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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.

rs4908329

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99602346 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.482617 (127744/264690, TOPMED)
C=0.460504 (99923/216986, ALFA)
T=0.498050 (69741/140028, GnomAD) (+ 18 more)
T=0.21718 (3640/16760, 8.3KJPN)
T=0.4185 (2096/5008, 1000G)
T=0.4987 (2234/4480, Estonian)
C=0.4276 (1648/3854, ALSPAC)
C=0.4307 (1597/3708, TWINSUK)
T=0.1481 (434/2930, KOREAN)
T=0.4036 (841/2084, HGDP_Stanford)
T=0.4081 (768/1882, HapMap)
T=0.1578 (289/1832, Korea1K)
T=0.4281 (476/1112, Daghestan)
C=0.417 (416/998, GoNL)
T=0.468 (281/600, NorthernSweden)
C=0.367 (124/338, SGDP_PRJ)
T=0.486 (105/216, Qatari)
T=0.336 (72/214, Vietnamese)
T=0.47 (19/40, GENOME_DK)
C=0.33 (10/30, Siberian)
C=0.40 (8/20, Ancient Sardinia)
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.99602346C>T
GRCh37.p13 chr 1 NC_000001.10:g.100067902C>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 216986 C=0.460504 T=0.539496
European Sub 186828 C=0.442691 T=0.557309
African Sub 9714 C=0.5737 T=0.4263
African Others Sub 348 C=0.647 T=0.353
African American Sub 9366 C=0.5710 T=0.4290
Asian Sub 746 C=0.714 T=0.286
East Asian Sub 600 C=0.718 T=0.282
Other Asian Sub 146 C=0.699 T=0.301
Latin American 1 Sub 844 C=0.475 T=0.525
Latin American 2 Sub 6906 C=0.6399 T=0.3601
South Asian Sub 5044 C=0.5724 T=0.4276
Other Sub 6904 C=0.4929 T=0.5071


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 C=0.517383 T=0.482617
gnomAD - Genomes Global Study-wide 140028 C=0.501950 T=0.498050
gnomAD - Genomes European Sub 75838 C=0.44840 T=0.55160
gnomAD - Genomes African Sub 41964 C=0.57108 T=0.42892
gnomAD - Genomes American Sub 13630 C=0.53529 T=0.46471
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.4804 T=0.5196
gnomAD - Genomes East Asian Sub 3126 C=0.7492 T=0.2508
gnomAD - Genomes Other Sub 2148 C=0.5037 T=0.4963
8.3KJPN JAPANESE Study-wide 16760 C=0.78282 T=0.21718
1000Genomes Global Study-wide 5008 C=0.5815 T=0.4185
1000Genomes African Sub 1322 C=0.6036 T=0.3964
1000Genomes East Asian Sub 1008 C=0.7202 T=0.2798
1000Genomes Europe Sub 1006 C=0.4254 T=0.5746
1000Genomes South Asian Sub 978 C=0.581 T=0.419
1000Genomes American Sub 694 C=0.565 T=0.435
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5013 T=0.4987
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.4276 T=0.5724
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.4307 T=0.5693
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8519 T=0.1481
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.5964 T=0.4036
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.762 T=0.238
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.594 T=0.406
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.463 T=0.537
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.428 T=0.572
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.632 T=0.368
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.764 T=0.236
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.31 T=0.69
HapMap Global Study-wide 1882 C=0.5919 T=0.4081
HapMap American Sub 764 C=0.580 T=0.420
HapMap African Sub 692 C=0.581 T=0.419
HapMap Asian Sub 250 C=0.784 T=0.216
HapMap Europe Sub 176 C=0.415 T=0.585
Korean Genome Project KOREAN Study-wide 1832 C=0.8422 T=0.1578
Genome-wide autozygosity in Daghestan Global Study-wide 1112 C=0.5719 T=0.4281
Genome-wide autozygosity in Daghestan Daghestan Sub 618 C=0.571 T=0.429
Genome-wide autozygosity in Daghestan Near_East Sub 140 C=0.564 T=0.436
Genome-wide autozygosity in Daghestan Central Asia Sub 120 C=0.708 T=0.292
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.380 T=0.620
Genome-wide autozygosity in Daghestan South Asian Sub 90 C=0.63 T=0.37
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.58 T=0.42
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.417 T=0.583
Northern Sweden ACPOP Study-wide 600 C=0.532 T=0.468
SGDP_PRJ Global Study-wide 338 C=0.367 T=0.633
Qatari Global Study-wide 216 C=0.514 T=0.486
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.664 T=0.336
The Danish reference pan genome Danish Study-wide 40 C=0.53 T=0.47
Siberian Global Study-wide 30 C=0.33 T=0.67
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 20 C=0.40 T=0.60
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 C= T
GRCh38.p13 chr 1 NC_000001.11:g.99602346= NC_000001.11:g.99602346C>T
GRCh37.p13 chr 1 NC_000001.10:g.100067902= NC_000001.10:g.100067902C>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#.

118 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6783697 Feb 20, 2003 (111)
2 BCM_SSAHASNP ss9829626 Jul 11, 2003 (116)
3 CSHL-HAPMAP ss16418513 Feb 27, 2004 (120)
4 SSAHASNP ss20567902 Apr 05, 2004 (121)
5 PERLEGEN ss24244138 Sep 20, 2004 (123)
6 ABI ss43886105 Mar 14, 2006 (126)
7 ILLUMINA ss66750247 Nov 29, 2006 (127)
8 ILLUMINA ss67396976 Nov 29, 2006 (127)
9 ILLUMINA ss67768050 Nov 29, 2006 (127)
10 PERLEGEN ss68775407 May 16, 2007 (127)
11 ILLUMINA ss70835186 May 26, 2008 (130)
12 ILLUMINA ss71418334 May 16, 2007 (127)
13 ILLUMINA ss75617188 Dec 06, 2007 (129)
14 ILLUMINA ss79201972 Dec 15, 2007 (130)
15 HGSV ss81018380 Dec 15, 2007 (130)
16 KRIBB_YJKIM ss84395095 Dec 15, 2007 (130)
17 HGSV ss86176378 Dec 15, 2007 (130)
18 BCMHGSC_JDW ss87656615 Mar 23, 2008 (129)
19 HUMANGENOME_JCVI ss99232663 Feb 06, 2009 (130)
20 1000GENOMES ss108453811 Jan 23, 2009 (130)
21 1000GENOMES ss110891267 Jan 25, 2009 (130)
22 ILLUMINA-UK ss118919290 Feb 15, 2009 (130)
23 ILLUMINA ss122427812 Dec 01, 2009 (131)
24 ENSEMBL ss138045123 Dec 01, 2009 (131)
25 ENSEMBL ss142516744 Dec 01, 2009 (131)
26 ILLUMINA ss154328021 Dec 01, 2009 (131)
27 GMI ss155415773 Dec 01, 2009 (131)
28 ILLUMINA ss159504532 Dec 01, 2009 (131)
29 ILLUMINA ss160726651 Dec 01, 2009 (131)
30 COMPLETE_GENOMICS ss163739415 Jul 04, 2010 (132)
31 COMPLETE_GENOMICS ss164869401 Jul 04, 2010 (132)
32 COMPLETE_GENOMICS ss166904908 Jul 04, 2010 (132)
33 ILLUMINA ss171972905 Jul 04, 2010 (132)
34 ILLUMINA ss173869771 Jul 04, 2010 (132)
35 BUSHMAN ss198832918 Jul 04, 2010 (132)
36 BCM-HGSC-SUB ss205299241 Jul 04, 2010 (132)
37 1000GENOMES ss218548716 Jul 14, 2010 (132)
38 1000GENOMES ss230656790 Jul 14, 2010 (132)
39 1000GENOMES ss238323755 Jul 15, 2010 (132)
40 GMI ss275945366 May 04, 2012 (137)
41 GMI ss284105708 Apr 25, 2013 (138)
42 PJP ss290580526 May 09, 2011 (134)
43 ILLUMINA ss481096265 May 04, 2012 (137)
44 ILLUMINA ss481118309 May 04, 2012 (137)
45 ILLUMINA ss482109627 Sep 08, 2015 (146)
46 ILLUMINA ss485343230 May 04, 2012 (137)
47 ILLUMINA ss537291935 Sep 08, 2015 (146)
48 TISHKOFF ss554480768 Apr 25, 2013 (138)
49 SSMP ss648254030 Apr 25, 2013 (138)
50 ILLUMINA ss780675947 Sep 08, 2015 (146)
51 ILLUMINA ss783117369 Sep 08, 2015 (146)
52 ILLUMINA ss784074217 Sep 08, 2015 (146)
53 ILLUMINA ss825532490 Apr 01, 2015 (144)
54 ILLUMINA ss832376103 Sep 08, 2015 (146)
55 ILLUMINA ss833015875 Jul 12, 2019 (153)
56 ILLUMINA ss836172315 Sep 08, 2015 (146)
57 EVA-GONL ss975483134 Aug 21, 2014 (142)
58 JMKIDD_LAB ss1068127804 Aug 21, 2014 (142)
59 1000GENOMES ss1292108224 Aug 21, 2014 (142)
60 HAMMER_LAB ss1397255157 Sep 08, 2015 (146)
61 DDI ss1425911031 Apr 01, 2015 (144)
62 EVA_GENOME_DK ss1574271710 Apr 01, 2015 (144)
63 EVA_DECODE ss1584861446 Apr 01, 2015 (144)
64 EVA_UK10K_ALSPAC ss1600817259 Apr 01, 2015 (144)
65 EVA_UK10K_TWINSUK ss1643811292 Apr 01, 2015 (144)
66 EVA_SVP ss1712357161 Apr 01, 2015 (144)
67 ILLUMINA ss1751859121 Sep 08, 2015 (146)
68 HAMMER_LAB ss1794807831 Sep 08, 2015 (146)
69 WEILL_CORNELL_DGM ss1918682721 Feb 12, 2016 (147)
70 GENOMED ss1966820819 Jul 19, 2016 (147)
71 JJLAB ss2019862878 Sep 14, 2016 (149)
72 USC_VALOUEV ss2147881575 Dec 20, 2016 (150)
73 HUMAN_LONGEVITY ss2165032297 Dec 20, 2016 (150)
74 TOPMED ss2327383079 Dec 20, 2016 (150)
75 SYSTEMSBIOZJU ss2624442847 Nov 08, 2017 (151)
76 ILLUMINA ss2632553638 Nov 08, 2017 (151)
77 GRF ss2697808911 Nov 08, 2017 (151)
78 ILLUMINA ss2710678279 Nov 08, 2017 (151)
79 GNOMAD ss2758639278 Nov 08, 2017 (151)
80 SWEGEN ss2987305878 Nov 08, 2017 (151)
81 BIOINF_KMB_FNS_UNIBA ss3023695028 Nov 08, 2017 (151)
82 TOPMED ss3084653508 Nov 08, 2017 (151)
83 CSHL ss3343595996 Nov 08, 2017 (151)
84 ILLUMINA ss3626165314 Oct 11, 2018 (152)
85 ILLUMINA ss3630587814 Oct 11, 2018 (152)
86 ILLUMINA ss3632903291 Oct 11, 2018 (152)
87 ILLUMINA ss3633598289 Oct 11, 2018 (152)
88 ILLUMINA ss3634339263 Oct 11, 2018 (152)
89 ILLUMINA ss3635291899 Oct 11, 2018 (152)
90 ILLUMINA ss3636016818 Oct 11, 2018 (152)
91 ILLUMINA ss3637042355 Oct 11, 2018 (152)
92 ILLUMINA ss3637775461 Oct 11, 2018 (152)
93 ILLUMINA ss3638905838 Oct 11, 2018 (152)
94 ILLUMINA ss3639450879 Oct 11, 2018 (152)
95 ILLUMINA ss3640046623 Oct 11, 2018 (152)
96 ILLUMINA ss3642785646 Oct 11, 2018 (152)
97 URBANLAB ss3646731483 Oct 11, 2018 (152)
98 EGCUT_WGS ss3655390980 Jul 12, 2019 (153)
99 EVA_DECODE ss3687367389 Jul 12, 2019 (153)
100 ACPOP ss3727314192 Jul 12, 2019 (153)
101 ILLUMINA ss3744640232 Jul 12, 2019 (153)
102 EVA ss3746574297 Jul 12, 2019 (153)
103 ILLUMINA ss3772141469 Jul 12, 2019 (153)
104 PACBIO ss3783495937 Jul 12, 2019 (153)
105 PACBIO ss3789140970 Jul 12, 2019 (153)
106 PACBIO ss3794013814 Jul 12, 2019 (153)
107 KHV_HUMAN_GENOMES ss3799575057 Jul 12, 2019 (153)
108 EVA ss3826326654 Apr 25, 2020 (154)
109 EVA ss3836553604 Apr 25, 2020 (154)
110 EVA ss3841961601 Apr 25, 2020 (154)
111 HGDP ss3847343748 Apr 25, 2020 (154)
112 SGDP_PRJ ss3849477846 Apr 25, 2020 (154)
113 KRGDB ss3894555920 Apr 25, 2020 (154)
114 KOGIC ss3945091588 Apr 25, 2020 (154)
115 EVA ss3984814986 Apr 25, 2021 (155)
116 EVA ss4016927700 Apr 25, 2021 (155)
117 TOPMED ss4460702707 Apr 25, 2021 (155)
118 TOMMO_GENOMICS ss5145313834 Apr 25, 2021 (155)
119 1000Genomes NC_000001.10 - 100067902 Oct 11, 2018 (152)
120 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100067902 Oct 11, 2018 (152)
121 Genome-wide autozygosity in Daghestan NC_000001.9 - 99840490 Apr 25, 2020 (154)
122 Genetic variation in the Estonian population NC_000001.10 - 100067902 Oct 11, 2018 (152)
123 The Danish reference pan genome NC_000001.10 - 100067902 Apr 25, 2020 (154)
124 gnomAD - Genomes NC_000001.11 - 99602346 Apr 25, 2021 (155)
125 Genome of the Netherlands Release 5 NC_000001.10 - 100067902 Apr 25, 2020 (154)
126 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99840490 Apr 25, 2020 (154)
127 HapMap NC_000001.11 - 99602346 Apr 25, 2020 (154)
128 KOREAN population from KRGDB NC_000001.10 - 100067902 Apr 25, 2020 (154)
129 Korean Genome Project NC_000001.11 - 99602346 Apr 25, 2020 (154)
130 Northern Sweden NC_000001.10 - 100067902 Jul 12, 2019 (153)
131 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100067902 Apr 25, 2021 (155)
132 Qatari NC_000001.10 - 100067902 Apr 25, 2020 (154)
133 SGDP_PRJ NC_000001.10 - 100067902 Apr 25, 2020 (154)
134 Siberian NC_000001.10 - 100067902 Apr 25, 2020 (154)
135 8.3KJPN NC_000001.10 - 100067902 Apr 25, 2021 (155)
136 TopMed NC_000001.11 - 99602346 Apr 25, 2021 (155)
137 UK 10K study - Twins NC_000001.10 - 100067902 Oct 11, 2018 (152)
138 A Vietnamese Genetic Variation Database NC_000001.10 - 100067902 Jul 12, 2019 (153)
139 ALFA NC_000001.11 - 99602346 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)
rs17413764 Oct 07, 2004 (123)
rs60624846 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81018380, ss86176378, ss3638905838, ss3639450879 NC_000001.8:99779922:C:T NC_000001.11:99602345:C:T (self)
16459, 21640, ss87656615, ss108453811, ss110891267, ss118919290, ss163739415, ss164869401, ss166904908, ss198832918, ss205299241, ss275945366, ss284105708, ss290580526, ss481096265, ss825532490, ss1397255157, ss1584861446, ss1712357161, ss3642785646, ss3847343748 NC_000001.9:99840489:C:T NC_000001.11:99602345:C:T (self)
2871808, 1584209, 1129228, 1629007, 687228, 1733314, 599057, 40913, 724651, 1494826, 397929, 3283141, 1584209, 341266, ss218548716, ss230656790, ss238323755, ss481118309, ss482109627, ss485343230, ss537291935, ss554480768, ss648254030, ss780675947, ss783117369, ss784074217, ss832376103, ss833015875, ss836172315, ss975483134, ss1068127804, ss1292108224, ss1425911031, ss1574271710, ss1600817259, ss1643811292, ss1751859121, ss1794807831, ss1918682721, ss1966820819, ss2019862878, ss2147881575, ss2327383079, ss2624442847, ss2632553638, ss2697808911, ss2710678279, ss2758639278, ss2987305878, ss3343595996, ss3626165314, ss3630587814, ss3632903291, ss3633598289, ss3634339263, ss3635291899, ss3636016818, ss3637042355, ss3637775461, ss3640046623, ss3655390980, ss3727314192, ss3744640232, ss3746574297, ss3772141469, ss3783495937, ss3789140970, ss3794013814, ss3826326654, ss3836553604, ss3849477846, ss3894555920, ss3984814986, ss4016927700, ss5145313834 NC_000001.10:100067901:C:T NC_000001.11:99602345:C:T (self)
20300840, 136602, 1469589, 15310511, 24309042, 11228588787, ss2165032297, ss3023695028, ss3084653508, ss3646731483, ss3687367389, ss3799575057, ss3841961601, ss3945091588, ss4460702707 NC_000001.11:99602345:C:T NC_000001.11:99602345:C:T (self)
ss9829626 NT_028050.12:941572:C:T NC_000001.11:99602345:C:T (self)
ss16418513, ss20567902 NT_028050.13:8256845:C:T NC_000001.11:99602345:C:T (self)
ss6783697, ss24244138, ss43886105, ss66750247, ss67396976, ss67768050, ss68775407, ss70835186, ss71418334, ss75617188, ss79201972, ss84395095, ss99232663, ss122427812, ss138045123, ss142516744, ss154328021, ss155415773, ss159504532, ss160726651, ss171972905, ss173869771 NT_032977.9:70039819:C:T NC_000001.11:99602345:C: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 rs4908329

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