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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.

rs1037208

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:27986211 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.27934 (35076/125568, TOPMED)
G=0.2578 (8084/31360, GnomAD)
G=0.310 (1553/5008, 1000G) (+ 5 more)
G=0.148 (663/4480, Estonian)
G=0.181 (698/3854, ALSPAC)
G=0.179 (663/3708, TWINSUK)
G=0.11 (67/600, NorthernSweden)
G=0.00 (1/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OCA2 : 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 15 NC_000015.10:g.27986211G>T
GRCh37.p13 chr 15 NC_000015.9:g.28231357G>T
OCA2 RefSeqGene NG_009846.1:g.118102C>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.120478T>G
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.120478T>G
Gene: OCA2, OCA2 melanosomal transmembrane protein (minus strand)
Molecule type Change Amino acid[Codon] SO Term
OCA2 transcript variant 1 NM_000275.3:c. N/A Intron Variant
OCA2 transcript variant 2 NM_001300984.2:c. N/A Intron Variant
OCA2 transcript variant X2 XM_011521640.2:c. N/A Intron Variant
OCA2 transcript variant X1 XM_017022255.1:c. N/A Intron Variant
OCA2 transcript variant X3 XM_017022256.1:c. N/A Intron Variant
OCA2 transcript variant X4 XM_017022257.1:c. N/A Intron Variant
OCA2 transcript variant X5 XM_017022258.1:c. N/A Intron Variant
OCA2 transcript variant X6 XM_017022259.1:c. N/A Intron Variant
OCA2 transcript variant X7 XM_017022260.1:c. N/A Intron Variant
OCA2 transcript variant X8 XM_017022261.1:c. N/A Intron Variant
OCA2 transcript variant X9 XM_017022262.1:c. N/A Intron Variant
OCA2 transcript variant X10 XM_017022263.1:c. N/A Intron Variant
OCA2 transcript variant X11 XM_017022264.1:c. N/A Intron Variant
OCA2 transcript variant X12 XM_017022265.1:c. N/A Intron Variant
OCA2 transcript variant X13 XR_001751294.1: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

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=0.27934 T=0.72066
gnomAD - Genomes Global Study-wide 31360 G=0.2578 T=0.7422
gnomAD - Genomes European Sub 18892 G=0.1591 T=0.8409
gnomAD - Genomes African Sub 8684 G=0.531 T=0.469
gnomAD - Genomes East Asian Sub 1560 G=0.001 T=0.999
gnomAD - Genomes Other Sub 1086 G=0.183 T=0.817
gnomAD - Genomes American Sub 848 G=0.26 T=0.74
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.15 T=0.85
1000Genomes Global Study-wide 5008 G=0.310 T=0.690
1000Genomes African Sub 1322 G=0.590 T=0.410
1000Genomes East Asian Sub 1008 G=0.001 T=0.999
1000Genomes Europe Sub 1006 G=0.183 T=0.817
1000Genomes South Asian Sub 978 G=0.41 T=0.59
1000Genomes American Sub 694 G=0.27 T=0.73
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.148 T=0.852
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.181 T=0.819
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.179 T=0.821
Northern Sweden ACPOP Study-wide 600 G=0.11 T=0.89
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.00 T=1.00
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= T Note
GRCh38.p12 chr 15 NC_000015.10:g.27986211= NC_000015.10:g.27986211G>T
GRCh37.p13 chr 15 NC_000015.9:g.28231357= NC_000015.9:g.28231357G>T
OCA2 RefSeqGene NG_009846.1:g.118102= NG_009846.1:g.118102C>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.120478T>G NW_011332701.1:g.120478=
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.120478T>G NT_187660.1:g.120478=
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, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1503344 Oct 05, 2000 (86)
2 WI_SSAHASNP ss6592599 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss10772748 Jul 11, 2003 (116)
4 CSHL-HAPMAP ss19324698 Feb 27, 2004 (120)
5 SSAHASNP ss21247098 Apr 05, 2004 (121)
6 PERLEGEN ss23752670 Sep 20, 2004 (123)
7 ABI ss43694179 Mar 15, 2006 (126)
8 ILLUMINA ss65762732 Oct 16, 2006 (127)
9 AFFY ss66501051 Dec 02, 2006 (127)
10 ILLUMINA ss74877976 Dec 06, 2007 (129)
11 AFFY ss76323973 Dec 06, 2007 (129)
12 HGSV ss77644047 Dec 06, 2007 (129)
13 HGSV ss78506449 Dec 06, 2007 (129)
14 KRIBB_YJKIM ss81452377 Dec 14, 2007 (130)
15 HGSV ss83616331 Dec 16, 2007 (130)
16 BCMHGSC_JDW ss90103788 Mar 24, 2008 (129)
17 BGI ss106418866 Feb 06, 2009 (130)
18 1000GENOMES ss108695789 Jan 23, 2009 (130)
19 ILLUMINA-UK ss118171754 Feb 14, 2009 (130)
20 ENSEMBL ss132383589 Dec 01, 2009 (131)
21 ENSEMBL ss134210122 Dec 01, 2009 (131)
22 GMI ss156359690 Dec 01, 2009 (131)
23 ILLUMINA ss159888548 Dec 01, 2009 (131)
24 COMPLETE_GENOMICS ss167715547 Jul 04, 2010 (132)
25 ILLUMINA ss170012211 Jul 04, 2010 (132)
26 AFFY ss173262037 Jul 04, 2010 (132)
27 BUSHMAN ss200653392 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss207304762 Jul 04, 2010 (132)
29 1000GENOMES ss211585517 Jul 14, 2010 (132)
30 1000GENOMES ss226812843 Jul 14, 2010 (132)
31 1000GENOMES ss236722447 Jul 15, 2010 (132)
32 BL ss254861760 May 09, 2011 (134)
33 GMI ss282192732 May 04, 2012 (137)
34 GMI ss286924576 Apr 25, 2013 (138)
35 PJP ss291808214 May 09, 2011 (134)
36 ILLUMINA ss479620070 Sep 08, 2015 (146)
37 TISHKOFF ss564383234 Apr 25, 2013 (138)
38 SSMP ss660095307 Apr 25, 2013 (138)
39 EVA-GONL ss991623841 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1080002897 Aug 21, 2014 (142)
41 1000GENOMES ss1352819065 Aug 21, 2014 (142)
42 HAMMER_LAB ss1397692492 Sep 08, 2015 (146)
43 DDI ss1427575751 Apr 01, 2015 (144)
44 EVA_GENOME_DK ss1577522708 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1632670092 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1675664125 Apr 01, 2015 (144)
47 EVA_DECODE ss1695635404 Apr 01, 2015 (144)
48 EVA_SVP ss1713477600 Apr 01, 2015 (144)
49 HAMMER_LAB ss1808131073 Sep 08, 2015 (146)
50 WEILL_CORNELL_DGM ss1935020889 Feb 12, 2016 (147)
51 GENOMED ss1968070654 Jul 19, 2016 (147)
52 JJLAB ss2028290775 Sep 14, 2016 (149)
53 USC_VALOUEV ss2156687760 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2205523984 Dec 20, 2016 (150)
55 TOPMED ss2370059280 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2628638524 Nov 08, 2017 (151)
57 GRF ss2701146781 Nov 08, 2017 (151)
58 GNOMAD ss2932980646 Nov 08, 2017 (151)
59 SWEGEN ss3013005261 Nov 08, 2017 (151)
60 BIOINF_KMB_FNS_UNIBA ss3027969636 Nov 08, 2017 (151)
61 TOPMED ss3223219573 Nov 08, 2017 (151)
62 CSHL ss3351041757 Nov 08, 2017 (151)
63 ILLUMINA ss3636288173 Oct 12, 2018 (152)
64 ILLUMINA ss3638075872 Oct 12, 2018 (152)
65 ILLUMINA ss3643060583 Oct 12, 2018 (152)
66 URBANLAB ss3650317104 Oct 12, 2018 (152)
67 EGCUT_WGS ss3680176789 Jul 13, 2019 (153)
68 EVA_DECODE ss3697583526 Jul 13, 2019 (153)
69 ACPOP ss3740786825 Jul 13, 2019 (153)
70 EVA ss3752890723 Jul 13, 2019 (153)
71 PACBIO ss3787801013 Jul 13, 2019 (153)
72 PACBIO ss3792820272 Jul 13, 2019 (153)
73 PACBIO ss3797704734 Jul 13, 2019 (153)
74 KHV_HUMAN_GENOMES ss3818207949 Jul 13, 2019 (153)
75 1000Genomes NC_000015.9 - 28231357 Oct 12, 2018 (152)
76 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28231357 Oct 12, 2018 (152)
77 Genetic variation in the Estonian population NC_000015.9 - 28231357 Oct 12, 2018 (152)
78 gnomAD - Genomes NC_000015.9 - 28231357 Jul 13, 2019 (153)
79 Northern Sweden NC_000015.9 - 28231357 Jul 13, 2019 (153)
80 TopMed NC_000015.10 - 27986211 Oct 12, 2018 (152)
81 UK 10K study - Twins NC_000015.9 - 28231357 Oct 12, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000015.9 - 28231357 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)
rs58068429 Feb 27, 2009 (130)
rs61149285 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss66501051, ss76323973, ss77644047, ss78506449, ss83616331, ss90103788, ss108695789, ss118171754, ss167715547, ss173262037, ss200653392, ss207304762, ss211585517, ss254861760, ss282192732, ss286924576, ss291808214, ss1397692492, ss1695635404, ss1713477600, ss3643060583 NC_000015.8:25904951:G:T NC_000015.10:27986210:G:T (self)
65866119, 36574053, 25915037, 179688869, 14071690, 36574053, 8137662, ss226812843, ss236722447, ss479620070, ss564383234, ss660095307, ss991623841, ss1080002897, ss1352819065, ss1427575751, ss1577522708, ss1632670092, ss1675664125, ss1808131073, ss1935020889, ss1968070654, ss2028290775, ss2156687760, ss2370059280, ss2628638524, ss2701146781, ss2932980646, ss3013005261, ss3351041757, ss3636288173, ss3638075872, ss3680176789, ss3740786825, ss3752890723, ss3787801013, ss3792820272, ss3797704734 NC_000015.9:28231356:G:T NC_000015.10:27986210:G:T (self)
125911149, ss2205523984, ss3027969636, ss3223219573, ss3650317104, ss3697583526, ss3818207949 NC_000015.10:27986210:G:T NC_000015.10:27986210:G:T (self)
ss10772748 NT_010280.15:596847:G:T NC_000015.10:27986210:G:T (self)
ss19324698, ss21247098 NT_010280.16:596847:G:T NC_000015.10:27986210:G:T (self)
ss1503344, ss6592599, ss23752670, ss43694179, ss65762732, ss74877976, ss81452377, ss106418866, ss132383589, ss134210122, ss156359690, ss159888548, ss170012211 NT_026446.14:4666503:G:T NC_000015.10:27986210:G:T (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 rs1037208
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
20158590 Predicting phenotype from genotype: normal pigmentation. Valenzuela RK et al. 2010 Journal of forensic sciences

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