Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs4649084

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:25426126 (GRCh38.p14) 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
A=0.395081 (104574/264690, TOPMED)
A=0.389661 (54565/140032, GnomAD)
A=0.39027 (30712/78694, PAGE_STUDY) (+ 17 more)
G=0.32447 (9169/28258, 14KJPN)
A=0.38790 (9889/25494, ALFA)
G=0.32709 (5482/16760, 8.3KJPN)
A=0.4742 (3037/6404, 1000G_30x)
A=0.4842 (2425/5008, 1000G)
A=0.4475 (2005/4480, Estonian)
A=0.4520 (1742/3854, ALSPAC)
A=0.4420 (1639/3708, TWINSUK)
G=0.3392 (994/2930, KOREAN)
A=0.4191 (793/1892, HapMap)
A=0.439 (438/998, GoNL)
A=0.400 (240/600, NorthernSweden)
A=0.318 (121/380, SGDP_PRJ)
A=0.380 (82/216, Qatari)
G=0.182 (39/214, Vietnamese)
A=0.40 (16/40, GENOME_DK)
A=0.32 (12/38, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RHCE : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 25494 A=0.38790 G=0.61210
European Sub 16044 A=0.45755 G=0.54245
African Sub 7178 A=0.2014 G=0.7986
African Others Sub 232 A=0.108 G=0.892
African American Sub 6946 A=0.2046 G=0.7954
Asian Sub 158 A=0.791 G=0.209
East Asian Sub 130 A=0.769 G=0.231
Other Asian Sub 28 A=0.89 G=0.11
Latin American 1 Sub 168 A=0.440 G=0.560
Latin American 2 Sub 670 A=0.527 G=0.473
South Asian Sub 104 A=0.577 G=0.423
Other Sub 1172 A=0.4181 G=0.5819


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=0.395081 G=0.604919
gnomAD - Genomes Global Study-wide 140032 A=0.389661 G=0.610339
gnomAD - Genomes European Sub 75834 A=0.45801 G=0.54199
gnomAD - Genomes African Sub 41964 A=0.20422 G=0.79578
gnomAD - Genomes American Sub 13636 A=0.46656 G=0.53344
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.5325 G=0.4675
gnomAD - Genomes East Asian Sub 3128 A=0.7177 G=0.2823
gnomAD - Genomes Other Sub 2150 A=0.4126 G=0.5874
The PAGE Study Global Study-wide 78694 A=0.39027 G=0.60973
The PAGE Study AfricanAmerican Sub 32514 A=0.21203 G=0.78797
The PAGE Study Mexican Sub 10810 A=0.53719 G=0.46281
The PAGE Study Asian Sub 8318 A=0.6780 G=0.3220
The PAGE Study PuertoRican Sub 7916 A=0.4066 G=0.5934
The PAGE Study NativeHawaiian Sub 4534 A=0.5759 G=0.4241
The PAGE Study Cuban Sub 4228 A=0.4584 G=0.5416
The PAGE Study Dominican Sub 3828 A=0.3362 G=0.6638
The PAGE Study CentralAmerican Sub 2450 A=0.4800 G=0.5200
The PAGE Study SouthAmerican Sub 1980 A=0.5071 G=0.4929
The PAGE Study NativeAmerican Sub 1260 A=0.4476 G=0.5524
The PAGE Study SouthAsian Sub 856 A=0.668 G=0.332
14KJPN JAPANESE Study-wide 28258 A=0.67553 G=0.32447
Allele Frequency Aggregator Total Global 25494 A=0.38790 G=0.61210
Allele Frequency Aggregator European Sub 16044 A=0.45755 G=0.54245
Allele Frequency Aggregator African Sub 7178 A=0.2014 G=0.7986
Allele Frequency Aggregator Other Sub 1172 A=0.4181 G=0.5819
Allele Frequency Aggregator Latin American 2 Sub 670 A=0.527 G=0.473
Allele Frequency Aggregator Latin American 1 Sub 168 A=0.440 G=0.560
Allele Frequency Aggregator Asian Sub 158 A=0.791 G=0.209
Allele Frequency Aggregator South Asian Sub 104 A=0.577 G=0.423
8.3KJPN JAPANESE Study-wide 16760 A=0.67291 G=0.32709
1000Genomes_30x Global Study-wide 6404 A=0.4742 G=0.5258
1000Genomes_30x African Sub 1786 A=0.1338 G=0.8662
1000Genomes_30x Europe Sub 1266 A=0.4494 G=0.5506
1000Genomes_30x South Asian Sub 1202 A=0.6789 G=0.3211
1000Genomes_30x East Asian Sub 1170 A=0.7786 G=0.2214
1000Genomes_30x American Sub 980 A=0.512 G=0.488
1000Genomes Global Study-wide 5008 A=0.4842 G=0.5158
1000Genomes African Sub 1322 A=0.1369 G=0.8631
1000Genomes East Asian Sub 1008 A=0.7718 G=0.2282
1000Genomes Europe Sub 1006 A=0.4493 G=0.5507
1000Genomes South Asian Sub 978 A=0.679 G=0.321
1000Genomes American Sub 694 A=0.504 G=0.496
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4475 G=0.5525
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.4520 G=0.5480
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.4420 G=0.5580
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6608 G=0.3392
HapMap Global Study-wide 1892 A=0.4191 G=0.5809
HapMap American Sub 770 A=0.529 G=0.471
HapMap African Sub 692 A=0.162 G=0.838
HapMap Asian Sub 254 A=0.740 G=0.260
HapMap Europe Sub 176 A=0.489 G=0.511
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.439 G=0.561
Northern Sweden ACPOP Study-wide 600 A=0.400 G=0.600
SGDP_PRJ Global Study-wide 380 A=0.318 G=0.682
Qatari Global Study-wide 216 A=0.380 G=0.620
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.818 G=0.182
The Danish reference pan genome Danish Study-wide 40 A=0.40 G=0.60
Siberian Global Study-wide 38 A=0.32 G=0.68
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.p14 chr 1 NC_000001.11:g.25426126A>G
GRCh37.p13 chr 1 NC_000001.10:g.25752617A>G
RHCE RefSeqGene (LRG_797) NG_009208.3:g.9067T>C
Gene: RHCE, Rh blood group CcEe antigens (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RHCE transcript variant 5 NM_001330430.4:c. N/A Genic Upstream Transcript Variant
RHCE transcript variant 1 NM_020485.8:c. N/A Genic Upstream Transcript Variant
RHCE transcript variant 3 NM_138616.5:c. N/A Genic Upstream Transcript Variant
RHCE transcript variant 4 NM_138617.5:c. N/A Genic Upstream Transcript Variant
RHCE transcript variant 2 NM_138618.6:c. N/A Genic Upstream Transcript Variant
RHCE transcript variant X2 XM_011541889.4:c.253+3814…

XM_011541889.4:c.253+3814T>C

N/A Intron Variant
RHCE transcript variant X3 XM_047427028.1:c.-21+2827…

XM_047427028.1:c.-21+2827T>C

N/A Intron Variant
RHCE transcript variant X5 XM_005245957.5:c. N/A Genic Upstream Transcript Variant
RHCE transcript variant X4 XM_006710810.4:c. N/A Genic Upstream Transcript Variant
RHCE transcript variant X1 XM_011541888.4:c. N/A Genic Upstream Transcript Variant
RHCE transcript variant X6 XM_017002014.3:c. N/A Genic Upstream Transcript 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
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.p14 chr 1 NC_000001.11:g.25426126= NC_000001.11:g.25426126A>G
GRCh37.p13 chr 1 NC_000001.10:g.25752617= NC_000001.10:g.25752617A>G
RHCE RefSeqGene (LRG_797) NG_009208.3:g.9067= NG_009208.3:g.9067T>C
RHCE transcript variant X2 XM_011541889.4:c.253+3814= XM_011541889.4:c.253+3814T>C
RHCE transcript variant X3 XM_047427028.1:c.-21+2827= XM_047427028.1:c.-21+2827T>C
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#.

81 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6397488 Feb 20, 2003 (111)
2 WI_SSAHASNP ss11133684 Jul 11, 2003 (116)
3 ABI ss41274821 Mar 13, 2006 (126)
4 ILLUMINA ss75008010 Dec 06, 2007 (129)
5 HUMANGENOME_JCVI ss99195249 Feb 04, 2009 (130)
6 1000GENOMES ss108072896 Jan 22, 2009 (130)
7 1000GENOMES ss110204024 Jan 24, 2009 (130)
8 ILLUMINA-UK ss118573501 Feb 14, 2009 (130)
9 KRIBB_YJKIM ss119482324 Dec 01, 2009 (131)
10 ENSEMBL ss131776707 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss163200112 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss163999534 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss166263363 Jul 04, 2010 (132)
14 ILLUMINA ss173768163 Jul 04, 2010 (132)
15 BUSHMAN ss198191643 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss205041483 Jul 04, 2010 (132)
17 1000GENOMES ss218290029 Jul 14, 2010 (132)
18 1000GENOMES ss230467107 Jul 14, 2010 (132)
19 1000GENOMES ss238173598 Jul 15, 2010 (132)
20 GMI ss275758339 May 04, 2012 (137)
21 GMI ss284021639 Apr 25, 2013 (138)
22 PJP ss290793124 May 09, 2011 (134)
23 ILLUMINA ss410934595 Sep 17, 2011 (135)
24 ILLUMINA ss537252932 Sep 08, 2015 (146)
25 TISHKOFF ss553907792 Apr 25, 2013 (138)
26 SSMP ss647648611 Apr 25, 2013 (138)
27 EVA-GONL ss974961034 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1067744634 Aug 21, 2014 (142)
29 1000GENOMES ss1290092518 Aug 21, 2014 (142)
30 DDI ss1425750700 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1573949226 Apr 01, 2015 (144)
32 EVA_DECODE ss1584319726 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1599755474 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1642749507 Apr 01, 2015 (144)
35 EVA_SVP ss1712318975 Apr 01, 2015 (144)
36 HAMMER_LAB ss1794082707 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1918173030 Feb 12, 2016 (147)
38 ILLUMINA ss1958254440 Feb 12, 2016 (147)
39 GENOMED ss1966707934 Jul 19, 2016 (147)
40 JJLAB ss2019598335 Sep 14, 2016 (149)
41 USC_VALOUEV ss2147604421 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2160837983 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2624316188 Nov 08, 2017 (151)
44 GRF ss2697510227 Nov 08, 2017 (151)
45 GNOMAD ss2752832810 Nov 08, 2017 (151)
46 SWEGEN ss2986490181 Nov 08, 2017 (151)
47 ILLUMINA ss3021068114 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3023564893 Nov 08, 2017 (151)
49 CSHL ss3343373698 Nov 08, 2017 (151)
50 ILLUMINA ss3626051899 Oct 11, 2018 (152)
51 ILLUMINA ss3637743998 Oct 11, 2018 (152)
52 ILLUMINA ss3642757234 Oct 11, 2018 (152)
53 URBANLAB ss3646626390 Oct 11, 2018 (152)
54 ILLUMINA ss3651393529 Oct 11, 2018 (152)
55 EGCUT_WGS ss3654555417 Jul 12, 2019 (153)
56 EVA_DECODE ss3686376397 Jul 12, 2019 (153)
57 ILLUMINA ss3725007279 Jul 12, 2019 (153)
58 ACPOP ss3726881115 Jul 12, 2019 (153)
59 EVA ss3745957975 Jul 12, 2019 (153)
60 PAGE_CC ss3770794340 Jul 12, 2019 (153)
61 KHV_HUMAN_GENOMES ss3798978488 Jul 12, 2019 (153)
62 EVA ss3826078753 Apr 25, 2020 (154)
63 EVA ss3836427516 Apr 25, 2020 (154)
64 EVA ss3841832312 Apr 25, 2020 (154)
65 SGDP_PRJ ss3848440453 Apr 25, 2020 (154)
66 KRGDB ss3893360339 Apr 25, 2020 (154)
67 EVA ss4016899082 Apr 27, 2021 (155)
68 TOPMED ss4442627445 Apr 27, 2021 (155)
69 TOMMO_GENOMICS ss5143000107 Apr 27, 2021 (155)
70 1000G_HIGH_COVERAGE ss5241560947 Oct 13, 2022 (156)
71 EVA ss5317428748 Oct 13, 2022 (156)
72 HUGCELL_USP ss5442704720 Oct 13, 2022 (156)
73 EVA ss5505793018 Oct 13, 2022 (156)
74 1000G_HIGH_COVERAGE ss5513493856 Oct 13, 2022 (156)
75 SANFORD_IMAGENETICS ss5625141064 Oct 13, 2022 (156)
76 TOMMO_GENOMICS ss5667463265 Oct 13, 2022 (156)
77 YY_MCH ss5800425148 Oct 13, 2022 (156)
78 EVA ss5831689378 Oct 13, 2022 (156)
79 EVA ss5848828512 Oct 13, 2022 (156)
80 EVA ss5907453867 Oct 13, 2022 (156)
81 EVA ss5936957255 Oct 13, 2022 (156)
82 1000Genomes NC_000001.10 - 25752617 Oct 11, 2018 (152)
83 1000Genomes_30x NC_000001.11 - 25426126 Oct 13, 2022 (156)
84 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 25752617 Oct 11, 2018 (152)
85 Genetic variation in the Estonian population NC_000001.10 - 25752617 Oct 11, 2018 (152)
86 The Danish reference pan genome NC_000001.10 - 25752617 Apr 25, 2020 (154)
87 gnomAD - Genomes NC_000001.11 - 25426126 Apr 27, 2021 (155)
88 Genome of the Netherlands Release 5 NC_000001.10 - 25752617 Apr 25, 2020 (154)
89 HapMap NC_000001.11 - 25426126 Apr 25, 2020 (154)
90 KOREAN population from KRGDB NC_000001.10 - 25752617 Apr 25, 2020 (154)
91 Northern Sweden NC_000001.10 - 25752617 Jul 12, 2019 (153)
92 The PAGE Study NC_000001.11 - 25426126 Jul 12, 2019 (153)
93 Qatari NC_000001.10 - 25752617 Apr 25, 2020 (154)
94 SGDP_PRJ NC_000001.10 - 25752617 Apr 25, 2020 (154)
95 Siberian NC_000001.10 - 25752617 Apr 25, 2020 (154)
96 8.3KJPN NC_000001.10 - 25752617 Apr 27, 2021 (155)
97 14KJPN NC_000001.11 - 25426126 Oct 13, 2022 (156)
98 TopMed NC_000001.11 - 25426126 Apr 27, 2021 (155)
99 UK 10K study - Twins NC_000001.10 - 25752617 Oct 11, 2018 (152)
100 A Vietnamese Genetic Variation Database NC_000001.10 - 25752617 Jul 12, 2019 (153)
101 ALFA NC_000001.11 - 25426126 Apr 27, 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
ss108072896, ss110204024, ss118573501, ss163200112, ss163999534, ss166263363, ss198191643, ss205041483, ss275758339, ss284021639, ss290793124, ss410934595, ss1584319726, ss1712318975, ss3642757234 NC_000001.9:25625203:A:G NC_000001.11:25426125:A:G (self)
782597, 415609, 293665, 1431089, 180369, 537733, 165980, 214960, 457433, 120775, 969414, 415609, 87532, ss218290029, ss230467107, ss238173598, ss537252932, ss553907792, ss647648611, ss974961034, ss1067744634, ss1290092518, ss1425750700, ss1573949226, ss1599755474, ss1642749507, ss1794082707, ss1918173030, ss1958254440, ss1966707934, ss2019598335, ss2147604421, ss2624316188, ss2697510227, ss2752832810, ss2986490181, ss3021068114, ss3343373698, ss3626051899, ss3637743998, ss3651393529, ss3654555417, ss3726881115, ss3745957975, ss3826078753, ss3836427516, ss3848440453, ss3893360339, ss4016899082, ss5143000107, ss5317428748, ss5505793018, ss5625141064, ss5831689378, ss5936957255 NC_000001.10:25752616:A:G NC_000001.11:25426125:A:G (self)
1019791, 5470813, 32625, 15809, 1300369, 6233780, 10718036612, ss2160837983, ss3023564893, ss3646626390, ss3686376397, ss3725007279, ss3770794340, ss3798978488, ss3841832312, ss4442627445, ss5241560947, ss5442704720, ss5513493856, ss5667463265, ss5800425148, ss5848828512, ss5907453867 NC_000001.11:25426125:A:G NC_000001.11:25426125:A:G (self)
ss6397488, ss41274821, ss75008010, ss99195249, ss119482324, ss131776707, ss173768163 NT_004610.19:12432704:A:G NC_000001.11:25426125:A:G (self)
ss11133684 NT_077384.1:56810:A:G NC_000001.11:25426125: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 rs4649084

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.post761+d5e8e07