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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.

rs2494124

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:194525064 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.073085 (19345/264690, TOPMED)
G=0.081613 (11359/139182, GnomAD)
G=0.09217 (1741/18890, ALFA) (+ 15 more)
G=0.00000 (0/16760, 8.3KJPN)
G=0.0417 (209/5008, 1000G)
G=0.1045 (468/4480, Estonian)
G=0.1134 (437/3854, ALSPAC)
G=0.1106 (410/3708, TWINSUK)
G=0.0003 (1/2930, KOREAN)
G=0.0005 (1/1832, Korea1K)
G=0.138 (138/998, GoNL)
G=0.178 (107/600, NorthernSweden)
G=0.072 (40/554, SGDP_PRJ)
G=0.052 (17/328, HapMap)
G=0.028 (6/216, Qatari)
G=0.000 (0/210, Vietnamese)
G=0.11 (6/56, Siberian)
G=0.10 (4/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.194525064G>A
GRCh38.p13 chr 1 NC_000001.11:g.194525064G>T
GRCh37.p13 chr 1 NC_000001.10:g.194494194G>A
GRCh37.p13 chr 1 NC_000001.10:g.194494194G>T
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 18890 G=0.09217 A=0.90783
European Sub 14286 G=0.10633 A=0.89367
African Sub 2946 G=0.0434 A=0.9566
African Others Sub 114 G=0.035 A=0.965
African American Sub 2832 G=0.0438 A=0.9562
Asian Sub 112 G=0.009 A=0.991
East Asian Sub 86 G=0.00 A=1.00
Other Asian Sub 26 G=0.04 A=0.96
Latin American 1 Sub 146 G=0.034 A=0.966
Latin American 2 Sub 610 G=0.059 A=0.941
South Asian Sub 98 G=0.06 A=0.94
Other Sub 692 G=0.066 A=0.934


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=0.073085 A=0.926915
gnomAD - Genomes Global Study-wide 139182 G=0.081613 A=0.918387
gnomAD - Genomes European Sub 75196 G=0.11197 A=0.88803
gnomAD - Genomes African Sub 41876 G=0.04647 A=0.95353
gnomAD - Genomes American Sub 13518 G=0.05215 A=0.94785
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.0443 A=0.9557
gnomAD - Genomes East Asian Sub 3132 G=0.0006 A=0.9994
gnomAD - Genomes Other Sub 2140 G=0.0650 A=0.9350
8.3KJPN JAPANESE Study-wide 16760 G=0.00000 A=1.00000
1000Genomes Global Study-wide 5008 G=0.0417 A=0.9583
1000Genomes African Sub 1322 G=0.0325 A=0.9675
1000Genomes East Asian Sub 1008 G=0.0000 A=1.0000
1000Genomes Europe Sub 1006 G=0.0954 A=0.9046
1000Genomes South Asian Sub 978 G=0.042 A=0.958
1000Genomes American Sub 694 G=0.042 A=0.958
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.1045 A=0.8955
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.1134 A=0.8866
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.1106 A=0.8894
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0003 A=0.9997, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.0005 A=0.9995
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.138 A=0.862
Northern Sweden ACPOP Study-wide 600 G=0.178 A=0.822
SGDP_PRJ Global Study-wide 554 G=0.072 A=0.928
HapMap Global Study-wide 328 G=0.052 A=0.948
HapMap African Sub 120 G=0.042 A=0.958
HapMap American Sub 120 G=0.100 A=0.900
HapMap Asian Sub 88 G=0.00 A=1.00
Qatari Global Study-wide 216 G=0.028 A=0.972
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.000 A=1.000
Siberian Global Study-wide 56 G=0.11 A=0.89
The Danish reference pan genome Danish Study-wide 40 G=0.10 A=0.90
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 T
GRCh38.p13 chr 1 NC_000001.11:g.194525064= NC_000001.11:g.194525064G>A NC_000001.11:g.194525064G>T
GRCh37.p13 chr 1 NC_000001.10:g.194494194= NC_000001.10:g.194494194G>A NC_000001.10:g.194494194G>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#.

61 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3499597 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss9811150 Jul 11, 2003 (116)
3 SC_SNP ss13010718 Dec 05, 2003 (123)
4 CSHL-HAPMAP ss17352438 Feb 27, 2004 (123)
5 CSHL-HAPMAP ss19852557 Feb 27, 2004 (123)
6 SSAHASNP ss20443920 Apr 05, 2004 (123)
7 PERLEGEN ss24272672 Sep 20, 2004 (123)
8 HGSV ss84524372 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss87920314 Mar 23, 2008 (129)
10 HUMANGENOME_JCVI ss97994574 Feb 05, 2009 (130)
11 BGI ss106620834 Feb 05, 2009 (130)
12 1000GENOMES ss108824238 Jan 23, 2009 (130)
13 1000GENOMES ss111567102 Jan 25, 2009 (130)
14 ILLUMINA-UK ss119158243 Dec 01, 2009 (131)
15 ENSEMBL ss139114688 Dec 01, 2009 (131)
16 GMI ss156100666 Dec 01, 2009 (131)
17 BUSHMAN ss199428141 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss205156110 Jul 04, 2010 (132)
19 1000GENOMES ss218801518 Jul 14, 2010 (132)
20 1000GENOMES ss230841379 Jul 14, 2010 (132)
21 GMI ss276157408 May 04, 2012 (137)
22 PJP ss290694187 May 09, 2011 (134)
23 SSMP ss648596768 Apr 25, 2013 (138)
24 EVA-GONL ss975978382 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1068484338 Aug 21, 2014 (142)
26 1000GENOMES ss1294035723 Aug 21, 2014 (142)
27 DDI ss1426064682 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1574578961 Apr 01, 2015 (144)
29 EVA_DECODE ss1585372995 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1601807829 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1644801862 Apr 01, 2015 (144)
32 HAMMER_LAB ss1795504004 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1919211465 Feb 12, 2016 (147)
34 JJLAB ss2020123610 Sep 14, 2016 (149)
35 USC_VALOUEV ss2148150483 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2168834265 Dec 20, 2016 (150)
37 TOPMED ss2331407546 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2624569720 Nov 08, 2017 (151)
39 GRF ss2698138171 Nov 08, 2017 (151)
40 GNOMAD ss2764473410 Nov 08, 2017 (151)
41 SWEGEN ss2988198276 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3023821126 Nov 08, 2017 (151)
43 TOPMED ss3099386676 Nov 08, 2017 (151)
44 CSHL ss3343840342 Nov 08, 2017 (151)
45 URBANLAB ss3646853157 Oct 11, 2018 (152)
46 EGCUT_WGS ss3656156273 Jul 12, 2019 (153)
47 EVA_DECODE ss3688325031 Jul 12, 2019 (153)
48 ACPOP ss3727726498 Jul 12, 2019 (153)
49 EVA ss3747146397 Jul 12, 2019 (153)
50 PACBIO ss3783645707 Jul 12, 2019 (153)
51 PACBIO ss3789264547 Jul 12, 2019 (153)
52 PACBIO ss3794136712 Jul 12, 2019 (153)
53 KHV_HUMAN_GENOMES ss3800152313 Jul 12, 2019 (153)
54 EVA ss3826566338 Apr 25, 2020 (154)
55 EVA ss3836681181 Apr 25, 2020 (154)
56 EVA ss3842092043 Apr 25, 2020 (154)
57 SGDP_PRJ ss3850580143 Apr 25, 2020 (154)
58 KRGDB ss3895856420 Apr 25, 2020 (154)
59 KOGIC ss3946187221 Apr 25, 2020 (154)
60 TOPMED ss4478152861 Apr 25, 2021 (155)
61 TOMMO_GENOMICS ss5147734280 Apr 25, 2021 (155)
62 1000Genomes NC_000001.10 - 194494194 Oct 11, 2018 (152)
63 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 194494194 Oct 11, 2018 (152)
64 Genetic variation in the Estonian population NC_000001.10 - 194494194 Oct 11, 2018 (152)
65 The Danish reference pan genome NC_000001.10 - 194494194 Apr 25, 2020 (154)
66 gnomAD - Genomes NC_000001.11 - 194525064 Apr 25, 2021 (155)
67 Genome of the Netherlands Release 5 NC_000001.10 - 194494194 Apr 25, 2020 (154)
68 HapMap NC_000001.11 - 194525064 Apr 25, 2020 (154)
69 KOREAN population from KRGDB NC_000001.10 - 194494194 Apr 25, 2020 (154)
70 Korean Genome Project NC_000001.11 - 194525064 Apr 25, 2020 (154)
71 Northern Sweden NC_000001.10 - 194494194 Jul 12, 2019 (153)
72 Qatari NC_000001.10 - 194494194 Apr 25, 2020 (154)
73 SGDP_PRJ NC_000001.10 - 194494194 Apr 25, 2020 (154)
74 Siberian NC_000001.10 - 194494194 Apr 25, 2020 (154)
75 8.3KJPN NC_000001.10 - 194494194 Apr 25, 2021 (155)
76 TopMed NC_000001.11 - 194525064 Apr 25, 2021 (155)
77 UK 10K study - Twins NC_000001.10 - 194494194 Oct 11, 2018 (152)
78 A Vietnamese Genetic Variation Database NC_000001.10 - 194494194 Jul 12, 2019 (153)
79 ALFA NC_000001.11 - 194525064 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)
rs9427600 Sep 24, 2004 (123)
rs17567804 Oct 07, 2004 (123)
rs59660356 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84524372 NC_000001.8:191225850:G:A NC_000001.11:194525063:G:A (self)
ss87920314, ss108824238, ss111567102, ss119158243, ss199428141, ss205156110, ss276157408, ss290694187, ss1585372995 NC_000001.9:192760816:G:A NC_000001.11:194525063:G:A (self)
4867970, 2673526, 1894521, 1822205, 1166237, 3033814, 1011363, 1253395, 2597123, 666837, 5703587, 2673526, 576978, ss218801518, ss230841379, ss648596768, ss975978382, ss1068484338, ss1294035723, ss1426064682, ss1574578961, ss1601807829, ss1644801862, ss1795504004, ss1919211465, ss2020123610, ss2148150483, ss2331407546, ss2624569720, ss2698138171, ss2764473410, ss2988198276, ss3343840342, ss3656156273, ss3727726498, ss3747146397, ss3783645707, ss3789264547, ss3794136712, ss3826566338, ss3836681181, ss3850580143, ss3895856420, ss5147734280 NC_000001.10:194494193:G:A NC_000001.11:194525063:G:A (self)
35112521, 234543, 2565222, 26232807, 41759196, 2760959786, ss2168834265, ss3023821126, ss3099386676, ss3646853157, ss3688325031, ss3800152313, ss3842092043, ss3946187221, ss4478152861 NC_000001.11:194525063:G:A NC_000001.11:194525063:G:A (self)
ss3499597, ss24272672, ss97994574, ss106620834, ss139114688, ss156100666 NT_004487.19:45982835:G:A NC_000001.11:194525063:G:A (self)
ss9811150, ss13010718, ss17352438, ss19852557, ss20443920 NT_004671.15:5849179:G:A NC_000001.11:194525063:G:A (self)
3033814, ss3895856420 NC_000001.10:194494193:G:T NC_000001.11:194525063: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 rs2494124

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