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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs6049782

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:2526440 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.276807 (73268/264690, TOPMED)
G=0.277884 (38861/139846, GnomAD)
A=0.48082 (13587/28258, 14KJPN) (+ 15 more)
G=0.30662 (5792/18890, ALFA)
A=0.47918 (8031/16760, 8.3KJPN)
G=0.3064 (1962/6404, 1000G_30x)
G=0.3069 (1537/5008, 1000G)
G=0.3828 (1715/4480, Estonian)
G=0.3277 (1263/3854, ALSPAC)
G=0.3077 (1141/3708, TWINSUK)
A=0.4485 (1314/2930, KOREAN)
G=0.330 (329/998, GoNL)
G=0.370 (222/600, NorthernSweden)
G=0.223 (103/462, SGDP_PRJ)
G=0.301 (65/216, Qatari)
A=0.404 (84/208, Vietnamese)
G=0.35 (14/40, GENOME_DK)
G=0.37 (14/38, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNF343 : 2KB Upstream 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 18890 G=0.30662 A=0.69338
European Sub 14286 G=0.33928 A=0.66072
African Sub 2946 G=0.1375 A=0.8625
African Others Sub 114 G=0.105 A=0.895
African American Sub 2832 G=0.1388 A=0.8612
Asian Sub 112 G=0.589 A=0.411
East Asian Sub 86 G=0.65 A=0.35
Other Asian Sub 26 G=0.38 A=0.62
Latin American 1 Sub 146 G=0.247 A=0.753
Latin American 2 Sub 610 G=0.370 A=0.630
South Asian Sub 98 G=0.30 A=0.70
Other Sub 692 G=0.264 A=0.736


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=0.276807 A=0.723193
gnomAD - Genomes Global Study-wide 139846 G=0.277884 A=0.722116
gnomAD - Genomes European Sub 75722 G=0.32158 A=0.67842
gnomAD - Genomes African Sub 41928 G=0.15174 A=0.84826
gnomAD - Genomes American Sub 13604 G=0.33520 A=0.66480
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.3511 A=0.6489
gnomAD - Genomes East Asian Sub 3122 G=0.5637 A=0.4363
gnomAD - Genomes Other Sub 2146 G=0.3080 A=0.6920
14KJPN JAPANESE Study-wide 28258 G=0.51918 A=0.48082
Allele Frequency Aggregator Total Global 18890 G=0.30662 A=0.69338
Allele Frequency Aggregator European Sub 14286 G=0.33928 A=0.66072
Allele Frequency Aggregator African Sub 2946 G=0.1375 A=0.8625
Allele Frequency Aggregator Other Sub 692 G=0.264 A=0.736
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.370 A=0.630
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.247 A=0.753
Allele Frequency Aggregator Asian Sub 112 G=0.589 A=0.411
Allele Frequency Aggregator South Asian Sub 98 G=0.30 A=0.70
8.3KJPN JAPANESE Study-wide 16760 G=0.52082 A=0.47918
1000Genomes_30x Global Study-wide 6404 G=0.3064 A=0.6936
1000Genomes_30x African Sub 1786 G=0.1041 A=0.8959
1000Genomes_30x Europe Sub 1266 G=0.3231 A=0.6769
1000Genomes_30x South Asian Sub 1202 G=0.2987 A=0.7013
1000Genomes_30x East Asian Sub 1170 G=0.5641 A=0.4359
1000Genomes_30x American Sub 980 G=0.355 A=0.645
1000Genomes Global Study-wide 5008 G=0.3069 A=0.6931
1000Genomes African Sub 1322 G=0.1021 A=0.8979
1000Genomes East Asian Sub 1008 G=0.5575 A=0.4425
1000Genomes Europe Sub 1006 G=0.3141 A=0.6859
1000Genomes South Asian Sub 978 G=0.291 A=0.709
1000Genomes American Sub 694 G=0.344 A=0.656
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.3828 A=0.6172
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.3277 A=0.6723
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.3077 A=0.6923
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5515 A=0.4485
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.330 A=0.670
Northern Sweden ACPOP Study-wide 600 G=0.370 A=0.630
SGDP_PRJ Global Study-wide 462 G=0.223 A=0.777
Qatari Global Study-wide 216 G=0.301 A=0.699
A Vietnamese Genetic Variation Database Global Study-wide 208 G=0.596 A=0.404
The Danish reference pan genome Danish Study-wide 40 G=0.35 A=0.65
Siberian Global Study-wide 38 G=0.37 A=0.63
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 20 NC_000020.11:g.2526440G>A
GRCh37.p13 chr 20 NC_000020.10:g.2507086G>A
Gene: ZNF343, zinc finger protein 343 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
ZNF343 transcript variant 2 NM_001282495.1:c. N/A Upstream Transcript Variant
ZNF343 transcript variant 3 NM_001282496.2:c. N/A N/A
ZNF343 transcript variant 4 NM_001282497.2:c. N/A N/A
ZNF343 transcript variant 5 NM_001282498.2:c. N/A N/A
ZNF343 transcript variant 6 NM_001282499.3:c. N/A N/A
ZNF343 transcript variant 7 NM_001321800.2:c. N/A N/A
ZNF343 transcript variant 8 NM_001321801.2:c. N/A N/A
ZNF343 transcript variant 9 NM_001321802.2:c. N/A N/A
ZNF343 transcript variant 10 NM_001321803.2:c. N/A N/A
ZNF343 transcript variant 11 NM_001321805.2:c. N/A N/A
ZNF343 transcript variant 1 NM_024325.6:c. N/A N/A
ZNF343 transcript variant X1 XM_047440474.1:c. N/A Upstream Transcript Variant
ZNF343 transcript variant X3 XM_047440476.1:c. N/A Upstream Transcript Variant
ZNF343 transcript variant X2 XM_047440475.1:c. N/A N/A
ZNF343 transcript variant X4 XM_047440477.1:c. N/A N/A
ZNF343 transcript variant X5 XM_047440478.1:c. N/A N/A
ZNF343 transcript variant X6 XM_047440479.1:c. N/A N/A
ZNF343 transcript variant X7 XM_047440480.1:c. N/A N/A
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 G= A
GRCh38.p14 chr 20 NC_000020.11:g.2526440= NC_000020.11:g.2526440G>A
GRCh37.p13 chr 20 NC_000020.10:g.2507086= NC_000020.10:g.2507086G>A
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#.

79 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8361733 Apr 21, 2003 (114)
2 WI_SSAHASNP ss12490914 Jul 11, 2003 (117)
3 CSHL-HAPMAP ss16897228 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss17697258 Feb 27, 2004 (120)
5 SSAHASNP ss21784696 Apr 05, 2004 (121)
6 ABI ss41388554 Mar 14, 2006 (126)
7 HGSV ss83638705 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss91617650 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss96181847 Feb 03, 2009 (130)
10 1000GENOMES ss111618272 Jan 25, 2009 (130)
11 1000GENOMES ss115373344 Jan 25, 2009 (130)
12 IGMI-SNU ss115458499 Feb 03, 2009 (130)
13 ILLUMINA-UK ss117460274 Dec 01, 2009 (131)
14 ENSEMBL ss135736761 Dec 01, 2009 (131)
15 ENSEMBL ss138199751 Dec 01, 2009 (131)
16 GMI ss156085298 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss167679011 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss168889389 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss171826895 Jul 04, 2010 (132)
20 BUSHMAN ss203810620 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss208633710 Jul 04, 2010 (132)
22 1000GENOMES ss228222107 Jul 14, 2010 (132)
23 1000GENOMES ss237738184 Jul 15, 2010 (132)
24 1000GENOMES ss243929826 Jul 15, 2010 (132)
25 BL ss255435695 May 09, 2011 (134)
26 GMI ss283276565 May 04, 2012 (137)
27 GMI ss287411949 Apr 25, 2013 (138)
28 PJP ss292564594 May 09, 2011 (134)
29 TISHKOFF ss566096130 Apr 25, 2013 (138)
30 SSMP ss661965972 Apr 25, 2013 (138)
31 EVA-GONL ss994477178 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1082024823 Aug 21, 2014 (142)
33 1000GENOMES ss1363838614 Aug 21, 2014 (142)
34 DDI ss1428977176 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1579411016 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1638289606 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1681283639 Apr 01, 2015 (144)
38 EVA_DECODE ss1698531342 Apr 01, 2015 (144)
39 HAMMER_LAB ss1809393780 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1937986078 Feb 12, 2016 (147)
41 GENOMED ss1969075979 Jul 19, 2016 (147)
42 JJLAB ss2029769479 Sep 14, 2016 (149)
43 USC_VALOUEV ss2158323306 Dec 20, 2016 (150)
44 HUMAN_LONGEVITY ss2240859738 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2629382227 Nov 08, 2017 (151)
46 GRF ss2703994861 Nov 08, 2017 (151)
47 GNOMAD ss2964800406 Nov 08, 2017 (151)
48 SWEGEN ss3017773631 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3028716660 Nov 08, 2017 (151)
50 CSHL ss3352389910 Nov 08, 2017 (151)
51 URBANLAB ss3650957464 Oct 12, 2018 (152)
52 EGCUT_WGS ss3684487545 Jul 13, 2019 (153)
53 EVA_DECODE ss3706443022 Jul 13, 2019 (153)
54 ACPOP ss3743196351 Jul 13, 2019 (153)
55 EVA ss3758350497 Jul 13, 2019 (153)
56 PACBIO ss3788582904 Jul 13, 2019 (153)
57 PACBIO ss3793485614 Jul 13, 2019 (153)
58 PACBIO ss3798372734 Jul 13, 2019 (153)
59 KHV_HUMAN_GENOMES ss3821522310 Jul 13, 2019 (153)
60 EVA ss3835555763 Apr 27, 2020 (154)
61 EVA ss3841401464 Apr 27, 2020 (154)
62 EVA ss3846908839 Apr 27, 2020 (154)
63 SGDP_PRJ ss3888610362 Apr 27, 2020 (154)
64 KRGDB ss3938788919 Apr 27, 2020 (154)
65 TOPMED ss5080335533 Apr 27, 2021 (155)
66 TOMMO_GENOMICS ss5228585096 Apr 27, 2021 (155)
67 1000G_HIGH_COVERAGE ss5307884445 Oct 13, 2022 (156)
68 EVA ss5435896608 Oct 13, 2022 (156)
69 HUGCELL_USP ss5500304804 Oct 13, 2022 (156)
70 EVA ss5512138597 Oct 13, 2022 (156)
71 1000G_HIGH_COVERAGE ss5613870083 Oct 13, 2022 (156)
72 SANFORD_IMAGENETICS ss5662748657 Oct 13, 2022 (156)
73 TOMMO_GENOMICS ss5787500193 Oct 13, 2022 (156)
74 YY_MCH ss5817764898 Oct 13, 2022 (156)
75 EVA ss5845363374 Oct 13, 2022 (156)
76 EVA ss5853042616 Oct 13, 2022 (156)
77 EVA ss5922445575 Oct 13, 2022 (156)
78 EVA ss5957646518 Oct 13, 2022 (156)
79 EVA ss5981072807 Oct 13, 2022 (156)
80 1000Genomes NC_000020.10 - 2507086 Oct 12, 2018 (152)
81 1000Genomes_30x NC_000020.11 - 2526440 Oct 13, 2022 (156)
82 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 2507086 Oct 12, 2018 (152)
83 Genetic variation in the Estonian population NC_000020.10 - 2507086 Oct 12, 2018 (152)
84 The Danish reference pan genome NC_000020.10 - 2507086 Apr 27, 2020 (154)
85 gnomAD - Genomes NC_000020.11 - 2526440 Apr 27, 2021 (155)
86 Genome of the Netherlands Release 5 NC_000020.10 - 2507086 Apr 27, 2020 (154)
87 KOREAN population from KRGDB NC_000020.10 - 2507086 Apr 27, 2020 (154)
88 Northern Sweden NC_000020.10 - 2507086 Jul 13, 2019 (153)
89 Qatari NC_000020.10 - 2507086 Apr 27, 2020 (154)
90 SGDP_PRJ NC_000020.10 - 2507086 Apr 27, 2020 (154)
91 Siberian NC_000020.10 - 2507086 Apr 27, 2020 (154)
92 8.3KJPN NC_000020.10 - 2507086 Apr 27, 2021 (155)
93 14KJPN NC_000020.11 - 2526440 Oct 13, 2022 (156)
94 TopMed NC_000020.11 - 2526440 Apr 27, 2021 (155)
95 UK 10K study - Twins NC_000020.10 - 2507086 Oct 12, 2018 (152)
96 A Vietnamese Genetic Variation Database NC_000020.10 - 2507086 Jul 13, 2019 (153)
97 ALFA NC_000020.11 - 2526440 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).

Associated ID History Updated (Build)
rs8122105 Aug 26, 2003 (117)
rs56966181 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83638705, ss91617650, ss111618272, ss115373344, ss117460274, ss167679011, ss168889389, ss171826895, ss203810620, ss208633710, ss255435695, ss283276565, ss287411949, ss292564594, ss1698531342 NC_000020.9:2455085:G:A NC_000020.11:2526439:G:A (self)
77270103, 42769904, 30225793, 5575955, 19057229, 45966313, 16481216, 20028000, 40627342, 10839660, 86554403, 42769904, 9441730, ss228222107, ss237738184, ss243929826, ss566096130, ss661965972, ss994477178, ss1082024823, ss1363838614, ss1428977176, ss1579411016, ss1638289606, ss1681283639, ss1809393780, ss1937986078, ss1969075979, ss2029769479, ss2158323306, ss2629382227, ss2703994861, ss2964800406, ss3017773631, ss3352389910, ss3684487545, ss3743196351, ss3758350497, ss3788582904, ss3793485614, ss3798372734, ss3835555763, ss3841401464, ss3888610362, ss3938788919, ss5228585096, ss5435896608, ss5512138597, ss5662748657, ss5845363374, ss5957646518, ss5981072807 NC_000020.10:2507085:G:A NC_000020.11:2526439:G:A (self)
101396018, 544878377, 121337297, 355444478, 8310021798, ss2240859738, ss3028716660, ss3650957464, ss3706443022, ss3821522310, ss3846908839, ss5080335533, ss5307884445, ss5500304804, ss5613870083, ss5787500193, ss5817764898, ss5853042616, ss5922445575 NC_000020.11:2526439:G:A NC_000020.11:2526439:G:A (self)
ss8361733, ss12490914, ss16897228, ss17697258, ss21784696, ss41388554, ss96181847, ss115458499, ss135736761, ss138199751, ss156085298 NT_011387.8:2447085:G:A NC_000020.11:2526439:G:A (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 rs6049782

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