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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.

rs1375164

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28046666 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.47990 (60260/125568, TOPMED)
T=0.4225 (13243/31344, GnomAD)
C=0.378 (1893/5008, 1000G) (+ 5 more)
T=0.167 (750/4480, Estonian)
T=0.206 (792/3854, ALSPAC)
T=0.207 (766/3708, TWINSUK)
T=0.17 (100/600, NorthernSweden)
C=0.10 (21/210, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OCA2 : Intron Variant
Publications
3 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.28046666C>A
GRCh38.p12 chr 15 NC_000015.10:g.28046666C>T
GRCh37.p13 chr 15 NC_000015.9:g.28291812C>A
GRCh37.p13 chr 15 NC_000015.9:g.28291812C>T
OCA2 RefSeqGene NG_009846.1:g.57647G>T
OCA2 RefSeqGene NG_009846.1:g.57647G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.180964C>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.180964C>T
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.180964C>A
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.180964C>T
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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.52010 T=0.47990
gnomAD - Genomes Global Study-wide 31344 C=0.5775 T=0.4225
gnomAD - Genomes European Sub 18884 C=0.8041 T=0.1959
gnomAD - Genomes African Sub 8682 C=0.138 T=0.862
gnomAD - Genomes East Asian Sub 1556 C=0.116 T=0.884
gnomAD - Genomes Other Sub 1086 C=0.732 T=0.268
gnomAD - Genomes American Sub 846 C=0.65 T=0.35
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.68 T=0.32
1000Genomes Global Study-wide 5008 C=0.378 T=0.622
1000Genomes African Sub 1322 C=0.039 T=0.961
1000Genomes East Asian Sub 1008 C=0.109 T=0.891
1000Genomes Europe Sub 1006 C=0.763 T=0.237
1000Genomes South Asian Sub 978 C=0.55 T=0.45
1000Genomes American Sub 694 C=0.61 T=0.39
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.833 T=0.167
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.794 T=0.206
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.793 T=0.207
Northern Sweden ACPOP Study-wide 600 C=0.83 T=0.17
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.10 T=0.90
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 C= A T Note
GRCh38.p12 chr 15 NC_000015.10:g.28...

NC_000015.10:g.28046666=

NC_000015.10:g.28...

NC_000015.10:g.28046666C>A

NC_000015.10:g.28...

NC_000015.10:g.28046666C>T

GRCh37.p13 chr 15 NC_000015.9:g.282...

NC_000015.9:g.28291812=

NC_000015.9:g.282...

NC_000015.9:g.28291812C>A

NC_000015.9:g.282...

NC_000015.9:g.28291812C>T

OCA2 RefSeqGene NG_009846.1:g.57647= NG_009846.1:g.576...

NG_009846.1:g.57647G>T

NG_009846.1:g.576...

NG_009846.1:g.57647G>A

chr 15 fix patch HG2139_PATCH NW_011332701.1:g....

NW_011332701.1:g.180964=

NW_011332701.1:g....

NW_011332701.1:g.180964C>A

NW_011332701.1:g....

NW_011332701.1:g.180964C>T

GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.180...

NT_187660.1:g.180964=

NT_187660.1:g.180...

NT_187660.1:g.180964C>A

NT_187660.1:g.180...

NT_187660.1:g.180964C>T

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#.

67 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2163423 Oct 23, 2000 (88)
2 CSHL-HAPMAP ss19320395 Feb 27, 2004 (120)
3 PERLEGEN ss24675774 Sep 20, 2004 (123)
4 ABI ss40635187 Mar 13, 2006 (126)
5 PERLEGEN ss69171481 May 17, 2007 (127)
6 ILLUMINA ss75235883 Dec 07, 2007 (129)
7 HGSV ss80654892 Dec 16, 2007 (130)
8 HGSV ss85187981 Dec 16, 2007 (130)
9 BGI ss106418893 Feb 06, 2009 (130)
10 1000GENOMES ss108695984 Jan 23, 2009 (130)
11 1000GENOMES ss113953532 Jan 25, 2009 (130)
12 ILLUMINA-UK ss118171867 Feb 14, 2009 (130)
13 KRIBB_YJKIM ss119389954 Dec 01, 2009 (131)
14 GMI ss156360258 Dec 01, 2009 (131)
15 ENSEMBL ss161704110 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss168985090 Jul 04, 2010 (132)
17 ILLUMINA ss172453471 Jul 04, 2010 (132)
18 BUSHMAN ss200654028 Jul 04, 2010 (132)
19 1000GENOMES ss226813090 Jul 14, 2010 (132)
20 1000GENOMES ss236722571 Jul 15, 2010 (132)
21 1000GENOMES ss243120565 Jul 15, 2010 (132)
22 GMI ss282192845 May 04, 2012 (137)
23 GMI ss286924630 Apr 25, 2013 (138)
24 PJP ss291808278 May 09, 2011 (134)
25 ILLUMINA ss536860543 Sep 08, 2015 (146)
26 TISHKOFF ss564383489 Apr 25, 2013 (138)
27 SSMP ss660095591 Apr 25, 2013 (138)
28 ILLUMINA ss778693926 Sep 08, 2015 (146)
29 ILLUMINA ss834152726 Sep 08, 2015 (146)
30 EVA-GONL ss991624194 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1080003211 Aug 21, 2014 (142)
32 1000GENOMES ss1352820719 Aug 21, 2014 (142)
33 DDI ss1427575849 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1577522862 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1632670920 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1675664953 Apr 01, 2015 (144)
37 EVA_DECODE ss1695635805 Apr 01, 2015 (144)
38 EVA_SVP ss1713477628 Apr 01, 2015 (144)
39 HAMMER_LAB ss1808131258 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1935021231 Feb 12, 2016 (147)
41 GENOMED ss1968070732 Jul 19, 2016 (147)
42 JJLAB ss2028290942 Sep 14, 2016 (149)
43 ILLUMINA ss2095057517 Dec 20, 2016 (150)
44 USC_VALOUEV ss2156687940 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2205527451 Dec 20, 2016 (150)
46 TOPMED ss2370062897 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2628638646 Nov 08, 2017 (151)
48 ILLUMINA ss2633208702 Nov 08, 2017 (151)
49 ILLUMINA ss2635056523 Nov 08, 2017 (151)
50 GRF ss2701146964 Nov 08, 2017 (151)
51 GNOMAD ss2932985230 Nov 08, 2017 (151)
52 SWEGEN ss3013005825 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3027969728 Nov 08, 2017 (151)
54 TOPMED ss3223230091 Nov 08, 2017 (151)
55 TOPMED ss3223230092 Nov 08, 2017 (151)
56 CSHL ss3351041929 Nov 08, 2017 (151)
57 ILLUMINA ss3627323344 Oct 12, 2018 (152)
58 ILLUMINA ss3631203025 Oct 12, 2018 (152)
59 ILLUMINA ss3638075895 Oct 12, 2018 (152)
60 ILLUMINA ss3641057865 Oct 12, 2018 (152)
61 ILLUMINA ss3643060605 Oct 12, 2018 (152)
62 ILLUMINA ss3652015576 Oct 12, 2018 (152)
63 EGCUT_WGS ss3680177397 Jul 13, 2019 (153)
64 EVA_DECODE ss3697584258 Jul 13, 2019 (153)
65 ACPOP ss3740787100 Jul 13, 2019 (153)
66 EVA ss3752891169 Jul 13, 2019 (153)
67 KHV_HUMAN_GENOMES ss3818208395 Jul 13, 2019 (153)
68 1000Genomes NC_000015.9 - 28291812 Oct 12, 2018 (152)
69 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28291812 Oct 12, 2018 (152)
70 Genetic variation in the Estonian population NC_000015.9 - 28291812 Oct 12, 2018 (152)
71 gnomAD - Genomes NC_000015.9 - 28291812 Jul 13, 2019 (153)
72 Northern Sweden NC_000015.9 - 28291812 Jul 13, 2019 (153)
73 TopMed NC_000015.10 - 28046666 Oct 12, 2018 (152)
74 UK 10K study - Twins NC_000015.9 - 28291812 Oct 12, 2018 (152)
75 A Vietnamese Genetic Variation Database NC_000015.9 - 28291812 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)
rs17567379 Oct 08, 2004 (123)
rs61270042 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3223230091 NC_000015.10:28046665:C:A NC_000015.10:28046665:C:A (self)
ss80654892, ss85187981, ss108695984, ss113953532, ss118171867, ss168985090, ss200654028, ss282192845, ss286924630, ss291808278, ss1695635805, ss1713477628, ss2635056523, ss3643060605 NC_000015.8:25965406:C:T NC_000015.10:28046665:C:T (self)
65867826, 36574953, 25915645, 179693437, 14071965, 36574953, 8137840, ss226813090, ss236722571, ss243120565, ss536860543, ss564383489, ss660095591, ss778693926, ss834152726, ss991624194, ss1080003211, ss1352820719, ss1427575849, ss1577522862, ss1632670920, ss1675664953, ss1808131258, ss1935021231, ss1968070732, ss2028290942, ss2095057517, ss2156687940, ss2370062897, ss2628638646, ss2633208702, ss2701146964, ss2932985230, ss3013005825, ss3351041929, ss3627323344, ss3631203025, ss3638075895, ss3641057865, ss3652015576, ss3680177397, ss3740787100, ss3752891169 NC_000015.9:28291811:C:T NC_000015.10:28046665:C:T (self)
125920181, ss2205527451, ss3027969728, ss3223230092, ss3697584258, ss3818208395 NC_000015.10:28046665:C:T NC_000015.10:28046665:C:T (self)
ss19320395 NT_010280.16:657302:C:T NC_000015.10:28046665:C:T (self)
ss2163423, ss24675774, ss40635187, ss69171481, ss75235883, ss106418893, ss119389954, ss156360258, ss161704110, ss172453471 NT_026446.14:4726958:C:T NC_000015.10:28046665:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

3 citations for rs1375164
PMID Title Author Year Journal
17236130 A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. Duffy DL et al. 2007 American journal of human genetics
18528436 Linkage and association analysis of spectrophotometrically quantified hair color in Australian adolescents: the effect of OCA2 and HERC2. Shekar SN et al. 2008 The Journal of investigative dermatology
22133426 Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing. de Gruijter JM et al. 2011 Investigative genetics

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