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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.

rs3212345

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:89915864 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.39151 (49161/125568, TOPMED)
T=0.4067 (12747/31346, GnomAD)
T=0.254 (1270/5008, 1000G) (+ 5 more)
C=0.459 (2058/4480, Estonian)
C=0.413 (1593/3854, ALSPAC)
C=0.430 (1596/3708, TWINSUK)
T=0.49 (292/600, NorthernSweden)
T=0.05 (10/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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 16 NC_000016.10:g.89915864T>C
GRCh37.p13 chr 16 NC_000016.9:g.89982272T>C
MC1R RefSeqGene NG_012026.1:g.2986T>C
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=0.39151 C=0.60849
gnomAD - Genomes Global Study-wide 31346 T=0.4067 C=0.5933
gnomAD - Genomes European Sub 18858 T=0.5553 C=0.4447
gnomAD - Genomes African Sub 8704 T=0.133 C=0.867
gnomAD - Genomes East Asian Sub 1558 T=0.082 C=0.918
gnomAD - Genomes Other Sub 1088 T=0.475 C=0.525
gnomAD - Genomes American Sub 848 T=0.37 C=0.63
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.57 C=0.43
1000Genomes Global Study-wide 5008 T=0.254 C=0.746
1000Genomes African Sub 1322 T=0.058 C=0.942
1000Genomes East Asian Sub 1008 T=0.078 C=0.922
1000Genomes Europe Sub 1006 T=0.576 C=0.424
1000Genomes South Asian Sub 978 T=0.29 C=0.71
1000Genomes American Sub 694 T=0.36 C=0.64
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.541 C=0.459
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.587 C=0.413
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.570 C=0.430
Northern Sweden ACPOP Study-wide 600 T=0.49 C=0.51
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.05 C=0.95
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= C Note
GRCh38.p12 chr 16 NC_000016.10:g.89915864= NC_000016.10:g.89915864T>C
GRCh37.p13 chr 16 NC_000016.9:g.89982272= NC_000016.9:g.89982272T>C
MC1R RefSeqGene NG_012026.1:g.2986= NG_012026.1:g.2986T>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, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 PGA-UW-FHCRC ss4472717 Jul 03, 2002 (106)
2 BCM_SSAHASNP ss10843047 Jul 11, 2003 (116)
3 CSHL-HAPMAP ss17552427 Feb 27, 2004 (120)
4 SSAHASNP ss21304330 Apr 05, 2004 (121)
5 ABI ss43959145 Mar 15, 2006 (126)
6 ILLUMINA ss65738608 Oct 14, 2006 (127)
7 ILLUMINA ss74892502 Dec 06, 2007 (129)
8 HGSV ss78759218 Dec 06, 2007 (129)
9 HGSV ss82023699 Dec 14, 2007 (130)
10 HGSV ss82409258 Dec 14, 2007 (130)
11 HGSV ss84718977 Dec 14, 2007 (130)
12 BGI ss106492473 Feb 04, 2009 (130)
13 1000GENOMES ss109578113 Jan 24, 2009 (130)
14 1000GENOMES ss113171484 Jan 25, 2009 (130)
15 KRIBB_YJKIM ss119456398 Dec 01, 2009 (131)
16 GMI ss157737049 Dec 01, 2009 (131)
17 ENSEMBL ss161821083 Dec 01, 2009 (131)
18 ILLUMINA ss173574951 Jul 04, 2010 (132)
19 BUSHMAN ss202102055 Jul 04, 2010 (132)
20 1000GENOMES ss227419547 Jul 14, 2010 (132)
21 1000GENOMES ss237150915 Jul 15, 2010 (132)
22 1000GENOMES ss243467190 Jul 15, 2010 (132)
23 GMI ss282656935 May 04, 2012 (137)
24 GMI ss287131160 Apr 25, 2013 (138)
25 PJP ss291905436 May 09, 2011 (134)
26 ILLUMINA ss537168141 Sep 08, 2015 (146)
27 TISHKOFF ss565112634 Apr 25, 2013 (138)
28 SSMP ss660891996 Apr 25, 2013 (138)
29 ILLUMINA ss778703442 Sep 08, 2015 (146)
30 ILLUMINA ss834162466 Sep 08, 2015 (146)
31 EVA-GONL ss992830682 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1080869811 Aug 21, 2014 (142)
33 1000GENOMES ss1357561293 Aug 21, 2014 (142)
34 DDI ss1427948748 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1578051474 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1635117151 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1678111184 Apr 01, 2015 (144)
38 EVA_DECODE ss1696872248 Apr 01, 2015 (144)
39 EVA_SVP ss1713563802 Apr 01, 2015 (144)
40 HAMMER_LAB ss1808662904 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1936272919 Feb 12, 2016 (147)
42 GENOMED ss1968333618 Jul 19, 2016 (147)
43 AMU ss1971464512 Jul 19, 2016 (147)
44 JJLAB ss2028926273 Sep 14, 2016 (149)
45 USC_VALOUEV ss2157367851 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2214823824 Dec 20, 2016 (150)
47 TOPMED ss2379649902 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2628953362 Nov 08, 2017 (151)
49 GRF ss2701904618 Nov 08, 2017 (151)
50 GNOMAD ss2946701709 Nov 08, 2017 (151)
51 AFFY ss2985080439 Nov 08, 2017 (151)
52 AFFY ss2985718374 Nov 08, 2017 (151)
53 SWEGEN ss3015041287 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3028280811 Nov 08, 2017 (151)
55 TOPMED ss3255025398 Nov 08, 2017 (151)
56 CSHL ss3351606467 Nov 08, 2017 (151)
57 ILLUMINA ss3627602912 Oct 12, 2018 (152)
58 ILLUMINA ss3631346715 Oct 12, 2018 (152)
59 ILLUMINA ss3638143969 Oct 12, 2018 (152)
60 ILLUMINA ss3643123666 Oct 12, 2018 (152)
61 ILLUMINA ss3653852535 Oct 12, 2018 (152)
62 EGCUT_WGS ss3682019117 Jul 13, 2019 (153)
63 EVA_DECODE ss3699905636 Jul 13, 2019 (153)
64 ACPOP ss3741791895 Jul 13, 2019 (153)
65 EVA ss3754343066 Jul 13, 2019 (153)
66 PACBIO ss3788124120 Jul 13, 2019 (153)
67 PACBIO ss3793095014 Jul 13, 2019 (153)
68 PACBIO ss3797980416 Jul 13, 2019 (153)
69 KHV_HUMAN_GENOMES ss3819613358 Jul 13, 2019 (153)
70 1000Genomes NC_000016.9 - 89982272 Oct 12, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 89982272 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000016.9 - 89982272 Oct 12, 2018 (152)
73 gnomAD - Genomes NC_000016.9 - 89982272 Jul 13, 2019 (153)
74 Northern Sweden NC_000016.9 - 89982272 Jul 13, 2019 (153)
75 TopMed NC_000016.10 - 89915864 Oct 12, 2018 (152)
76 UK 10K study - Twins NC_000016.9 - 89982272 Oct 12, 2018 (152)
77 A Vietnamese Genetic Variation Database NC_000016.9 - 89982272 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)
rs57502984 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78759218, ss82023699, ss82409258, ss84718977, ss109578113, ss113171484, ss202102055, ss282656935, ss287131160, ss291905436, ss1696872248, ss1713563802, ss3643123666 NC_000016.8:88509772:T:C NC_000016.10:89915863:T:C (self)
70762652, 39253413, 27757365, 193093314, 15076760, 39253413, 8697199, ss227419547, ss237150915, ss243467190, ss537168141, ss565112634, ss660891996, ss778703442, ss834162466, ss992830682, ss1080869811, ss1357561293, ss1427948748, ss1578051474, ss1635117151, ss1678111184, ss1808662904, ss1936272919, ss1968333618, ss1971464512, ss2028926273, ss2157367851, ss2379649902, ss2628953362, ss2701904618, ss2946701709, ss2985080439, ss2985718374, ss3015041287, ss3351606467, ss3627602912, ss3631346715, ss3638143969, ss3653852535, ss3682019117, ss3741791895, ss3754343066, ss3788124120, ss3793095014, ss3797980416 NC_000016.9:89982271:T:C NC_000016.10:89915863:T:C (self)
151102987, ss2214823824, ss3028280811, ss3255025398, ss3699905636, ss3819613358 NC_000016.10:89915863:T:C NC_000016.10:89915863:T:C (self)
ss10843047 NT_010542.13:1538024:T:C NC_000016.10:89915863:T:C (self)
ss17552427, ss21304330 NT_010542.14:1538179:T:C NC_000016.10:89915863:T:C (self)
ss4472717, ss43959145, ss65738608, ss74892502, ss106492473, ss119456398, ss157737049, ss161821083, ss173574951 NT_010542.15:1542888:T:C NC_000016.10:89915863:T:C (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 rs3212345
PMID Title Author Year Journal
22961816 Polymorphisms upstream of the melanocortin-1 receptor coding region are associated with human pigmentation variation in a Brazilian population. Neitzke-Montinelli V et al. 2012 American journal of human biology

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