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dbSNP Short Genetic Variations

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.

rs2402130

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr14:92334859 (GRCh38.p12) 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=0.29021 (36441/125568, TOPMED)
G=0.3349 (26279/78466, PAGE_STUDY)
G=0.2766 (8658/31298, GnomAD) (+ 6 more)
G=0.269 (1347/5008, 1000G)
G=0.156 (698/4480, Estonian)
G=0.203 (783/3854, ALSPAC)
G=0.206 (765/3708, TWINSUK)
G=0.15 (90/600, NorthernSweden)
G=0.06 (13/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC24A4 : Intron Variant
Publications
2 citations
Genomic View
See rs on genome
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.p12 chr 14 NC_000014.9:g.92334859G>A
GRCh37.p13 chr 14 NC_000014.8:g.92801203G>A
SLC24A4 RefSeqGene NG_023408.1:g.17279G>A
Gene: SLC24A4, solute carrier family 24 member 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC24A4 transcript variant 1 NM_153646.3:c. N/A Intron Variant
SLC24A4 transcript variant 2 NM_153647.4:c. N/A Intron Variant
SLC24A4 transcript variant 3 NM_153648.3:c. N/A Intron Variant
SLC24A4 transcript variant X1 XM_011536436.2:c. N/A Intron Variant
SLC24A4 transcript variant X2 XM_011536437.2:c. N/A Intron Variant
SLC24A4 transcript variant X3 XM_011536438.2:c. N/A Intron Variant
SLC24A4 transcript variant X4 XM_011536439.2:c. N/A Intron Variant
SLC24A4 transcript variant X5 XM_024449478.1:c. N/A Intron Variant
SLC24A4 transcript variant X7 XM_005267342.2:c. N/A Genic Upstream Transcript Variant
SLC24A4 transcript variant X6 XM_011536440.2:c. N/A Genic Upstream Transcript 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

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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 G=0.29021 A=0.70979
The PAGE Study Global Study-wide 78466 G=0.3349 A=0.6651
The PAGE Study AfricanAmerican Sub 32364 G=0.5222 A=0.4778
The PAGE Study Mexican Sub 10802 G=0.1936 A=0.8064
The PAGE Study Asian Sub 8300 G=0.075 A=0.925
The PAGE Study PuertoRican Sub 7906 G=0.306 A=0.694
The PAGE Study NativeHawaiian Sub 4512 G=0.083 A=0.917
The PAGE Study Cuban Sub 4226 G=0.279 A=0.721
The PAGE Study Dominican Sub 3812 G=0.371 A=0.629
The PAGE Study CentralAmerican Sub 2448 G=0.199 A=0.801
The PAGE Study SouthAmerican Sub 1980 G=0.173 A=0.827
The PAGE Study NativeAmerican Sub 1260 G=0.242 A=0.758
The PAGE Study SouthAsian Sub 856 G=0.17 A=0.83
gnomAD - Genomes Global Study-wide 31298 G=0.2766 A=0.7234
gnomAD - Genomes European Sub 18850 G=0.1794 A=0.8206
gnomAD - Genomes African Sub 8666 G=0.545 A=0.455
gnomAD - Genomes East Asian Sub 1556 G=0.055 A=0.945
gnomAD - Genomes Other Sub 1088 G=0.210 A=0.790
gnomAD - Genomes American Sub 848 G=0.22 A=0.78
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.17 A=0.83
1000Genomes Global Study-wide 5008 G=0.269 A=0.731
1000Genomes African Sub 1322 G=0.600 A=0.400
1000Genomes East Asian Sub 1008 G=0.061 A=0.939
1000Genomes Europe Sub 1006 G=0.213 A=0.787
1000Genomes South Asian Sub 978 G=0.14 A=0.86
1000Genomes American Sub 694 G=0.21 A=0.79
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.156 A=0.844
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.203 A=0.797
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.206 A=0.794
Northern Sweden ACPOP Study-wide 600 G=0.15 A=0.85
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.06 A=0.94
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 Note
GRCh38.p12 chr 14 NC_000014.9:g.92334859= NC_000014.9:g.92334859G>A
GRCh37.p13 chr 14 NC_000014.8:g.92801203= NC_000014.8:g.92801203G>A
SLC24A4 RefSeqGene NG_023408.1:g.17279= NG_023408.1:g.17279G>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#.

116 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3366586 Sep 28, 2001 (100)
2 CSHL-HAPMAP ss16661234 Feb 27, 2004 (120)
3 SSAHASNP ss21221148 Apr 05, 2004 (121)
4 AFFY ss66422318 Dec 02, 2006 (127)
5 ILLUMINA ss66677979 Dec 02, 2006 (127)
6 ILLUMINA ss67252031 Dec 02, 2006 (127)
7 ILLUMINA ss67649855 Dec 02, 2006 (127)
8 PERLEGEN ss69166362 May 18, 2007 (127)
9 ILLUMINA ss70730373 May 25, 2008 (130)
10 ILLUMINA ss71299773 May 18, 2007 (127)
11 ILLUMINA ss75684747 Dec 07, 2007 (129)
12 AFFY ss76188715 Dec 08, 2007 (130)
13 ILLUMINA ss79133588 Dec 15, 2007 (130)
14 HGSV ss83483882 Dec 15, 2007 (130)
15 KRIBB_YJKIM ss84045818 Dec 15, 2007 (130)
16 BCMHGSC_JDW ss90039320 Mar 24, 2008 (129)
17 HUMANGENOME_JCVI ss96879072 Feb 06, 2009 (130)
18 BGI ss106407311 Feb 06, 2009 (130)
19 1000GENOMES ss108563382 Jan 23, 2009 (130)
20 1000GENOMES ss113713649 Jan 25, 2009 (130)
21 ILLUMINA-UK ss118698207 Feb 14, 2009 (130)
22 ILLUMINA ss122026845 Dec 01, 2009 (131)
23 ENSEMBL ss134118193 Dec 01, 2009 (131)
24 ENSEMBL ss136966483 Dec 01, 2009 (131)
25 ILLUMINA ss153909865 Dec 01, 2009 (131)
26 GMI ss156132605 Dec 01, 2009 (131)
27 ILLUMINA ss159387702 Dec 01, 2009 (131)
28 ILLUMINA ss160544234 Dec 01, 2009 (131)
29 COMPLETE_GENOMICS ss168509398 Jul 04, 2010 (132)
30 COMPLETE_GENOMICS ss170342735 Jul 04, 2010 (132)
31 ILLUMINA ss171241924 Jul 04, 2010 (132)
32 COMPLETE_GENOMICS ss171505469 Jul 04, 2010 (132)
33 AFFY ss172751692 Jul 04, 2010 (132)
34 ILLUMINA ss173328031 Jul 04, 2010 (132)
35 BUSHMAN ss200419333 Jul 04, 2010 (132)
36 BCM-HGSC-SUB ss206867776 Jul 04, 2010 (132)
37 1000GENOMES ss226721378 Jul 14, 2010 (132)
38 1000GENOMES ss236654109 Jul 15, 2010 (132)
39 1000GENOMES ss243065738 Jul 15, 2010 (132)
40 BL ss255201235 May 09, 2011 (134)
41 GMI ss282113090 May 04, 2012 (137)
42 GMI ss286892457 Apr 25, 2013 (138)
43 PJP ss291653387 May 09, 2011 (134)
44 ILLUMINA ss480558622 May 04, 2012 (137)
45 ILLUMINA ss480572873 May 04, 2012 (137)
46 ILLUMINA ss481391251 Sep 08, 2015 (146)
47 ILLUMINA ss485074917 May 04, 2012 (137)
48 ILLUMINA ss537086932 Sep 08, 2015 (146)
49 TISHKOFF ss564272257 Apr 25, 2013 (138)
50 SSMP ss659967959 Apr 25, 2013 (138)
51 ILLUMINA ss778868098 Sep 08, 2015 (146)
52 ILLUMINA ss782983742 Sep 08, 2015 (146)
53 ILLUMINA ss783944707 Sep 08, 2015 (146)
54 ILLUMINA ss825464106 Apr 01, 2015 (144)
55 ILLUMINA ss832240353 Sep 08, 2015 (146)
56 ILLUMINA ss832899461 Jul 13, 2019 (153)
57 ILLUMINA ss834328966 Sep 08, 2015 (146)
58 EVA-GONL ss991449025 Aug 21, 2014 (142)
59 JMKIDD_LAB ss1079883112 Aug 21, 2014 (142)
60 1000GENOMES ss1352147172 Aug 21, 2014 (142)
61 HAMMER_LAB ss1397688751 Sep 08, 2015 (146)
62 DDI ss1427510694 Apr 01, 2015 (144)
63 EVA_GENOME_DK ss1577431579 Apr 01, 2015 (144)
64 EVA_UK10K_ALSPAC ss1632351389 Apr 01, 2015 (144)
65 EVA_UK10K_TWINSUK ss1675345422 Apr 01, 2015 (144)
66 EVA_DECODE ss1695462925 Apr 01, 2015 (144)
67 EVA_MGP ss1711381155 Apr 01, 2015 (144)
68 EVA_SVP ss1713466489 Apr 01, 2015 (144)
69 ILLUMINA ss1752147912 Sep 08, 2015 (146)
70 HAMMER_LAB ss1808046502 Sep 08, 2015 (146)
71 WEILL_CORNELL_DGM ss1934818938 Feb 12, 2016 (147)
72 ILLUMINA ss1959577168 Feb 12, 2016 (147)
73 GENOMED ss1968030164 Jul 19, 2016 (147)
74 JJLAB ss2028193519 Sep 14, 2016 (149)
75 ILLUMINA ss2095055883 Dec 20, 2016 (150)
76 USC_VALOUEV ss2156576518 Dec 20, 2016 (150)
77 HUMAN_LONGEVITY ss2204353825 Dec 20, 2016 (150)
78 TOPMED ss2368757982 Dec 20, 2016 (150)
79 SYSTEMSBIOZJU ss2628586076 Nov 08, 2017 (151)
80 ILLUMINA ss2633188208 Nov 08, 2017 (151)
81 GRF ss2701012290 Nov 08, 2017 (151)
82 GNOMAD ss2930936133 Nov 08, 2017 (151)
83 SWEGEN ss3012668230 Nov 08, 2017 (151)
84 ILLUMINA ss3021594700 Nov 08, 2017 (151)
85 BIOINF_KMB_FNS_UNIBA ss3027923848 Nov 08, 2017 (151)
86 TOPMED ss3218619671 Nov 08, 2017 (151)
87 CSHL ss3350940223 Nov 08, 2017 (151)
88 ILLUMINA ss3627286328 Oct 12, 2018 (152)
89 ILLUMINA ss3631184170 Oct 12, 2018 (152)
90 ILLUMINA ss3633086272 Oct 12, 2018 (152)
91 ILLUMINA ss3633790153 Oct 12, 2018 (152)
92 ILLUMINA ss3634590359 Oct 12, 2018 (152)
93 ILLUMINA ss3635479401 Oct 12, 2018 (152)
94 ILLUMINA ss3636279899 Oct 12, 2018 (152)
95 ILLUMINA ss3637230592 Oct 12, 2018 (152)
96 ILLUMINA ss3638066881 Oct 12, 2018 (152)
97 ILLUMINA ss3639047115 Oct 12, 2018 (152)
98 ILLUMINA ss3639528525 Oct 12, 2018 (152)
99 ILLUMINA ss3640297686 Oct 12, 2018 (152)
100 ILLUMINA ss3641054687 Oct 12, 2018 (152)
101 ILLUMINA ss3641349773 Oct 12, 2018 (152)
102 ILLUMINA ss3643052435 Oct 12, 2018 (152)
103 URBANLAB ss3650264897 Oct 12, 2018 (152)
104 ILLUMINA ss3651992513 Oct 12, 2018 (152)
105 EGCUT_WGS ss3679933051 Jul 13, 2019 (153)
106 EVA_DECODE ss3697248601 Jul 13, 2019 (153)
107 ILLUMINA ss3725471407 Jul 13, 2019 (153)
108 ACPOP ss3740637154 Jul 13, 2019 (153)
109 ILLUMINA ss3744890960 Jul 13, 2019 (153)
110 EVA ss3752677422 Jul 13, 2019 (153)
111 PAGE_CC ss3771807942 Jul 13, 2019 (153)
112 ILLUMINA ss3772389714 Jul 13, 2019 (153)
113 PACBIO ss3787746810 Jul 13, 2019 (153)
114 PACBIO ss3792772551 Jul 13, 2019 (153)
115 PACBIO ss3797657077 Jul 13, 2019 (153)
116 KHV_HUMAN_GENOMES ss3818004592 Jul 13, 2019 (153)
117 1000Genomes NC_000014.8 - 92801203 Oct 12, 2018 (152)
118 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 92801203 Oct 12, 2018 (152)
119 Genetic variation in the Estonian population NC_000014.8 - 92801203 Oct 12, 2018 (152)
120 gnomAD - Genomes NC_000014.8 - 92801203 Jul 13, 2019 (153)
121 Northern Sweden NC_000014.8 - 92801203 Jul 13, 2019 (153)
122 The PAGE Study NC_000014.9 - 92334859 Jul 13, 2019 (153)
123 TopMed NC_000014.9 - 92334859 Oct 12, 2018 (152)
124 UK 10K study - Twins NC_000014.8 - 92801203 Oct 12, 2018 (152)
125 A Vietnamese Genetic Variation Database NC_000014.8 - 92801203 Jul 13, 2019 (153)
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)
rs56585488 May 25, 2008 (130)
rs60171479 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss83483882, ss90039320, ss108563382, ss113713649, ss118698207, ss168509398, ss170342735, ss171505469, ss200419333, ss206867776, ss255201235, ss282113090, ss286892457, ss291653387, ss480558622, ss825464106, ss1397688751, ss1695462925, ss1713466489, ss3639047115, ss3639528525, ss3643052435 NC_000014.7:91870955:G:A NC_000014.9:92334858:G:A (self)
65171489, 36223069, 25671299, 177892586, 13922019, 36223069, 8058200, ss226721378, ss236654109, ss243065738, ss480572873, ss481391251, ss485074917, ss537086932, ss564272257, ss659967959, ss778868098, ss782983742, ss783944707, ss832240353, ss832899461, ss834328966, ss991449025, ss1079883112, ss1352147172, ss1427510694, ss1577431579, ss1632351389, ss1675345422, ss1711381155, ss1752147912, ss1808046502, ss1934818938, ss1959577168, ss1968030164, ss2028193519, ss2095055883, ss2156576518, ss2368757982, ss2628586076, ss2633188208, ss2701012290, ss2930936133, ss3012668230, ss3021594700, ss3350940223, ss3627286328, ss3631184170, ss3633086272, ss3633790153, ss3634590359, ss3635479401, ss3636279899, ss3637230592, ss3638066881, ss3640297686, ss3641054687, ss3641349773, ss3651992513, ss3679933051, ss3740637154, ss3744890960, ss3752677422, ss3772389714, ss3787746810, ss3792772551, ss3797657077 NC_000014.8:92801202:G:A NC_000014.9:92334858:G:A (self)
1029411, 122693207, ss2204353825, ss3027923848, ss3218619671, ss3650264897, ss3697248601, ss3725471407, ss3771807942, ss3818004592 NC_000014.9:92334858:G:A NC_000014.9:92334858:G:A (self)
ss16661234, ss21221148 NT_026437.10:72721243:G:A NC_000014.9:92334858:G:A (self)
ss3366586, ss66422318, ss66677979, ss67252031, ss67649855, ss69166362, ss70730373, ss71299773, ss75684747, ss76188715, ss79133588, ss84045818, ss96879072, ss106407311, ss122026845, ss134118193, ss136966483, ss153909865, ss156132605, ss159387702, ss160544234, ss171241924, ss172751692, ss173328031 NT_026437.12:73801202:G:A NC_000014.9:92334858: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.

2 citations for rs2402130
PMID Title Author Year Journal
21197618 Model-based prediction of human hair color using DNA variants. Branicki W et al. 2011 Human genetics
26547235 Crowdsourced direct-to-consumer genomic analysis of a family quartet. Corpas M et al. 2015 BMC genomics

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.post104+4a6ee9c