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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.

rs6089771

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:63763035 (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
G=0.483611 (128007/264690, TOPMED)
G=0.493862 (69033/139782, GnomAD)
G=0.13989 (3953/28258, 14KJPN) (+ 16 more)
A=0.49852 (9417/18890, ALFA)
G=0.13896 (2329/16760, 8.3KJPN)
G=0.4625 (2962/6404, 1000G_30x)
G=0.4573 (2290/5008, 1000G)
A=0.4616 (2068/4480, Estonian)
G=0.4497 (1733/3854, ALSPAC)
G=0.4617 (1712/3708, TWINSUK)
G=0.1628 (477/2930, KOREAN)
G=0.1496 (274/1832, Korea1K)
G=0.453 (452/998, GoNL)
G=0.477 (286/600, NorthernSweden)
A=0.338 (108/320, SGDP_PRJ)
A=0.449 (97/216, Qatari)
G=0.132 (28/212, Vietnamese)
G=0.42 (17/40, GENOME_DK)
A=0.45 (10/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZBTB46 : 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 18890 A=0.49852 G=0.50148
European Sub 14286 A=0.50469 G=0.49531
African Sub 2946 A=0.4162 G=0.5838
African Others Sub 114 A=0.377 G=0.623
African American Sub 2832 A=0.4177 G=0.5823
Asian Sub 112 A=0.875 G=0.125
East Asian Sub 86 A=0.86 G=0.14
Other Asian Sub 26 A=0.92 G=0.08
Latin American 1 Sub 146 A=0.527 G=0.473
Latin American 2 Sub 610 A=0.680 G=0.320
South Asian Sub 98 A=0.39 G=0.61
Other Sub 692 A=0.510 G=0.490


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=0.516389 G=0.483611
gnomAD - Genomes Global Study-wide 139782 A=0.506138 G=0.493862
gnomAD - Genomes European Sub 75750 A=0.52218 G=0.47782
gnomAD - Genomes African Sub 41856 A=0.42288 G=0.57712
gnomAD - Genomes American Sub 13590 A=0.57954 G=0.42046
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.5443 G=0.4557
gnomAD - Genomes East Asian Sub 3118 A=0.8672 G=0.1328
gnomAD - Genomes Other Sub 2148 A=0.5154 G=0.4846
14KJPN JAPANESE Study-wide 28258 A=0.86011 G=0.13989
Allele Frequency Aggregator Total Global 18890 A=0.49852 G=0.50148
Allele Frequency Aggregator European Sub 14286 A=0.50469 G=0.49531
Allele Frequency Aggregator African Sub 2946 A=0.4162 G=0.5838
Allele Frequency Aggregator Other Sub 692 A=0.510 G=0.490
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.680 G=0.320
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.527 G=0.473
Allele Frequency Aggregator Asian Sub 112 A=0.875 G=0.125
Allele Frequency Aggregator South Asian Sub 98 A=0.39 G=0.61
8.3KJPN JAPANESE Study-wide 16760 A=0.86104 G=0.13896
1000Genomes_30x Global Study-wide 6404 A=0.5375 G=0.4625
1000Genomes_30x African Sub 1786 A=0.3639 G=0.6361
1000Genomes_30x Europe Sub 1266 A=0.4874 G=0.5126
1000Genomes_30x South Asian Sub 1202 A=0.4118 G=0.5882
1000Genomes_30x East Asian Sub 1170 A=0.8803 G=0.1197
1000Genomes_30x American Sub 980 A=0.663 G=0.337
1000Genomes Global Study-wide 5008 A=0.5427 G=0.4573
1000Genomes African Sub 1322 A=0.3691 G=0.6309
1000Genomes East Asian Sub 1008 A=0.8770 G=0.1230
1000Genomes Europe Sub 1006 A=0.5060 G=0.4940
1000Genomes South Asian Sub 978 A=0.401 G=0.599
1000Genomes American Sub 694 A=0.641 G=0.359
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4616 G=0.5384
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.5503 G=0.4497
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.5383 G=0.4617
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.8372 G=0.1628
Korean Genome Project KOREAN Study-wide 1832 A=0.8504 G=0.1496
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.547 G=0.453
Northern Sweden ACPOP Study-wide 600 A=0.523 G=0.477
SGDP_PRJ Global Study-wide 320 A=0.338 G=0.662
Qatari Global Study-wide 216 A=0.449 G=0.551
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.868 G=0.132
The Danish reference pan genome Danish Study-wide 40 A=0.57 G=0.42
Siberian Global Study-wide 22 A=0.45 G=0.55
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.63763035A>G
GRCh37.p13 chr 20 NC_000020.10:g.62394388A>G
Gene: ZBTB46, zinc finger and BTB domain containing 46 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZBTB46 transcript variant 1 NM_001369741.1:c.1223-101…

NM_001369741.1:c.1223-10174T>C

N/A Intron Variant
ZBTB46 transcript variant 2 NM_025224.4:c.1223-10174T…

NM_025224.4:c.1223-10174T>C

N/A Intron Variant
ZBTB46 transcript variant X6 XM_005260195.5:c.1223-101…

XM_005260195.5:c.1223-10174T>C

N/A Intron Variant
ZBTB46 transcript variant X2 XM_005260197.5:c.1223-101…

XM_005260197.5:c.1223-10174T>C

N/A Intron Variant
ZBTB46 transcript variant X5 XM_005260198.5:c.1223-101…

XM_005260198.5:c.1223-10174T>C

N/A Intron Variant
ZBTB46 transcript variant X4 XM_006723700.4:c.1223-101…

XM_006723700.4:c.1223-10174T>C

N/A Intron Variant
ZBTB46 transcript variant X1 XM_011528548.3:c.1223-101…

XM_011528548.3:c.1223-10174T>C

N/A Intron Variant
ZBTB46 transcript variant X7 XM_047439901.1:c.1223-101…

XM_047439901.1:c.1223-10174T>C

N/A Intron Variant
ZBTB46 transcript variant X10 XM_011528549.3:c. N/A Genic Downstream Transcript Variant
ZBTB46 transcript variant X9 XM_017027667.2:c. N/A Genic Downstream Transcript Variant
ZBTB46 transcript variant X8 XR_001754167.2:n. N/A Intron Variant
ZBTB46 transcript variant X3 XR_936500.3:n. N/A Intron 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 20 NC_000020.11:g.63763035= NC_000020.11:g.63763035A>G
GRCh37.p13 chr 20 NC_000020.10:g.62394388= NC_000020.10:g.62394388A>G
ZBTB46 transcript variant 1 NM_001369741.1:c.1223-10174= NM_001369741.1:c.1223-10174T>C
ZBTB46 transcript NM_025224.3:c.1223-10174= NM_025224.3:c.1223-10174T>C
ZBTB46 transcript variant 2 NM_025224.4:c.1223-10174= NM_025224.4:c.1223-10174T>C
ZBTB46 transcript variant X1 XM_005260195.1:c.1223-10174= XM_005260195.1:c.1223-10174T>C
ZBTB46 transcript variant X6 XM_005260195.5:c.1223-10174= XM_005260195.5:c.1223-10174T>C
ZBTB46 transcript variant X2 XM_005260196.1:c.1223-10174= XM_005260196.1:c.1223-10174T>C
ZBTB46 transcript variant X3 XM_005260197.1:c.1223-10174= XM_005260197.1:c.1223-10174T>C
ZBTB46 transcript variant X2 XM_005260197.5:c.1223-10174= XM_005260197.5:c.1223-10174T>C
ZBTB46 transcript variant X4 XM_005260198.1:c.1223-10174= XM_005260198.1:c.1223-10174T>C
ZBTB46 transcript variant X5 XM_005260198.5:c.1223-10174= XM_005260198.5:c.1223-10174T>C
ZBTB46 transcript variant X4 XM_006723700.4:c.1223-10174= XM_006723700.4:c.1223-10174T>C
ZBTB46 transcript variant X1 XM_011528548.3:c.1223-10174= XM_011528548.3:c.1223-10174T>C
ZBTB46 transcript variant X7 XM_047439901.1:c.1223-10174= XM_047439901.1:c.1223-10174T>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#.

67 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8413259 Apr 21, 2003 (114)
2 BCM_SSAHASNP ss10972528 Jul 11, 2003 (117)
3 WI_SSAHASNP ss12498479 Jul 11, 2003 (117)
4 CSHL-HAPMAP ss16904193 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss19482615 Feb 27, 2004 (120)
6 ABI ss41421764 Mar 13, 2006 (126)
7 HGSV ss86026181 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss91757131 Mar 24, 2008 (129)
9 1000GENOMES ss113575201 Jan 25, 2009 (130)
10 ILLUMINA-UK ss117611600 Dec 01, 2009 (131)
11 ENSEMBL ss138272720 Dec 01, 2009 (131)
12 ENSEMBL ss161340119 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss170110074 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss172211933 Jul 04, 2010 (132)
15 BUSHMAN ss203947089 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss208746868 Jul 04, 2010 (132)
17 1000GENOMES ss210963346 Jul 14, 2010 (132)
18 1000GENOMES ss228452942 Jul 14, 2010 (132)
19 1000GENOMES ss237902695 Jul 15, 2010 (132)
20 1000GENOMES ss244058028 Jul 15, 2010 (132)
21 PJP ss292599834 May 09, 2011 (134)
22 TISHKOFF ss566369221 Apr 25, 2013 (138)
23 SSMP ss662250698 Apr 25, 2013 (138)
24 EVA-GONL ss994911167 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1082340603 Aug 21, 2014 (142)
26 1000GENOMES ss1365500132 Aug 21, 2014 (142)
27 DDI ss1429107308 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1579578867 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1639169703 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1682163736 Apr 01, 2015 (144)
31 EVA_DECODE ss1698975922 Apr 01, 2015 (144)
32 HAMMER_LAB ss1809586779 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1938434474 Feb 12, 2016 (147)
34 GENOMED ss1969172550 Jul 19, 2016 (147)
35 JJLAB ss2029997525 Sep 14, 2016 (149)
36 USC_VALOUEV ss2158569812 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2244256939 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2629491176 Nov 08, 2017 (151)
39 GRF ss2704267182 Nov 08, 2017 (151)
40 GNOMAD ss2969459293 Nov 08, 2017 (151)
41 SWEGEN ss3018479884 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3028832205 Nov 08, 2017 (151)
43 CSHL ss3352597936 Nov 08, 2017 (151)
44 EGCUT_WGS ss3685164949 Jul 13, 2019 (153)
45 EVA_DECODE ss3707319451 Jul 13, 2019 (153)
46 ACPOP ss3743554892 Jul 13, 2019 (153)
47 EVA ss3758872718 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3822026058 Jul 13, 2019 (153)
49 EVA ss3835766621 Apr 27, 2020 (154)
50 SGDP_PRJ ss3889493633 Apr 27, 2020 (154)
51 KRGDB ss3939821905 Apr 27, 2020 (154)
52 KOGIC ss3982648668 Apr 27, 2020 (154)
53 TOPMED ss5094788665 Apr 27, 2021 (155)
54 TOMMO_GENOMICS ss5230482424 Apr 27, 2021 (155)
55 1000G_HIGH_COVERAGE ss5309447322 Oct 16, 2022 (156)
56 EVA ss5438591952 Oct 16, 2022 (156)
57 HUGCELL_USP ss5501661533 Oct 16, 2022 (156)
58 EVA ss5512264109 Oct 16, 2022 (156)
59 1000G_HIGH_COVERAGE ss5616207287 Oct 16, 2022 (156)
60 SANFORD_IMAGENETICS ss5663574680 Oct 16, 2022 (156)
61 TOMMO_GENOMICS ss5790551054 Oct 16, 2022 (156)
62 YY_MCH ss5818202716 Oct 16, 2022 (156)
63 EVA ss5845949172 Oct 16, 2022 (156)
64 EVA ss5853218146 Oct 16, 2022 (156)
65 EVA ss5924171783 Oct 16, 2022 (156)
66 EVA ss5958507782 Oct 16, 2022 (156)
67 EVA ss5981100106 Oct 16, 2022 (156)
68 1000Genomes NC_000020.10 - 62394388 Oct 12, 2018 (152)
69 1000Genomes_30x NC_000020.11 - 63763035 Oct 16, 2022 (156)
70 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 62394388 Oct 12, 2018 (152)
71 Genetic variation in the Estonian population NC_000020.10 - 62394388 Oct 12, 2018 (152)
72 The Danish reference pan genome NC_000020.10 - 62394388 Apr 27, 2020 (154)
73 gnomAD - Genomes NC_000020.11 - 63763035 Apr 27, 2021 (155)
74 Genome of the Netherlands Release 5 NC_000020.10 - 62394388 Apr 27, 2020 (154)
75 KOREAN population from KRGDB NC_000020.10 - 62394388 Apr 27, 2020 (154)
76 Korean Genome Project NC_000020.11 - 63763035 Apr 27, 2020 (154)
77 Northern Sweden NC_000020.10 - 62394388 Jul 13, 2019 (153)
78 Qatari NC_000020.10 - 62394388 Apr 27, 2020 (154)
79 SGDP_PRJ NC_000020.10 - 62394388 Apr 27, 2020 (154)
80 Siberian NC_000020.10 - 62394388 Apr 27, 2020 (154)
81 8.3KJPN NC_000020.10 - 62394388 Apr 27, 2021 (155)
82 14KJPN NC_000020.11 - 63763035 Oct 16, 2022 (156)
83 TopMed NC_000020.11 - 63763035 Apr 27, 2021 (155)
84 UK 10K study - Twins NC_000020.10 - 62394388 Oct 12, 2018 (152)
85 A Vietnamese Genetic Variation Database NC_000020.10 - 62394388 Jul 13, 2019 (153)
86 ALFA NC_000020.11 - 63763035 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)
rs6512286 Aug 26, 2003 (117)
rs57266646 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss86026181, ss91757131, ss113575201, ss117611600, ss170110074, ss172211933, ss203947089, ss208746868, ss210963346, ss292599834, ss1698975922 NC_000020.9:61864831:A:G NC_000020.11:63763034:A:G (self)
78988669, 43735476, 30903197, 5743806, 19476403, 46999299, 16839757, 20476396, 41510613, 11086166, 88451731, 43735476, 9644027, ss228452942, ss237902695, ss244058028, ss566369221, ss662250698, ss994911167, ss1082340603, ss1365500132, ss1429107308, ss1579578867, ss1639169703, ss1682163736, ss1809586779, ss1938434474, ss1969172550, ss2029997525, ss2158569812, ss2629491176, ss2704267182, ss2969459293, ss3018479884, ss3352597936, ss3685164949, ss3743554892, ss3758872718, ss3835766621, ss3889493633, ss3939821905, ss5230482424, ss5438591952, ss5512264109, ss5663574680, ss5845949172, ss5958507782, ss5981100106 NC_000020.10:62394387:A:G NC_000020.11:63763034:A:G (self)
103733222, 557040445, 39026669, 124388158, 369897610, 14851590680, ss2244256939, ss3028832205, ss3707319451, ss3822026058, ss3982648668, ss5094788665, ss5309447322, ss5501661533, ss5616207287, ss5790551054, ss5818202716, ss5853218146, ss5924171783 NC_000020.11:63763034:A:G NC_000020.11:63763034:A:G (self)
ss8413259, ss10972528, ss12498479, ss16904193, ss19482615 NT_011333.5:1131017:A:G NC_000020.11:63763034:A:G (self)
ss41421764, ss138272720, ss161340119 NT_011333.6:1131018:A:G NC_000020.11:63763034: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 rs6089771

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