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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.

rs6413547

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:187729216 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.354452 (93820/264690, TOPMED)
T=0.349508 (48913/139948, GnomAD)
T=0.32984 (9320/28256, 14KJPN) (+ 16 more)
T=0.33674 (6361/18890, ALFA)
T=0.33556 (5624/16760, 8.3KJPN)
T=0.3690 (2363/6404, 1000G_30x)
T=0.3626 (1816/5008, 1000G)
T=0.3118 (1397/4480, Estonian)
T=0.3272 (1261/3854, ALSPAC)
T=0.3145 (1166/3708, TWINSUK)
T=0.2898 (849/2930, KOREAN)
T=0.2686 (492/1832, Korea1K)
T=0.307 (306/998, GoNL)
T=0.332 (199/600, NorthernSweden)
T=0.205 (99/482, SGDP_PRJ)
T=0.495 (107/216, Qatari)
T=0.236 (51/216, Vietnamese)
T=0.28 (11/40, GENOME_DK)
T=0.30 (12/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 18890 T=0.33674 C=0.66326
European Sub 14286 T=0.31681 C=0.68319
African Sub 2946 T=0.4240 C=0.5760
African Others Sub 114 T=0.456 C=0.544
African American Sub 2832 T=0.4227 C=0.5773
Asian Sub 112 T=0.250 C=0.750
East Asian Sub 86 T=0.26 C=0.74
Other Asian Sub 26 T=0.23 C=0.77
Latin American 1 Sub 146 T=0.404 C=0.596
Latin American 2 Sub 610 T=0.357 C=0.643
South Asian Sub 98 T=0.35 C=0.65
Other Sub 692 T=0.357 C=0.643


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 T=0.354452 C=0.645548
gnomAD - Genomes Global Study-wide 139948 T=0.349508 C=0.650492
gnomAD - Genomes European Sub 75846 T=0.31087 C=0.68913
gnomAD - Genomes African Sub 41870 T=0.42006 C=0.57994
gnomAD - Genomes American Sub 13636 T=0.36902 C=0.63098
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.3613 C=0.6387
gnomAD - Genomes East Asian Sub 3130 T=0.2425 C=0.7575
gnomAD - Genomes Other Sub 2142 T=0.3525 C=0.6475
14KJPN JAPANESE Study-wide 28256 T=0.32984 C=0.67016
Allele Frequency Aggregator Total Global 18890 T=0.33674 C=0.66326
Allele Frequency Aggregator European Sub 14286 T=0.31681 C=0.68319
Allele Frequency Aggregator African Sub 2946 T=0.4240 C=0.5760
Allele Frequency Aggregator Other Sub 692 T=0.357 C=0.643
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.357 C=0.643
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.404 C=0.596
Allele Frequency Aggregator Asian Sub 112 T=0.250 C=0.750
Allele Frequency Aggregator South Asian Sub 98 T=0.35 C=0.65
8.3KJPN JAPANESE Study-wide 16760 T=0.33556 C=0.66444
1000Genomes_30x Global Study-wide 6404 T=0.3690 C=0.6310
1000Genomes_30x African Sub 1786 T=0.4546 C=0.5454
1000Genomes_30x Europe Sub 1266 T=0.3404 C=0.6596
1000Genomes_30x South Asian Sub 1202 T=0.3270 C=0.6730
1000Genomes_30x East Asian Sub 1170 T=0.2701 C=0.7299
1000Genomes_30x American Sub 980 T=0.419 C=0.581
1000Genomes Global Study-wide 5008 T=0.3626 C=0.6374
1000Genomes African Sub 1322 T=0.4561 C=0.5439
1000Genomes East Asian Sub 1008 T=0.2738 C=0.7262
1000Genomes Europe Sub 1006 T=0.3310 C=0.6690
1000Genomes South Asian Sub 978 T=0.328 C=0.672
1000Genomes American Sub 694 T=0.408 C=0.592
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.3118 C=0.6882
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.3272 C=0.6728
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.3145 C=0.6855
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.2898 C=0.7102
Korean Genome Project KOREAN Study-wide 1832 T=0.2686 C=0.7314
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.307 C=0.693
Northern Sweden ACPOP Study-wide 600 T=0.332 C=0.668
SGDP_PRJ Global Study-wide 482 T=0.205 C=0.795
Qatari Global Study-wide 216 T=0.495 C=0.505
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.236 C=0.764
The Danish reference pan genome Danish Study-wide 40 T=0.28 C=0.72
Siberian Global Study-wide 40 T=0.30 C=0.70
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.187729216T>C
GRCh37.p13 chr 1 NC_000001.10:g.187698347T>C
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 T= C
GRCh38.p14 chr 1 NC_000001.11:g.187729216= NC_000001.11:g.187729216T>C
GRCh37.p13 chr 1 NC_000001.10:g.187698347= NC_000001.10:g.187698347T>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#.

77 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8820742 Jul 11, 2003 (116)
2 BCM_SSAHASNP ss9830621 Jul 11, 2003 (116)
3 SC_JCM ss11199340 Jul 11, 2003 (116)
4 WI_SSAHASNP ss11362078 Jul 11, 2003 (116)
5 PERLEGEN ss23200447 Sep 20, 2004 (123)
6 ABI ss41232513 Mar 15, 2006 (126)
7 HGSV ss78152190 Dec 06, 2007 (129)
8 HGSV ss81290113 Dec 14, 2007 (130)
9 HUMANGENOME_JCVI ss99269861 Feb 04, 2009 (130)
10 1000GENOMES ss108779615 Jan 23, 2009 (130)
11 1000GENOMES ss111492505 Jan 25, 2009 (130)
12 ILLUMINA-UK ss119136165 Dec 01, 2009 (131)
13 ENSEMBL ss144212577 Dec 01, 2009 (131)
14 GMI ss156037035 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss164675386 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss165563848 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss167371386 Jul 04, 2010 (132)
18 BUSHMAN ss199366878 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss205198520 Jul 04, 2010 (132)
20 1000GENOMES ss218773783 Jul 14, 2010 (132)
21 1000GENOMES ss230821507 Jul 14, 2010 (132)
22 1000GENOMES ss238449570 Jul 15, 2010 (132)
23 BL ss253679665 May 09, 2011 (134)
24 GMI ss276137679 May 04, 2012 (137)
25 GMI ss284191620 Apr 25, 2013 (138)
26 PJP ss290683134 May 09, 2011 (134)
27 TISHKOFF ss554959737 Apr 25, 2013 (138)
28 SSMP ss648564834 Apr 25, 2013 (138)
29 EVA-GONL ss975922828 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1068444366 Aug 21, 2014 (142)
31 1000GENOMES ss1293840201 Aug 21, 2014 (142)
32 DDI ss1426048303 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1574541756 Apr 01, 2015 (144)
34 EVA_DECODE ss1585315515 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1601704378 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1644698411 Apr 01, 2015 (144)
37 HAMMER_LAB ss1795430002 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1919157241 Feb 12, 2016 (147)
39 GENOMED ss1966921896 Jul 19, 2016 (147)
40 JJLAB ss2020095101 Sep 14, 2016 (149)
41 USC_VALOUEV ss2148123555 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2168416605 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2624555401 Nov 08, 2017 (151)
44 GRF ss2698108049 Nov 08, 2017 (151)
45 GNOMAD ss2763907500 Nov 08, 2017 (151)
46 SWEGEN ss2988118966 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3023806870 Nov 08, 2017 (151)
48 CSHL ss3343816556 Nov 08, 2017 (151)
49 URBANLAB ss3646840001 Oct 11, 2018 (152)
50 EGCUT_WGS ss3656071529 Jul 12, 2019 (153)
51 EVA_DECODE ss3688225855 Jul 12, 2019 (153)
52 ACPOP ss3727681908 Jul 12, 2019 (153)
53 EVA ss3747087323 Jul 12, 2019 (153)
54 PACBIO ss3783631046 Jul 12, 2019 (153)
55 PACBIO ss3789251790 Jul 12, 2019 (153)
56 PACBIO ss3794123928 Jul 12, 2019 (153)
57 KHV_HUMAN_GENOMES ss3800088704 Jul 12, 2019 (153)
58 EVA ss3826541112 Apr 25, 2020 (154)
59 EVA ss3836667364 Apr 25, 2020 (154)
60 EVA ss3842077854 Apr 25, 2020 (154)
61 SGDP_PRJ ss3850475914 Apr 25, 2020 (154)
62 KRGDB ss3895744202 Apr 25, 2020 (154)
63 KOGIC ss3946099142 Apr 25, 2020 (154)
64 TOPMED ss4476380223 Apr 25, 2021 (155)
65 TOMMO_GENOMICS ss5147511163 Apr 25, 2021 (155)
66 1000G_HIGH_COVERAGE ss5245084680 Oct 12, 2022 (156)
67 EVA ss5323500567 Oct 12, 2022 (156)
68 HUGCELL_USP ss5445590232 Oct 12, 2022 (156)
69 EVA ss5506113269 Oct 12, 2022 (156)
70 1000G_HIGH_COVERAGE ss5518813237 Oct 12, 2022 (156)
71 SANFORD_IMAGENETICS ss5627041997 Oct 12, 2022 (156)
72 TOMMO_GENOMICS ss5675006190 Oct 12, 2022 (156)
73 YY_MCH ss5801458000 Oct 12, 2022 (156)
74 EVA ss5832978091 Oct 12, 2022 (156)
75 EVA ss5849199052 Oct 12, 2022 (156)
76 EVA ss5911159753 Oct 12, 2022 (156)
77 EVA ss5938861996 Oct 12, 2022 (156)
78 1000Genomes NC_000001.10 - 187698347 Oct 11, 2018 (152)
79 1000Genomes_30x NC_000001.11 - 187729216 Oct 12, 2022 (156)
80 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 187698347 Oct 11, 2018 (152)
81 Genetic variation in the Estonian population NC_000001.10 - 187698347 Oct 11, 2018 (152)
82 The Danish reference pan genome NC_000001.10 - 187698347 Apr 25, 2020 (154)
83 gnomAD - Genomes NC_000001.11 - 187729216 Apr 25, 2021 (155)
84 Genome of the Netherlands Release 5 NC_000001.10 - 187698347 Apr 25, 2020 (154)
85 KOREAN population from KRGDB NC_000001.10 - 187698347 Apr 25, 2020 (154)
86 Korean Genome Project NC_000001.11 - 187729216 Apr 25, 2020 (154)
87 Northern Sweden NC_000001.10 - 187698347 Jul 12, 2019 (153)
88 Qatari NC_000001.10 - 187698347 Apr 25, 2020 (154)
89 SGDP_PRJ NC_000001.10 - 187698347 Apr 25, 2020 (154)
90 Siberian NC_000001.10 - 187698347 Apr 25, 2020 (154)
91 8.3KJPN NC_000001.10 - 187698347 Apr 25, 2021 (155)
92 14KJPN NC_000001.11 - 187729216 Oct 12, 2022 (156)
93 TopMed NC_000001.11 - 187729216 Apr 25, 2021 (155)
94 UK 10K study - Twins NC_000001.10 - 187698347 Oct 11, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000001.10 - 187698347 Jul 12, 2019 (153)
96 ALFA NC_000001.11 - 187729216 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)
rs17266896 Oct 07, 2004 (123)
rs57086045 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78152190, ss81290113 NC_000001.8:184430003:T:C NC_000001.11:187729215:T:C (self)
ss108779615, ss111492505, ss119136165, ss164675386, ss165563848, ss167371386, ss199366878, ss205198520, ss253679665, ss276137679, ss284191620, ss290683134, ss1585315515 NC_000001.9:185964969:T:C NC_000001.11:187729215:T:C (self)
4664587, 2559408, 1809777, 1800522, 1112293, 2921596, 966773, 1199171, 2492894, 639909, 5480470, 2559408, 549257, ss218773783, ss230821507, ss238449570, ss554959737, ss648564834, ss975922828, ss1068444366, ss1293840201, ss1426048303, ss1574541756, ss1601704378, ss1644698411, ss1795430002, ss1919157241, ss1966921896, ss2020095101, ss2148123555, ss2624555401, ss2698108049, ss2763907500, ss2988118966, ss3343816556, ss3656071529, ss3727681908, ss3747087323, ss3783631046, ss3789251790, ss3794123928, ss3826541112, ss3836667364, ss3850475914, ss3895744202, ss5147511163, ss5323500567, ss5506113269, ss5627041997, ss5832978091, ss5938861996 NC_000001.10:187698346:T:C NC_000001.11:187729215:T:C (self)
6339172, 33647328, 2477143, 8843294, 39986558, 9564207965, ss2168416605, ss3023806870, ss3646840001, ss3688225855, ss3800088704, ss3842077854, ss3946099142, ss4476380223, ss5245084680, ss5445590232, ss5518813237, ss5675006190, ss5801458000, ss5849199052, ss5911159753 NC_000001.11:187729215:T:C NC_000001.11:187729215:T:C (self)
ss9830621, ss11199340, ss11362078 NT_004487.15:16490994:T:C NC_000001.11:187729215:T:C (self)
ss8820742, ss23200447, ss41232513, ss99269861, ss144212577, ss156037035 NT_004487.19:39186988:T:C NC_000001.11:187729215:T:C (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 rs6413547

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