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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.

rs12015135

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:16052921 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.147063 (38926/264690, TOPMED)
C=0.153241 (21466/140080, GnomAD)
C=0.01692 (478/28258, 14KJPN) (+ 17 more)
C=0.13656 (3455/25300, ALFA)
C=0.01724 (289/16760, 8.3KJPN)
C=0.1220 (781/6404, 1000G_30x)
C=0.1134 (568/5008, 1000G)
C=0.1279 (493/3854, ALSPAC)
C=0.1254 (465/3708, TWINSUK)
C=0.0126 (37/2930, KOREAN)
C=0.1501 (280/1866, HapMap)
C=0.0115 (21/1832, Korea1K)
C=0.119 (119/998, GoNL)
C=0.140 (84/600, NorthernSweden)
C=0.083 (18/216, Qatari)
C=0.005 (1/216, Vietnamese)
A=0.44 (37/84, SGDP_PRJ)
C=0.15 (6/40, GENOME_DK)
A=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CLCNKB : 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 25300 A=0.86344 C=0.13656
European Sub 16842 A=0.87442 C=0.12558
African Sub 3682 A=0.7341 C=0.2659
African Others Sub 128 A=0.750 C=0.250
African American Sub 3554 A=0.7335 C=0.2665
Asian Sub 168 A=0.988 C=0.012
East Asian Sub 110 A=0.991 C=0.009
Other Asian Sub 58 A=0.98 C=0.02
Latin American 1 Sub 292 A=0.846 C=0.154
Latin American 2 Sub 2764 A=0.9439 C=0.0561
South Asian Sub 110 A=0.955 C=0.045
Other Sub 1442 A=0.8932 C=0.1068


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=0.852937 C=0.147063
gnomAD - Genomes Global Study-wide 140080 A=0.846759 C=0.153241
gnomAD - Genomes European Sub 75886 A=0.88194 C=0.11806
gnomAD - Genomes African Sub 41930 A=0.73995 C=0.26005
gnomAD - Genomes American Sub 13658 A=0.92005 C=0.07995
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.9446 C=0.0554
gnomAD - Genomes East Asian Sub 3132 A=0.9888 C=0.0112
gnomAD - Genomes Other Sub 2154 A=0.8644 C=0.1356
14KJPN JAPANESE Study-wide 28258 A=0.98308 C=0.01692
Allele Frequency Aggregator Total Global 25300 A=0.86344 C=0.13656
Allele Frequency Aggregator European Sub 16842 A=0.87442 C=0.12558
Allele Frequency Aggregator African Sub 3682 A=0.7341 C=0.2659
Allele Frequency Aggregator Latin American 2 Sub 2764 A=0.9439 C=0.0561
Allele Frequency Aggregator Other Sub 1442 A=0.8932 C=0.1068
Allele Frequency Aggregator Latin American 1 Sub 292 A=0.846 C=0.154
Allele Frequency Aggregator Asian Sub 168 A=0.988 C=0.012
Allele Frequency Aggregator South Asian Sub 110 A=0.955 C=0.045
8.3KJPN JAPANESE Study-wide 16760 A=0.98276 C=0.01724
1000Genomes_30x Global Study-wide 6404 A=0.8780 C=0.1220
1000Genomes_30x African Sub 1786 A=0.7156 C=0.2844
1000Genomes_30x Europe Sub 1266 A=0.8965 C=0.1035
1000Genomes_30x South Asian Sub 1202 A=0.9509 C=0.0491
1000Genomes_30x East Asian Sub 1170 A=0.9915 C=0.0085
1000Genomes_30x American Sub 980 A=0.926 C=0.074
1000Genomes Global Study-wide 5008 A=0.8866 C=0.1134
1000Genomes African Sub 1322 A=0.7315 C=0.2685
1000Genomes East Asian Sub 1008 A=0.9901 C=0.0099
1000Genomes Europe Sub 1006 A=0.9016 C=0.0984
1000Genomes South Asian Sub 978 A=0.947 C=0.053
1000Genomes American Sub 694 A=0.925 C=0.075
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8721 C=0.1279
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8746 C=0.1254
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.9874 C=0.0126
HapMap Global Study-wide 1866 A=0.8499 C=0.1501
HapMap American Sub 756 A=0.902 C=0.098
HapMap African Sub 686 A=0.727 C=0.273
HapMap Asian Sub 254 A=0.980 C=0.020
HapMap Europe Sub 170 A=0.918 C=0.082
Korean Genome Project KOREAN Study-wide 1832 A=0.9885 C=0.0115
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.881 C=0.119
Northern Sweden ACPOP Study-wide 600 A=0.860 C=0.140
Qatari Global Study-wide 216 A=0.917 C=0.083
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.995 C=0.005
SGDP_PRJ Global Study-wide 84 A=0.44 C=0.56
The Danish reference pan genome Danish Study-wide 40 A=0.85 C=0.15
Siberian Global Study-wide 6 A=0.5 C=0.5
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.16052921A>C
GRCh37.p13 chr 1 NC_000001.10:g.16379416A>C
CLCNKB RefSeqGene NG_013079.1:g.14170A>C
LOC106501713 genomic region NG_042865.1:g.8429A>C
Gene: CLCNKB, chloride voltage-gated channel Kb (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CLCNKB transcript variant 1 NM_000085.5:c.1622+510A>C N/A Intron Variant
CLCNKB transcript variant 2 NM_001165945.2:c.1115+510…

NM_001165945.2:c.1115+510A>C

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= C
GRCh38.p14 chr 1 NC_000001.11:g.16052921= NC_000001.11:g.16052921A>C
GRCh37.p13 chr 1 NC_000001.10:g.16379416= NC_000001.10:g.16379416A>C
CLCNKB RefSeqGene NG_013079.1:g.14170= NG_013079.1:g.14170A>C
LOC106501713 genomic region NG_042865.1:g.8429= NG_042865.1:g.8429A>C
CLCNKB transcript variant 1 NM_000085.4:c.1622+510= NM_000085.4:c.1622+510A>C
CLCNKB transcript variant 1 NM_000085.5:c.1622+510= NM_000085.5:c.1622+510A>C
CLCNKB transcript variant 2 NM_001165945.2:c.1115+510= NM_001165945.2:c.1115+510A>C
CLCNKB transcript variant X1 XM_005245733.1:c.1622+510= XM_005245733.1:c.1622+510A>C
CLCNKB transcript variant X2 XM_005245734.1:c.971+510= XM_005245734.1:c.971+510A>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#.

69 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18052650 Feb 28, 2004 (120)
2 AFFY ss76454437 Dec 07, 2007 (129)
3 HGSV ss78471365 Dec 07, 2007 (129)
4 HGSV ss85618387 Dec 14, 2007 (130)
5 KRIBB_YJKIM ss105044360 Feb 04, 2009 (130)
6 1000GENOMES ss108017333 Jan 22, 2009 (130)
7 1000GENOMES ss110106606 Jan 24, 2009 (130)
8 ILLUMINA ss159200110 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss163118687 Jul 04, 2010 (132)
10 BUSHMAN ss198073784 Jul 04, 2010 (132)
11 1000GENOMES ss218254454 Jul 14, 2010 (132)
12 1000GENOMES ss230440085 Jul 14, 2010 (132)
13 ILLUMINA ss244274960 Jul 04, 2010 (132)
14 GMI ss275728778 May 04, 2012 (137)
15 PJP ss290699601 May 09, 2011 (134)
16 ILLUMINA ss479350672 May 04, 2012 (137)
17 ILLUMINA ss482126436 May 04, 2012 (137)
18 ILLUMINA ss532916230 Sep 08, 2015 (146)
19 TISHKOFF ss553833208 Apr 25, 2013 (138)
20 SSMP ss647601157 Apr 25, 2013 (138)
21 ILLUMINA ss780636836 Sep 08, 2015 (146)
22 ILLUMINA ss780959743 Sep 08, 2015 (146)
23 ILLUMINA ss832712567 Jul 12, 2019 (153)
24 ILLUMINA ss836130957 Sep 08, 2015 (146)
25 EVA-GONL ss974891790 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1067695507 Aug 21, 2014 (142)
27 1000GENOMES ss1289821208 Aug 21, 2014 (142)
28 DDI ss1425724838 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1573908201 Apr 01, 2015 (144)
30 EVA_DECODE ss1584248982 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1599617549 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1642611582 Apr 01, 2015 (144)
33 EVA_SVP ss1712313782 Apr 01, 2015 (144)
34 HAMMER_LAB ss1793966314 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1918095201 Feb 12, 2016 (147)
36 JJLAB ss2019561268 Sep 14, 2016 (149)
37 ILLUMINA ss2094782518 Dec 20, 2016 (150)
38 USC_VALOUEV ss2147560674 Dec 20, 2016 (150)
39 ILLUMINA ss2632482247 Nov 08, 2017 (151)
40 GRF ss2697461736 Nov 08, 2017 (151)
41 GNOMAD ss2752026999 Nov 08, 2017 (151)
42 SWEGEN ss2986364944 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023544872 Nov 08, 2017 (151)
44 CSHL ss3343336189 Nov 08, 2017 (151)
45 ILLUMINA ss3626034713 Oct 11, 2018 (152)
46 ILLUMINA ss3630520354 Oct 11, 2018 (152)
47 ILLUMINA ss3641574515 Oct 11, 2018 (152)
48 EVA_DECODE ss3686235457 Jul 12, 2019 (153)
49 ACPOP ss3726822365 Jul 12, 2019 (153)
50 EVA ss3745873123 Jul 12, 2019 (153)
51 KHV_HUMAN_GENOMES ss3798894123 Jul 12, 2019 (153)
52 EVA ss3836408275 Apr 25, 2020 (154)
53 EVA ss3841812509 Apr 25, 2020 (154)
54 SGDP_PRJ ss3848282383 Apr 25, 2020 (154)
55 KRGDB ss3893177584 Apr 25, 2020 (154)
56 KOGIC ss3943906307 Apr 25, 2020 (154)
57 TOPMED ss4440373654 Apr 26, 2021 (155)
58 TOMMO_GENOMICS ss5142654381 Apr 26, 2021 (155)
59 1000G_HIGH_COVERAGE ss5241312531 Oct 13, 2022 (156)
60 EVA ss5316985138 Oct 13, 2022 (156)
61 HUGCELL_USP ss5442490979 Oct 13, 2022 (156)
62 EVA ss5505774732 Oct 13, 2022 (156)
63 1000G_HIGH_COVERAGE ss5513130698 Oct 13, 2022 (156)
64 SANFORD_IMAGENETICS ss5625001917 Oct 13, 2022 (156)
65 TOMMO_GENOMICS ss5667017482 Oct 13, 2022 (156)
66 YY_MCH ss5800359888 Oct 13, 2022 (156)
67 EVA ss5831589189 Oct 13, 2022 (156)
68 EVA ss5907182388 Oct 13, 2022 (156)
69 EVA ss5936821844 Oct 13, 2022 (156)
70 1000Genomes NC_000001.10 - 16379416 Oct 11, 2018 (152)
71 1000Genomes_30x NC_000001.11 - 16052921 Oct 13, 2022 (156)
72 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 16379416 Oct 11, 2018 (152)
73 The Danish reference pan genome NC_000001.10 - 16379416 Apr 25, 2020 (154)
74 gnomAD - Genomes NC_000001.11 - 16052921 Apr 26, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000001.10 - 16379416 Apr 25, 2020 (154)
76 HapMap NC_000001.11 - 16052921 Apr 25, 2020 (154)
77 KOREAN population from KRGDB NC_000001.10 - 16379416 Apr 25, 2020 (154)
78 Korean Genome Project NC_000001.11 - 16052921 Apr 25, 2020 (154)
79 Northern Sweden NC_000001.10 - 16379416 Jul 12, 2019 (153)
80 Qatari NC_000001.10 - 16379416 Apr 25, 2020 (154)
81 SGDP_PRJ NC_000001.10 - 16379416 Apr 25, 2020 (154)
82 Siberian NC_000001.10 - 16379416 Apr 25, 2020 (154)
83 8.3KJPN NC_000001.10 - 16379416 Apr 26, 2021 (155)
84 14KJPN NC_000001.11 - 16052921 Oct 13, 2022 (156)
85 TopMed NC_000001.11 - 16052921 Apr 26, 2021 (155)
86 UK 10K study - Twins NC_000001.10 - 16379416 Oct 11, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000001.10 - 16379416 Jul 12, 2019 (153)
88 ALFA NC_000001.11 - 16052921 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).

Associated ID History Updated (Build)
rs57492240 May 23, 2008 (130)
rs386423704 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78471365, ss85618387 NC_000001.8:16124721:A:C NC_000001.11:16052920:A:C (self)
ss76454437, ss108017333, ss110106606, ss163118687, ss198073784, ss275728778, ss290699601, ss482126436, ss1584248982, ss1712313782 NC_000001.9:16252002:A:C NC_000001.11:16052920:A:C (self)
502143, 263136, 1404062, 114309, 354978, 107230, 137131, 299363, 77028, 623688, 263136, 56116, ss218254454, ss230440085, ss479350672, ss532916230, ss553833208, ss647601157, ss780636836, ss780959743, ss832712567, ss836130957, ss974891790, ss1067695507, ss1289821208, ss1425724838, ss1573908201, ss1599617549, ss1642611582, ss1793966314, ss1918095201, ss2019561268, ss2094782518, ss2147560674, ss2632482247, ss2697461736, ss2752026999, ss2986364944, ss3343336189, ss3626034713, ss3630520354, ss3641574515, ss3726822365, ss3745873123, ss3836408275, ss3848282383, ss3893177584, ss5142654381, ss5316985138, ss5505774732, ss5625001917, ss5831589189, ss5936821844 NC_000001.10:16379415:A:C NC_000001.11:16052920:A:C (self)
656633, 3504018, 19634, 284308, 854586, 3979989, 13107801680, ss3023544872, ss3686235457, ss3798894123, ss3841812509, ss3943906307, ss4440373654, ss5241312531, ss5442490979, ss5513130698, ss5667017482, ss5800359888, ss5907182388 NC_000001.11:16052920:A:C NC_000001.11:16052920:A:C (self)
ss18052650, ss105044360, ss159200110, ss244274960 NT_004610.19:3059503:A:C NC_000001.11:16052920:A: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 rs12015135

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