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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.

rs183671

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr5:33964105 (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
T>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.34160 (42894/125568, TOPMED)
T=0.2764 (8669/31360, GnomAD)
G=0.378 (1895/5008, 1000G) (+ 5 more)
T=0.013 (58/4480, Estonian)
T=0.031 (119/3854, ALSPAC)
T=0.024 (90/3708, TWINSUK)
T=0.03 (15/600, NorthernSweden)
G=0.08 (17/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC45A2 : Intron Variant
Publications
4 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 5 NC_000005.10:g.33964105T>A
GRCh38.p12 chr 5 NC_000005.10:g.33964105T>G
GRCh37.p13 chr 5 NC_000005.9:g.33964210T>A
GRCh37.p13 chr 5 NC_000005.9:g.33964210T>G
SLC45A2 RefSeqGene NG_011691.2:g.25571A>T
SLC45A2 RefSeqGene NG_011691.2:g.25571A>C
Gene: SLC45A2, solute carrier family 45 member 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC45A2 transcript variant 2 NM_001012509.4:c. N/A Intron Variant
SLC45A2 transcript variant 3 NM_001297417.3:c. N/A Intron Variant
SLC45A2 transcript variant 1 NM_016180.5: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

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 T=0.34160 G=0.65840
gnomAD - Genomes Global Study-wide 31360 T=0.2764 G=0.7236
gnomAD - Genomes European Sub 18896 T=0.0264 G=0.9736
gnomAD - Genomes African Sub 8688 T=0.704 G=0.296
gnomAD - Genomes East Asian Sub 1552 T=0.903 G=0.097
gnomAD - Genomes Other Sub 1086 T=0.160 G=0.840
gnomAD - Genomes American Sub 848 T=0.53 G=0.47
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.09 G=0.91
1000Genomes Global Study-wide 5008 T=0.622 G=0.378
1000Genomes African Sub 1322 T=0.790 G=0.210
1000Genomes East Asian Sub 1008 T=0.909 G=0.091
1000Genomes Europe Sub 1006 T=0.047 G=0.953
1000Genomes South Asian Sub 978 T=0.77 G=0.23
1000Genomes American Sub 694 T=0.51 G=0.49
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.013 G=0.987
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.031 G=0.969
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.024 G=0.976
Northern Sweden ACPOP Study-wide 600 T=0.03 G=0.97
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.92 G=0.08
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 Note
GRCh38.p12 chr 5 NC_000005.10:g.33...

NC_000005.10:g.33964105=

NC_000005.10:g.33...

NC_000005.10:g.33964105T>A

NC_000005.10:g.33...

NC_000005.10:g.33964105T>G

GRCh37.p13 chr 5 NC_000005.9:g.339...

NC_000005.9:g.33964210=

NC_000005.9:g.339...

NC_000005.9:g.33964210T>A

NC_000005.9:g.339...

NC_000005.9:g.33964210T>G

SLC45A2 RefSeqGene NG_011691.2:g.25571= NG_011691.2:g.255...

NG_011691.2:g.25571A>T

NG_011691.2:g.255...

NG_011691.2:g.25571A>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#.

91 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss243648 Jul 12, 2000 (79)
2 KWOK ss245537 Jul 12, 2000 (85)
3 KWOK ss1280821 Oct 04, 2000 (86)
4 KWOK ss1282854 Oct 04, 2000 (86)
5 KWOK ss1657071 Oct 18, 2000 (87)
6 KWOK ss1657944 Oct 18, 2000 (87)
7 SC_JCM ss3576396 Sep 28, 2001 (100)
8 WI_SSAHASNP ss11718750 Jul 11, 2003 (116)
9 CSHL-HAPMAP ss17852229 Feb 27, 2004 (120)
10 SSAHASNP ss22248758 Apr 05, 2004 (121)
11 PERLEGEN ss23457085 Sep 20, 2004 (123)
12 ABI ss44677949 Mar 14, 2006 (126)
13 HGSV ss77528309 Dec 07, 2007 (129)
14 BCMHGSC_JDW ss93054704 Mar 24, 2008 (129)
15 HUMANGENOME_JCVI ss98610248 Feb 06, 2009 (130)
16 BGI ss104184547 Dec 01, 2009 (131)
17 1000GENOMES ss108947833 Jan 23, 2009 (130)
18 1000GENOMES ss111672338 Jan 25, 2009 (130)
19 ENSEMBL ss143019624 Dec 01, 2009 (131)
20 ENSEMBL ss143237086 Dec 01, 2009 (131)
21 ILLUMINA ss160465676 Dec 01, 2009 (131)
22 COMPLETE_GENOMICS ss162160858 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss164667303 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss166398283 Jul 04, 2010 (132)
25 BUSHMAN ss200096259 Jul 04, 2010 (132)
26 BCM-HGSC-SUB ss206945707 Jul 04, 2010 (132)
27 1000GENOMES ss221616082 Jul 14, 2010 (132)
28 1000GENOMES ss232898728 Jul 14, 2010 (132)
29 1000GENOMES ss240082380 Jul 15, 2010 (132)
30 BL ss253359542 May 09, 2011 (134)
31 GMI ss278239247 May 04, 2012 (137)
32 GMI ss285153640 Apr 25, 2013 (138)
33 PJP ss293564877 May 09, 2011 (134)
34 ILLUMINA ss480309071 May 04, 2012 (137)
35 ILLUMINA ss480320119 May 04, 2012 (137)
36 ILLUMINA ss481078453 Sep 08, 2015 (146)
37 ILLUMINA ss484952260 May 04, 2012 (137)
38 ILLUMINA ss536995416 Sep 08, 2015 (146)
39 TISHKOFF ss558314462 Apr 25, 2013 (138)
40 SSMP ss652168516 Apr 25, 2013 (138)
41 ILLUMINA ss778842384 Sep 08, 2015 (146)
42 ILLUMINA ss782922436 Sep 08, 2015 (146)
43 ILLUMINA ss783885398 Sep 08, 2015 (146)
44 ILLUMINA ss832177601 Sep 08, 2015 (146)
45 ILLUMINA ss834302950 Sep 08, 2015 (146)
46 EVA-GONL ss981430642 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1072530308 Aug 21, 2014 (142)
48 1000GENOMES ss1314583396 Aug 21, 2014 (142)
49 HAMMER_LAB ss1397409776 Sep 08, 2015 (146)
50 DDI ss1430303054 Apr 01, 2015 (144)
51 EVA_GENOME_DK ss1581086790 Apr 01, 2015 (144)
52 EVA_DECODE ss1590953197 Apr 01, 2015 (144)
53 EVA_UK10K_ALSPAC ss1612627194 Apr 01, 2015 (144)
54 EVA_UK10K_TWINSUK ss1655621227 Apr 01, 2015 (144)
55 EVA_MGP ss1711083770 Apr 01, 2015 (144)
56 ILLUMINA ss1752572702 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1924692433 Feb 12, 2016 (147)
58 GENOMED ss1970059632 Jul 19, 2016 (147)
59 JJLAB ss2022948896 Sep 14, 2016 (149)
60 USC_VALOUEV ss2151099580 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2272761442 Dec 20, 2016 (150)
62 TOPMED ss2440793285 Dec 20, 2016 (150)
63 ILLUMINA ss2634265924 Nov 08, 2017 (151)
64 GRF ss2706634645 Nov 08, 2017 (151)
65 GNOMAD ss2823087920 Nov 08, 2017 (151)
66 SWEGEN ss2996714533 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3025259944 Nov 08, 2017 (151)
68 CSHL ss3346328205 Nov 08, 2017 (151)
69 TOPMED ss3460632673 Nov 08, 2017 (151)
70 TOPMED ss3460632674 Nov 08, 2017 (151)
71 ILLUMINA ss3629211393 Oct 12, 2018 (152)
72 ILLUMINA ss3632193750 Oct 12, 2018 (152)
73 ILLUMINA ss3633370620 Oct 12, 2018 (152)
74 ILLUMINA ss3634091062 Oct 12, 2018 (152)
75 ILLUMINA ss3634997055 Oct 12, 2018 (152)
76 ILLUMINA ss3635773188 Oct 12, 2018 (152)
77 ILLUMINA ss3636707678 Oct 12, 2018 (152)
78 ILLUMINA ss3637525778 Oct 12, 2018 (152)
79 ILLUMINA ss3640704348 Oct 12, 2018 (152)
80 OMUKHERJEE_ADBS ss3646317973 Oct 12, 2018 (152)
81 URBANLAB ss3648028585 Oct 12, 2018 (152)
82 EGCUT_WGS ss3664611021 Jul 13, 2019 (153)
83 EVA_DECODE ss3714441206 Jul 13, 2019 (153)
84 ACPOP ss3732244997 Jul 13, 2019 (153)
85 ILLUMINA ss3745297196 Jul 13, 2019 (153)
86 EVA ss3763276504 Jul 13, 2019 (153)
87 ILLUMINA ss3772791510 Jul 13, 2019 (153)
88 PACBIO ss3785077421 Jul 13, 2019 (153)
89 PACBIO ss3790489151 Jul 13, 2019 (153)
90 PACBIO ss3795365577 Jul 13, 2019 (153)
91 KHV_HUMAN_GENOMES ss3806451748 Jul 13, 2019 (153)
92 1000Genomes NC_000005.9 - 33964210 Oct 12, 2018 (152)
93 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 33964210 Oct 12, 2018 (152)
94 Genetic variation in the Estonian population NC_000005.9 - 33964210 Oct 12, 2018 (152)
95 gnomAD - Genomes NC_000005.9 - 33964210 Jul 13, 2019 (153)
96 Northern Sweden NC_000005.9 - 33964210 Jul 13, 2019 (153)
97 TopMed NC_000005.10 - 33964105 Oct 12, 2018 (152)
98 UK 10K study - Twins NC_000005.9 - 33964210 Oct 12, 2018 (152)
99 A Vietnamese Genetic Variation Database NC_000005.9 - 33964210 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)
rs185229 Sep 19, 2000 (85)
rs16892031 Oct 08, 2004 (123)
rs386546303 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3460632673 NC_000005.10:33964104:T:A NC_000005.10:33964104:T:A (self)
ss77528309, ss93054704, ss108947833, ss111672338, ss162160858, ss164667303, ss166398283, ss200096259, ss206945707, ss253359542, ss278239247, ss285153640, ss293564877, ss480309071, ss1397409776, ss1590953197 NC_000005.8:33999966:T:G NC_000005.10:33964104:T:G (self)
26165582, 14554646, 10349269, 71440353, 5529862, 14554646, 3235187, ss221616082, ss232898728, ss240082380, ss480320119, ss481078453, ss484952260, ss536995416, ss558314462, ss652168516, ss778842384, ss782922436, ss783885398, ss832177601, ss834302950, ss981430642, ss1072530308, ss1314583396, ss1430303054, ss1581086790, ss1612627194, ss1655621227, ss1711083770, ss1752572702, ss1924692433, ss1970059632, ss2022948896, ss2151099580, ss2440793285, ss2634265924, ss2706634645, ss2823087920, ss2996714533, ss3346328205, ss3629211393, ss3632193750, ss3633370620, ss3634091062, ss3634997055, ss3635773188, ss3636707678, ss3637525778, ss3640704348, ss3646317973, ss3664611021, ss3732244997, ss3745297196, ss3763276504, ss3772791510, ss3785077421, ss3790489151, ss3795365577 NC_000005.9:33964209:T:G NC_000005.10:33964104:T:G (self)
308122525, ss2272761442, ss3025259944, ss3460632674, ss3648028585, ss3714441206, ss3806451748 NC_000005.10:33964104:T:G NC_000005.10:33964104:T:G (self)
ss11718750 NT_006576.13:16390402:T:G NC_000005.10:33964104:T:G (self)
ss17852229, ss22248758 NT_006576.14:16416315:T:G NC_000005.10:33964104:T:G (self)
ss243648, ss245537, ss1280821, ss1282854, ss1657071, ss1657944, ss3576396, ss23457085, ss44677949, ss98610248, ss104184547, ss143019624, ss143237086, ss160465676 NT_006576.16:33954209:T:G NC_000005.10:33964104: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.

4 citations for rs183671
PMID Title Author Year Journal
17999355 A genomewide association study of skin pigmentation in a South Asian population. Stokowski RP et al. 2007 American journal of human genetics
23118974 Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four European populations. Candille SI et al. 2012 PloS one
26921301 Latitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes. Tiosano D et al. 2016 G3 (Bethesda, Md.)
26926045 A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features. Adhikari K et al. 2016 Nature communications

Genomic regions, transcripts, and products
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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