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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.

rs4466264

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:124744140 (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>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.379618 (100481/264690, TOPMED)
A=0.385218 (53805/139674, GnomAD)
A=0.37376 (10561/28256, 14KJPN) (+ 16 more)
A=0.37845 (6875/18166, ALFA)
A=0.37595 (6301/16760, 8.3KJPN)
A=0.3823 (2448/6404, 1000G_30x)
A=0.3788 (1897/5008, 1000G)
A=0.4451 (1994/4480, Estonian)
A=0.3570 (1376/3854, ALSPAC)
A=0.3722 (1380/3708, TWINSUK)
A=0.3304 (968/2930, KOREAN)
A=0.3477 (637/1832, Korea1K)
A=0.367 (366/998, GoNL)
A=0.370 (222/600, NorthernSweden)
T=0.370 (125/338, SGDP_PRJ)
T=0.486 (105/216, Qatari)
A=0.361 (78/216, Vietnamese)
A=0.35 (14/40, GENOME_DK)
T=0.28 (11/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NKAIN2 : Intron Variant
Publications
1 citation
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 18166 T=0.62155 A=0.37845, G=0.00000
European Sub 13892 T=0.61921 A=0.38079, G=0.00000
African Sub 2620 T=0.6630 A=0.3370, G=0.0000
African Others Sub 100 T=0.69 A=0.31, G=0.00
African American Sub 2520 T=0.6619 A=0.3381, G=0.0000
Asian Sub 112 T=0.661 A=0.339, G=0.000
East Asian Sub 86 T=0.65 A=0.35, G=0.00
Other Asian Sub 26 T=0.69 A=0.31, G=0.00
Latin American 1 Sub 146 T=0.548 A=0.452, G=0.000
Latin American 2 Sub 610 T=0.489 A=0.511, G=0.000
South Asian Sub 98 T=0.62 A=0.38, G=0.00
Other Sub 688 T=0.638 A=0.362, G=0.000


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=0.620382 A=0.379618
gnomAD - Genomes Global Study-wide 139674 T=0.614782 A=0.385218
gnomAD - Genomes European Sub 75692 T=0.61460 A=0.38540
gnomAD - Genomes African Sub 41876 T=0.62764 A=0.37236
gnomAD - Genomes American Sub 13570 T=0.54819 A=0.45181
gnomAD - Genomes Ashkenazi Jewish Sub 3316 T=0.6680 A=0.3320
gnomAD - Genomes East Asian Sub 3074 T=0.6848 A=0.3152
gnomAD - Genomes Other Sub 2146 T=0.6090 A=0.3910
14KJPN JAPANESE Study-wide 28256 T=0.62624 A=0.37376
Allele Frequency Aggregator Total Global 18166 T=0.62155 A=0.37845, G=0.00000
Allele Frequency Aggregator European Sub 13892 T=0.61921 A=0.38079, G=0.00000
Allele Frequency Aggregator African Sub 2620 T=0.6630 A=0.3370, G=0.0000
Allele Frequency Aggregator Other Sub 688 T=0.638 A=0.362, G=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.489 A=0.511, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.548 A=0.452, G=0.000
Allele Frequency Aggregator Asian Sub 112 T=0.661 A=0.339, G=0.000
Allele Frequency Aggregator South Asian Sub 98 T=0.62 A=0.38, G=0.00
8.3KJPN JAPANESE Study-wide 16760 T=0.62405 A=0.37595
1000Genomes_30x Global Study-wide 6404 T=0.6177 A=0.3823
1000Genomes_30x African Sub 1786 T=0.6260 A=0.3740
1000Genomes_30x Europe Sub 1266 T=0.6098 A=0.3902
1000Genomes_30x South Asian Sub 1202 T=0.6780 A=0.3220
1000Genomes_30x East Asian Sub 1170 T=0.6513 A=0.3487
1000Genomes_30x American Sub 980 T=0.499 A=0.501
1000Genomes Global Study-wide 5008 T=0.6212 A=0.3788
1000Genomes African Sub 1322 T=0.6324 A=0.3676
1000Genomes East Asian Sub 1008 T=0.6548 A=0.3452
1000Genomes Europe Sub 1006 T=0.6064 A=0.3936
1000Genomes South Asian Sub 978 T=0.670 A=0.330
1000Genomes American Sub 694 T=0.504 A=0.496
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5549 A=0.4451
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6430 A=0.3570
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6278 A=0.3722
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.6696 A=0.3304
Korean Genome Project KOREAN Study-wide 1832 T=0.6523 A=0.3477
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.633 A=0.367
Northern Sweden ACPOP Study-wide 600 T=0.630 A=0.370
SGDP_PRJ Global Study-wide 338 T=0.370 A=0.630
Qatari Global Study-wide 216 T=0.486 A=0.514
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.639 A=0.361
The Danish reference pan genome Danish Study-wide 40 T=0.65 A=0.35
Siberian Global Study-wide 40 T=0.28 A=0.72
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 6 NC_000006.12:g.124744140T>A
GRCh38.p14 chr 6 NC_000006.12:g.124744140T>G
GRCh37.p13 chr 6 NC_000006.11:g.125065286T>A
GRCh37.p13 chr 6 NC_000006.11:g.125065286T>G
NKAIN2 RefSeqGene NG_021365.2:g.945277T>A
NKAIN2 RefSeqGene NG_021365.2:g.945277T>G
NKAIN2 RefSeqGene NG_021365.1:g.945218T>A
NKAIN2 RefSeqGene NG_021365.1:g.945218T>G
Gene: NKAIN2, sodium/potassium transporting ATPase interacting 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NKAIN2 transcript variant 1 NM_001040214.3:c.475-4719…

NM_001040214.3:c.475-47199T>A

N/A Intron Variant
NKAIN2 transcript variant 3 NM_001300737.2:c.472-4719…

NM_001300737.2:c.472-47199T>A

N/A Intron Variant
NKAIN2 transcript variant 4 NM_001300738.2:c.205-4719…

NM_001300738.2:c.205-47199T>A

N/A Intron Variant
NKAIN2 transcript variant 5 NM_001300740.1:c.169-4719…

NM_001300740.1:c.169-47199T>A

N/A Intron Variant
NKAIN2 transcript variant 2 NM_153355.5:c.274-47199T>A N/A Intron Variant
NKAIN2 transcript variant X3 XM_017010318.3:c.394-4719…

XM_017010318.3:c.394-47199T>A

N/A Intron Variant
NKAIN2 transcript variant X1 XR_007059213.1:n. N/A Intron Variant
NKAIN2 transcript variant X2 XR_007059214.1:n. N/A Intron Variant
NKAIN2 transcript variant X4 XR_007059215.1: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 T= A G
GRCh38.p14 chr 6 NC_000006.12:g.124744140= NC_000006.12:g.124744140T>A NC_000006.12:g.124744140T>G
GRCh37.p13 chr 6 NC_000006.11:g.125065286= NC_000006.11:g.125065286T>A NC_000006.11:g.125065286T>G
NKAIN2 RefSeqGene NG_021365.2:g.945277= NG_021365.2:g.945277T>A NG_021365.2:g.945277T>G
NKAIN2 RefSeqGene NG_021365.1:g.945218= NG_021365.1:g.945218T>A NG_021365.1:g.945218T>G
NKAIN2 transcript variant 1 NM_001040214.1:c.475-47199= NM_001040214.1:c.475-47199T>A NM_001040214.1:c.475-47199T>G
NKAIN2 transcript variant 1 NM_001040214.3:c.475-47199= NM_001040214.3:c.475-47199T>A NM_001040214.3:c.475-47199T>G
NKAIN2 transcript variant 3 NM_001300737.2:c.472-47199= NM_001300737.2:c.472-47199T>A NM_001300737.2:c.472-47199T>G
NKAIN2 transcript variant 4 NM_001300738.2:c.205-47199= NM_001300738.2:c.205-47199T>A NM_001300738.2:c.205-47199T>G
NKAIN2 transcript variant 5 NM_001300740.1:c.169-47199= NM_001300740.1:c.169-47199T>A NM_001300740.1:c.169-47199T>G
NKAIN2 transcript variant 2 NM_153355.3:c.274-47199= NM_153355.3:c.274-47199T>A NM_153355.3:c.274-47199T>G
NKAIN2 transcript variant 2 NM_153355.5:c.274-47199= NM_153355.5:c.274-47199T>A NM_153355.5:c.274-47199T>G
NKAIN2 transcript variant X1 XM_005266833.1:c.472-47199= XM_005266833.1:c.472-47199T>A XM_005266833.1:c.472-47199T>G
NKAIN2 transcript variant X2 XM_005266834.1:c.475-47199= XM_005266834.1:c.475-47199T>A XM_005266834.1:c.475-47199T>G
NKAIN2 transcript variant X3 XM_005266835.1:c.475-47199= XM_005266835.1:c.475-47199T>A XM_005266835.1:c.475-47199T>G
NKAIN2 transcript variant X3 XM_017010318.3:c.394-47199= XM_017010318.3:c.394-47199T>A XM_017010318.3:c.394-47199T>G
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#.

74 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5999133 Feb 20, 2003 (111)
2 PERLEGEN ss12673931 Dec 05, 2003 (119)
3 SC_SNP ss12853862 Dec 05, 2003 (119)
4 SC_SNP ss15756352 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss17906702 Feb 27, 2004 (120)
6 PERLEGEN ss23368158 Sep 20, 2004 (123)
7 ABI ss44745539 Mar 14, 2006 (126)
8 AFFY ss66024722 Dec 02, 2006 (127)
9 PERLEGEN ss68990345 May 18, 2007 (127)
10 BCMHGSC_JDW ss93554825 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss98538547 Feb 04, 2009 (130)
12 BGI ss104357406 Dec 01, 2009 (131)
13 1000GENOMES ss110871847 Jan 25, 2009 (130)
14 1000GENOMES ss115063743 Jan 25, 2009 (130)
15 ILLUMINA-UK ss116706473 Feb 14, 2009 (130)
16 ENSEMBL ss139890287 Dec 01, 2009 (131)
17 ENSEMBL ss144290159 Dec 01, 2009 (131)
18 GMI ss157558685 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss162791892 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss164472760 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss167241062 Jul 04, 2010 (132)
22 1000GENOMES ss222658086 Jul 14, 2010 (132)
23 1000GENOMES ss233672751 Jul 15, 2010 (132)
24 1000GENOMES ss240690508 Jul 15, 2010 (132)
25 GMI ss279012591 May 04, 2012 (137)
26 PJP ss293718696 May 09, 2011 (134)
27 TISHKOFF ss559504512 Apr 25, 2013 (138)
28 SSMP ss653718689 Apr 25, 2013 (138)
29 EVA-GONL ss983469709 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1074011003 Aug 21, 2014 (142)
31 1000GENOMES ss1322150270 Aug 21, 2014 (142)
32 DDI ss1430887545 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1581887235 Apr 01, 2015 (144)
34 EVA_DECODE ss1593036053 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1616630689 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1659624722 Apr 01, 2015 (144)
37 HAMMER_LAB ss1804657733 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1926713760 Feb 12, 2016 (147)
39 GENOMED ss1970520103 Jul 19, 2016 (147)
40 JJLAB ss2024013044 Sep 14, 2016 (149)
41 USC_VALOUEV ss2152207836 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2288125944 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2626502334 Nov 08, 2017 (151)
44 GRF ss2707838260 Nov 08, 2017 (151)
45 GNOMAD ss2844771812 Nov 08, 2017 (151)
46 SWEGEN ss2999906234 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3025801180 Nov 08, 2017 (151)
48 CSHL ss3347217444 Nov 08, 2017 (151)
49 URBANLAB ss3648466470 Oct 12, 2018 (152)
50 EGCUT_WGS ss3667816189 Jul 13, 2019 (153)
51 EVA_DECODE ss3718219857 Jul 13, 2019 (153)
52 ACPOP ss3733959103 Jul 13, 2019 (153)
53 EVA ss3765635769 Jul 13, 2019 (153)
54 KHV_HUMAN_GENOMES ss3808792350 Jul 13, 2019 (153)
55 EVA ss3830179728 Apr 26, 2020 (154)
56 EVA ss3838576305 Apr 26, 2020 (154)
57 EVA ss3844026177 Apr 26, 2020 (154)
58 SGDP_PRJ ss3865645599 Apr 26, 2020 (154)
59 KRGDB ss3912595984 Apr 26, 2020 (154)
60 KOGIC ss3960026916 Apr 26, 2020 (154)
61 TOPMED ss4720780162 Apr 26, 2021 (155)
62 TOMMO_GENOMICS ss5179799074 Apr 26, 2021 (155)
63 1000G_HIGH_COVERAGE ss5270244725 Oct 13, 2022 (156)
64 EVA ss5368811980 Oct 13, 2022 (156)
65 HUGCELL_USP ss5467695514 Oct 13, 2022 (156)
66 1000G_HIGH_COVERAGE ss5557132851 Oct 13, 2022 (156)
67 SANFORD_IMAGENETICS ss5641432060 Oct 13, 2022 (156)
68 TOMMO_GENOMICS ss5718647121 Oct 13, 2022 (156)
69 YY_MCH ss5807935932 Oct 13, 2022 (156)
70 EVA ss5842949451 Oct 13, 2022 (156)
71 EVA ss5855572536 Oct 13, 2022 (156)
72 EVA ss5885831990 Oct 13, 2022 (156)
73 EVA ss5970056056 Oct 13, 2022 (156)
74 EVA ss5970056057 Oct 13, 2022 (156)
75 1000Genomes NC_000006.11 - 125065286 Oct 12, 2018 (152)
76 1000Genomes_30x NC_000006.12 - 124744140 Oct 13, 2022 (156)
77 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 125065286 Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000006.11 - 125065286 Oct 12, 2018 (152)
79 The Danish reference pan genome NC_000006.11 - 125065286 Apr 26, 2020 (154)
80 gnomAD - Genomes NC_000006.12 - 124744140 Apr 26, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000006.11 - 125065286 Apr 26, 2020 (154)
82 KOREAN population from KRGDB NC_000006.11 - 125065286 Apr 26, 2020 (154)
83 Korean Genome Project NC_000006.12 - 124744140 Apr 26, 2020 (154)
84 Northern Sweden NC_000006.11 - 125065286 Jul 13, 2019 (153)
85 Qatari NC_000006.11 - 125065286 Apr 26, 2020 (154)
86 SGDP_PRJ NC_000006.11 - 125065286 Apr 26, 2020 (154)
87 Siberian NC_000006.11 - 125065286 Apr 26, 2020 (154)
88 8.3KJPN NC_000006.11 - 125065286 Apr 26, 2021 (155)
89 14KJPN NC_000006.12 - 124744140 Oct 13, 2022 (156)
90 TopMed NC_000006.12 - 124744140 Apr 26, 2021 (155)
91 UK 10K study - Twins NC_000006.11 - 125065286 Oct 12, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000006.11 - 125065286 Jul 13, 2019 (153)
93 ALFA NC_000006.12 - 124744140 Apr 26, 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
ss93554825, ss110871847, ss115063743, ss116706473, ss162791892, ss164472760, ss167241062, ss279012591, ss293718696, ss1593036053 NC_000006.10:125106984:T:A NC_000006.12:124744139:T:A (self)
34014904, 18956022, 13554437, 8052174, 8445054, 19773378, 7243968, 8755690, 17662579, 4724190, 37768381, 18956022, 4221612, ss222658086, ss233672751, ss240690508, ss559504512, ss653718689, ss983469709, ss1074011003, ss1322150270, ss1430887545, ss1581887235, ss1616630689, ss1659624722, ss1804657733, ss1926713760, ss1970520103, ss2024013044, ss2152207836, ss2626502334, ss2707838260, ss2844771812, ss2999906234, ss3347217444, ss3667816189, ss3733959103, ss3765635769, ss3830179728, ss3838576305, ss3865645599, ss3912595984, ss5179799074, ss5368811980, ss5641432060, ss5842949451, ss5970056056, ss5970056057 NC_000006.11:125065285:T:A NC_000006.12:124744139:T:A (self)
44658786, 240214204, 16404917, 52484225, 558157720, 7288711017, ss2288125944, ss3025801180, ss3648466470, ss3718219857, ss3808792350, ss3844026177, ss3960026916, ss4720780162, ss5270244725, ss5467695514, ss5557132851, ss5718647121, ss5807935932, ss5855572536, ss5885831990 NC_000006.12:124744139:T:A NC_000006.12:124744139:T:A (self)
ss12853862 NT_025741.12:29169720:T:A NC_000006.12:124744139:T:A (self)
ss15756352, ss17906702 NT_025741.13:29169720:T:A NC_000006.12:124744139:T:A (self)
ss5999133, ss12673931, ss23368158, ss44745539, ss66024722, ss68990345, ss98538547, ss104357406, ss139890287, ss144290159, ss157558685 NT_025741.15:29234742:T:A NC_000006.12:124744139:T:A (self)
7288711017 NC_000006.12:124744139:T:G NC_000006.12:124744139:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs4466264
PMID Title Author Year Journal
14740319 Matching strategies for genetic association studies in structured populations. Hinds DA et al. 2004 American journal of human genetics
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