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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.

rs4970362

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1159358 (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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.394890 (55272/139968, GnomAD)
A=0.36998 (32720/88438, ALFA)
A=0.42697 (7156/16760, 8.3KJPN) (+ 14 more)
A=0.3960 (1983/5008, 1000G)
A=0.4326 (1938/4480, Estonian)
A=0.3446 (1328/3854, ALSPAC)
A=0.3503 (1299/3708, TWINSUK)
A=0.4413 (1293/2930, KOREAN)
A=0.3567 (737/2066, HGDP_Stanford)
A=0.4101 (776/1892, HapMap)
A=0.381 (380/998, GoNL)
A=0.393 (236/600, NorthernSweden)
A=0.227 (108/476, SGDP_PRJ)
A=0.347 (75/216, Qatari)
A=0.431 (93/216, Vietnamese)
A=0.22 (20/90, Ancient Sardinia)
A=0.23 (11/48, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
2 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.1159358A>C
GRCh38.p13 chr 1 NC_000001.11:g.1159358A>G
GRCh38.p13 chr 1 NC_000001.11:g.1159358A>T
GRCh37.p13 chr 1 NC_000001.10:g.1094738A>C
GRCh37.p13 chr 1 NC_000001.10:g.1094738A>G
GRCh37.p13 chr 1 NC_000001.10:g.1094738A>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 88438 A=0.36998 C=0.00000, G=0.63002
European Sub 69256 A=0.36972 C=0.00000, G=0.63028
African Sub 4724 A=0.5409 C=0.0000, G=0.4591
African Others Sub 168 A=0.542 C=0.000, G=0.458
African American Sub 4556 A=0.5408 C=0.0000, G=0.4592
Asian Sub 448 A=0.509 C=0.000, G=0.491
East Asian Sub 382 A=0.508 C=0.000, G=0.492
Other Asian Sub 66 A=0.52 C=0.00, G=0.48
Latin American 1 Sub 550 A=0.405 C=0.000, G=0.595
Latin American 2 Sub 4954 A=0.2277 C=0.0000, G=0.7723
South Asian Sub 4930 A=0.3467 C=0.0000, G=0.6533
Other Sub 3576 A=0.3557 C=0.0000, G=0.6443


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
gnomAD - Genomes Global Study-wide 139968 A=0.394890 G=0.605110
gnomAD - Genomes European Sub 75786 A=0.37058 G=0.62942
gnomAD - Genomes African Sub 41938 A=0.48297 G=0.51703
gnomAD - Genomes American Sub 13648 A=0.26846 G=0.73154
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.2991 G=0.7009
gnomAD - Genomes East Asian Sub 3124 A=0.4830 G=0.5170
gnomAD - Genomes Other Sub 2152 A=0.3559 G=0.6441
8.3KJPN JAPANESE Study-wide 16760 A=0.42697 G=0.57303
1000Genomes Global Study-wide 5008 A=0.3960 G=0.6040
1000Genomes African Sub 1322 A=0.5023 G=0.4977
1000Genomes East Asian Sub 1008 A=0.4494 G=0.5506
1000Genomes Europe Sub 1006 A=0.3499 G=0.6501
1000Genomes South Asian Sub 978 A=0.344 G=0.656
1000Genomes American Sub 694 A=0.256 G=0.744
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4326 G=0.5674
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.3446 G=0.6554
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.3503 G=0.6497
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.4413 G=0.5587, T=0.0000
HGDP-CEPH-db Supplement 1 Global Study-wide 2066 A=0.3567 G=0.6433
HGDP-CEPH-db Supplement 1 Est_Asia Sub 468 A=0.400 G=0.600
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 406 A=0.362 G=0.638
HGDP-CEPH-db Supplement 1 Middle_Est Sub 346 A=0.402 G=0.598
HGDP-CEPH-db Supplement 1 Europe Sub 316 A=0.294 G=0.706
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=0.517 G=0.483
HGDP-CEPH-db Supplement 1 America Sub 216 A=0.167 G=0.833
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=0.14 G=0.86
HapMap Global Study-wide 1892 A=0.4101 G=0.5899
HapMap American Sub 770 A=0.342 G=0.658
HapMap African Sub 692 A=0.480 G=0.520
HapMap Asian Sub 254 A=0.457 G=0.543
HapMap Europe Sub 176 A=0.369 G=0.631
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.381 G=0.619
Northern Sweden ACPOP Study-wide 600 A=0.393 G=0.607
SGDP_PRJ Global Study-wide 476 A=0.227 G=0.773
Qatari Global Study-wide 216 A=0.347 G=0.653
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.431 G=0.569
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 90 A=0.22 G=0.78
Siberian Global Study-wide 48 A=0.23 G=0.77
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= C G T
GRCh38.p13 chr 1 NC_000001.11:g.1159358= NC_000001.11:g.1159358A>C NC_000001.11:g.1159358A>G NC_000001.11:g.1159358A>T
GRCh37.p13 chr 1 NC_000001.10:g.1094738= NC_000001.10:g.1094738A>C NC_000001.10:g.1094738A>G NC_000001.10:g.1094738A>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#.

100 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6879499 Feb 20, 2003 (111)
2 WI_SSAHASNP ss11422119 Jul 11, 2003 (116)
3 SC_SNP ss13052139 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss16412681 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss19116925 Feb 27, 2004 (120)
6 SSAHASNP ss20512854 Apr 05, 2004 (121)
7 PERLEGEN ss23803635 Sep 20, 2004 (123)
8 ABI ss41270920 Mar 15, 2006 (126)
9 ILLUMINA ss66685657 Dec 02, 2006 (127)
10 ILLUMINA ss67406326 Dec 02, 2006 (127)
11 ILLUMINA ss67773317 Dec 02, 2006 (127)
12 PERLEGEN ss68756323 May 18, 2007 (127)
13 ILLUMINA ss70839925 May 25, 2008 (130)
14 ILLUMINA ss71423664 May 18, 2007 (127)
15 ILLUMINA ss75581891 Dec 07, 2007 (129)
16 HGSV ss78365015 Dec 07, 2007 (129)
17 ILLUMINA ss79204983 Dec 15, 2007 (130)
18 KRIBB_YJKIM ss84414092 Dec 15, 2007 (130)
19 HUMANGENOME_JCVI ss99179793 Feb 05, 2009 (130)
20 BGI ss102713657 Dec 01, 2009 (131)
21 1000GENOMES ss107938604 Jan 22, 2009 (130)
22 ILLUMINA-UK ss118440427 Feb 14, 2009 (130)
23 ILLUMINA ss122445798 Dec 01, 2009 (131)
24 ENSEMBL ss131636747 Dec 01, 2009 (131)
25 ILLUMINA ss154333133 Dec 01, 2009 (131)
26 GMI ss154528350 Dec 01, 2009 (131)
27 ILLUMINA ss159509635 Dec 01, 2009 (131)
28 ILLUMINA ss160733842 Dec 01, 2009 (131)
29 COMPLETE_GENOMICS ss162983781 Jul 04, 2010 (132)
30 COMPLETE_GENOMICS ss163707978 Jul 04, 2010 (132)
31 ILLUMINA ss171999168 Jul 04, 2010 (132)
32 ILLUMINA ss173896320 Jul 04, 2010 (132)
33 BUSHMAN ss197889342 Jul 04, 2010 (132)
34 BCM-HGSC-SUB ss205451345 Jul 04, 2010 (132)
35 1000GENOMES ss210449668 Jul 14, 2010 (132)
36 1000GENOMES ss218192150 Jul 14, 2010 (132)
37 1000GENOMES ss230396540 Jul 14, 2010 (132)
38 1000GENOMES ss238116064 Jul 15, 2010 (132)
39 BL ss252866401 May 09, 2011 (134)
40 GMI ss275682567 May 04, 2012 (137)
41 GMI ss283988039 Apr 25, 2013 (138)
42 PJP ss290494398 May 09, 2011 (134)
43 ILLUMINA ss482131216 Sep 08, 2015 (146)
44 ILLUMINA ss537300526 Sep 08, 2015 (146)
45 TISHKOFF ss553714116 Apr 25, 2013 (138)
46 SSMP ss647518701 Apr 25, 2013 (138)
47 ILLUMINA ss825535501 Apr 01, 2015 (144)
48 ILLUMINA ss833020955 Aug 21, 2014 (142)
49 ILLUMINA ss833611783 Aug 21, 2014 (142)
50 EVA-GONL ss974772421 Aug 21, 2014 (142)
51 JMKIDD_LAB ss1067613905 Aug 21, 2014 (142)
52 1000GENOMES ss1289351975 Aug 21, 2014 (142)
53 DDI ss1425685961 Apr 01, 2015 (144)
54 EVA_DECODE ss1584132326 Apr 01, 2015 (144)
55 EVA_UK10K_ALSPAC ss1599383317 Apr 01, 2015 (144)
56 EVA_UK10K_TWINSUK ss1642377350 Apr 01, 2015 (144)
57 EVA_SVP ss1712305562 Apr 01, 2015 (144)
58 HAMMER_LAB ss1793717872 Sep 08, 2015 (146)
59 WEILL_CORNELL_DGM ss1917964435 Feb 12, 2016 (147)
60 GENOMED ss1966667775 Jul 19, 2016 (147)
61 JJLAB ss2019500056 Sep 14, 2016 (149)
62 USC_VALOUEV ss2147486902 Dec 20, 2016 (150)
63 HUMAN_LONGEVITY ss2159389514 Dec 20, 2016 (150)
64 TOPMED ss2321528754 Dec 20, 2016 (150)
65 SYSTEMSBIOZJU ss2624265613 Nov 08, 2017 (151)
66 ILLUMINA ss2634995311 Nov 08, 2017 (151)
67 GRF ss2697377747 Nov 08, 2017 (151)
68 GNOMAD ss2750676593 Nov 08, 2017 (151)
69 SWEGEN ss2986155067 Nov 08, 2017 (151)
70 BIOINF_KMB_FNS_UNIBA ss3023514379 Nov 08, 2017 (151)
71 TOPMED ss3066482510 Nov 08, 2017 (151)
72 CSHL ss3343274535 Nov 08, 2017 (151)
73 ILLUMINA ss3626007166 Oct 11, 2018 (152)
74 ILLUMINA ss3635978730 Oct 11, 2018 (152)
75 ILLUMINA ss3637732513 Oct 11, 2018 (152)
76 ILLUMINA ss3638887877 Oct 11, 2018 (152)
77 ILLUMINA ss3639440643 Oct 11, 2018 (152)
78 ILLUMINA ss3640973180 Oct 11, 2018 (152)
79 ILLUMINA ss3641266995 Oct 11, 2018 (152)
80 ILLUMINA ss3642746793 Oct 11, 2018 (152)
81 URBANLAB ss3646582004 Oct 11, 2018 (152)
82 EGCUT_WGS ss3654266106 Jul 12, 2019 (153)
83 EVA_DECODE ss3685998868 Jul 12, 2019 (153)
84 ACPOP ss3726719089 Jul 12, 2019 (153)
85 EVA ss3745724808 Jul 12, 2019 (153)
86 PACBIO ss3783303112 Jul 12, 2019 (153)
87 PACBIO ss3788980888 Jul 12, 2019 (153)
88 PACBIO ss3793853449 Jul 12, 2019 (153)
89 KHV_HUMAN_GENOMES ss3798747445 Jul 12, 2019 (153)
90 EVA ss3825982800 Apr 25, 2020 (154)
91 EVA ss3836379078 Apr 25, 2020 (154)
92 EVA ss3841783108 Apr 25, 2020 (154)
93 HGDP ss3847322128 Apr 25, 2020 (154)
94 SGDP_PRJ ss3848005290 Apr 25, 2020 (154)
95 KRGDB ss3892848223 Apr 25, 2020 (154)
96 EVA ss3984774106 Apr 25, 2021 (155)
97 EVA ss4016889131 Apr 25, 2021 (155)
98 TOPMED ss4436532303 Apr 25, 2021 (155)
99 TOPMED ss4436532304 Apr 25, 2021 (155)
100 TOMMO_GENOMICS ss5142068957 Apr 25, 2021 (155)
101 1000Genomes NC_000001.10 - 1094738 Oct 11, 2018 (152)
102 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1094738 Oct 11, 2018 (152)
103 Genetic variation in the Estonian population NC_000001.10 - 1094738 Oct 11, 2018 (152)
104 gnomAD - Genomes NC_000001.11 - 1159358 Apr 25, 2021 (155)
105 Genome of the Netherlands Release 5 NC_000001.10 - 1094738 Apr 25, 2020 (154)
106 HGDP-CEPH-db Supplement 1 NC_000001.9 - 1084601 Apr 25, 2020 (154)
107 HapMap NC_000001.11 - 1159358 Apr 25, 2020 (154)
108 KOREAN population from KRGDB NC_000001.10 - 1094738 Apr 25, 2020 (154)
109 Northern Sweden NC_000001.10 - 1094738 Jul 12, 2019 (153)
110 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 1094738 Apr 25, 2021 (155)
111 Qatari NC_000001.10 - 1094738 Apr 25, 2020 (154)
112 SGDP_PRJ NC_000001.10 - 1094738 Apr 25, 2020 (154)
113 Siberian NC_000001.10 - 1094738 Apr 25, 2020 (154)
114 8.3KJPN NC_000001.10 - 1094738 Apr 25, 2021 (155)
115 TopMed

Submission ignored due to conflicting rows:
Row 138638 (NC_000001.11:1159357:A:C 1/264690)
Row 138639 (NC_000001.11:1159357:A:G 163131/264690)

- Apr 25, 2021 (155)
116 TopMed

Submission ignored due to conflicting rows:
Row 138638 (NC_000001.11:1159357:A:C 1/264690)
Row 138639 (NC_000001.11:1159357:A:G 163131/264690)

- Apr 25, 2021 (155)
117 UK 10K study - Twins NC_000001.10 - 1094738 Oct 11, 2018 (152)
118 A Vietnamese Genetic Variation Database NC_000001.10 - 1094738 Jul 12, 2019 (153)
119 ALFA NC_000001.11 - 1159358 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)
rs59238685 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
13205471974, ss4436532303 NC_000001.11:1159357:A:C NC_000001.11:1159357:A:C
ss78365015, ss3638887877, ss3639440643 NC_000001.8:1134660:A:G NC_000001.11:1159357:A:G (self)
20, ss107938604, ss118440427, ss160733842, ss162983781, ss163707978, ss197889342, ss205451345, ss210449668, ss252866401, ss275682567, ss283988039, ss290494398, ss825535501, ss1584132326, ss1712305562, ss2634995311, ss3642746793, ss3847322128 NC_000001.9:1084600:A:G NC_000001.11:1159357:A:G (self)
17140, 5741, 4354, 2587, 25617, 3954, 33, 6365, 22270, 3256, 38264, 5741, 1272, ss218192150, ss230396540, ss238116064, ss482131216, ss537300526, ss553714116, ss647518701, ss833020955, ss833611783, ss974772421, ss1067613905, ss1289351975, ss1425685961, ss1599383317, ss1642377350, ss1793717872, ss1917964435, ss1966667775, ss2019500056, ss2147486902, ss2321528754, ss2624265613, ss2697377747, ss2750676593, ss2986155067, ss3343274535, ss3626007166, ss3635978730, ss3637732513, ss3640973180, ss3641266995, ss3654266106, ss3726719089, ss3745724808, ss3783303112, ss3788980888, ss3793853449, ss3825982800, ss3836379078, ss3848005290, ss3892848223, ss3984774106, ss4016889131, ss5142068957 NC_000001.10:1094737:A:G NC_000001.11:1159357:A:G (self)
152940, 253, 79109, 13205471974, ss2159389514, ss3023514379, ss3066482510, ss3646582004, ss3685998868, ss3798747445, ss3841783108, ss4436532304 NC_000001.11:1159357:A:G NC_000001.11:1159357:A:G (self)
ss6879499, ss23803635, ss41270920, ss66685657, ss67406326, ss67773317, ss68756323, ss70839925, ss71423664, ss75581891, ss79204983, ss84414092, ss99179793, ss102713657, ss122445798, ss131636747, ss154333133, ss154528350, ss159509635, ss171999168, ss173896320 NT_004350.19:573369:A:G NC_000001.11:1159357:A:G (self)
ss16412681, ss19116925, ss20512854 NT_077913.2:98448:A:G NC_000001.11:1159357:A:G (self)
ss11422119, ss13052139 NT_077960.1:164178:A:G NC_000001.11:1159357:A:G (self)
25617, ss3892848223 NC_000001.10:1094737:A:T NC_000001.11:1159357:A:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs4970362
PMID Title Author Year Journal
19176549 Genome-wide association analysis by lasso penalized logistic regression. Wu TT et al. 2009 Bioinformatics (Oxford, England)
20964851 CCRaVAT and QuTie-enabling analysis of rare variants in large-scale case control and quantitative trait association studies. Lawrence R et al. 2010 BMC bioinformatics
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