 Sep 14, 2016 (149)
39 USC_VALOUEV ss2147822260 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2164133567 Dec 20, 2016 (150)
41 TOPMED ss2326425819 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2624413858 Nov 08, 2017 (151)
43 GRF ss2697744416 Nov 08, 2017 (151)
44 GNOMAD ss2757366627 Nov 08, 2017 (151)
45 SWEGEN ss2987126094 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023665386 Nov 08, 2017 (151)
47 TOPMED ss3081742244 Nov 08, 2017 (151)
48 CSHL ss3343543957 Nov 08, 2017 (151)
49 EGCUT_WGS ss3655206689 Jul 12, 2019 (153)
50 EVA_DECODE ss3687151882 Jul 12, 2019 (153)
51 ACPOP ss3727217499 Jul 12, 2019 (153)
52 EVA ss3746440983 Jul 12, 2019 (153)
53 PACBIO ss3783464063 Jul 12, 2019 (153)
54 PACBIO ss3789114202 Jul 12, 2019 (153)
55 PACBIO ss3793986992 Jul 12, 2019 (153)
56 KHV_HUMAN_GENOMES ss3799446985 Jul 12, 2019 (153)
57 EVA ss3826271648 Apr 25, 2020 (154)
58 EVA ss3836524775 Apr 25, 2020 (154)
59 EVA ss3841931986 Apr 25, 2020 (154)
60 SGDP_PRJ ss3849251189 Apr 25, 2020 (154)
61 KRGDB ss3894302616 Apr 25, 2020 (154)
62 KOGIC ss3944882217 Apr 25, 2020 (154)
63 TOPMED ss4456704874 Apr 25, 2021 (155)
64 TOMMO_GENOMICS ss5144813579 Apr 25, 2021 (155)
65 1000Genomes NC_000001.10 - 83597210 Oct 11, 2018 (152)
66 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 83597210 Oct 11, 2018 (152)
67 Chileans NC_000001.10 - 83597210 Apr 25, 2020 (154)
68 Genetic variation in the Estonian population NC_000001.10 - 83597210 Oct 11, 2018 (152)
69 The Danish reference pan genome NC_000001.10 - 83597210 Apr 25, 2020 (154)
70 gnomAD - Genomes NC_000001.11 - 83131527 Apr 25, 2021 (155)
71 Genome of the Netherlands Release 5 NC_000001.10 - 83597210 Apr 25, 2020 (154)
72 HapMap NC_000001.11 - 83131527 Apr 25, 2020 (154)
73 KOREAN population from KRGDB NC_000001.10 - 83597210 Apr 25, 2020 (154)
74 Korean Genome Project NC_000001.11 - 83131527 Apr 25, 2020 (154)
75 Northern Sweden NC_000001.10 - 83597210 Jul 12, 2019 (153)
76 Qatari NC_000001.10 - 83597210 Apr 25, 2020 (154)
77 SGDP_PRJ NC_000001.10 - 83597210 Apr 25, 2020 (154)
78 Siberian NC_000001.10 - 83597210 Apr 25, 2020 (154)
79 8.3KJPN NC_000001.10 - 83597210 Apr 25, 2021 (155)
80 TopMed NC_000001.11 - 83131527 Apr 25, 2021 (155)
81 UK 10K study - Twins NC_000001.10 - 83597210 Oct 11, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000001.10 - 83597210 Jul 12, 2019 (153)
83 ALFA NC_000001.11 - 83131527 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)
rs60737339 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84200083, ss84222749 NC_000001.8:83309230:A:G NC_000001.11:83131526:A:G (self)
ss87583964, ss108367176, ss118850810, ss205323197, ss210573153, ss275903168, ss290550957, ss1584740012, ss1712348381 NC_000001.9:83369797:A:G NC_000001.11:83131526:A:G (self)
2417873, 1327235, 13840, 944937, 1583296, 573060, 1480010, 502364, 610877, 1268169, 338614, 2782886, 1327235, 284704, ss218492058, ss230612972, ss238291045, ss554362554, ss648176425, ss975366067, ss1068043933, ss1291670594, ss1425876317, ss1574191947, ss1600583807, ss1643577840, ss1794652618, ss1918568947, ss1966794197, ss2019805147, ss2147822260, ss2326425819, ss2624413858, ss2697744416, ss2757366627, ss2987126094, ss3343543957, ss3655206689, ss3727217499, ss3746440983, ss3783464063, ss3789114202, ss3793986992, ss3826271648, ss3836524775, ss3849251189, ss3894302616, ss5144813579 NC_000001.10:83597209:A:G NC_000001.11:83131526:A:G (self)
17065003, 113063, 1260218, 12793721, 20311209, 4911267024, ss2164133567, ss3023665386, ss3081742244, ss3687151882, ss3799446985, ss3841931986, ss3944882217, ss4456704874 NC_000001.11:83131526:A:G NC_000001.11:83131526:A:G (self)
ss13020155 NT_004902.14:465502:A:G NC_000001.11:83131526:A:G (self)
ss15556856 NT_026943.13:8417383:A:G NC_000001.11:83131526:A:G (self)
ss414357, ss595601, ss1023556, ss23145056, ss44001633, ss76844663, ss104815088, ss138025314, ss155265383 NT_032977.9:53569127:A:G NC_000001.11:83131526: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 rs323952

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