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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.

rs4778232

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28036619 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.45437 (57054/125568, TOPMED)
C=0.3759 (29583/78696, PAGE_STUDY)
T=0.4002 (12539/31330, GnomAD) (+ 6 more)
C=0.411 (2058/5008, 1000G)
T=0.172 (772/4480, Estonian)
T=0.206 (795/3854, ALSPAC)
T=0.211 (782/3708, TWINSUK)
T=0.18 (106/600, NorthernSweden)
C=0.10 (21/214, 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.28036619C>T
GRCh37.p13 chr 15 NC_000015.9:g.28281765C>T
OCA2 RefSeqGene NG_009846.1:g.67694G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.170917C>T
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.170917C>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=0.54563 T=0.45437
The PAGE Study Global Study-wide 78696 C=0.3759 T=0.6241
The PAGE Study AfricanAmerican Sub 32514 C=0.2523 T=0.7477
The PAGE Study Mexican Sub 10810 C=0.6245 T=0.3755
The PAGE Study Asian Sub 8314 C=0.100 T=0.900
The PAGE Study PuertoRican Sub 7918 C=0.559 T=0.441
The PAGE Study NativeHawaiian Sub 4534 C=0.245 T=0.755
The PAGE Study Cuban Sub 4230 C=0.583 T=0.417
The PAGE Study Dominican Sub 3828 C=0.460 T=0.540
The PAGE Study CentralAmerican Sub 2450 C=0.582 T=0.418
The PAGE Study SouthAmerican Sub 1982 C=0.644 T=0.356
The PAGE Study NativeAmerican Sub 1260 C=0.663 T=0.337
The PAGE Study SouthAsian Sub 856 C=0.58 T=0.42
gnomAD - Genomes Global Study-wide 31330 C=0.5998 T=0.4002
gnomAD - Genomes European Sub 18880 C=0.8002 T=0.1998
gnomAD - Genomes African Sub 8674 C=0.227 T=0.773
gnomAD - Genomes East Asian Sub 1556 C=0.111 T=0.889
gnomAD - Genomes Other Sub 1084 C=0.724 T=0.276
gnomAD - Genomes American Sub 846 C=0.66 T=0.34
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.68 T=0.32
1000Genomes Global Study-wide 5008 C=0.411 T=0.589
1000Genomes African Sub 1322 C=0.163 T=0.837
1000Genomes East Asian Sub 1008 C=0.102 T=0.898
1000Genomes Europe Sub 1006 C=0.760 T=0.240
1000Genomes South Asian Sub 978 C=0.55 T=0.45
1000Genomes American Sub 694 C=0.62 T=0.38
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.828 T=0.172
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=0.789 T=0.211
Northern Sweden ACPOP Study-wide 600 C=0.82 T=0.18
A Vietnamese Genetic Variation Database Global Study-wide 214 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= T Note
GRCh38.p12 chr 15 NC_000015.10:g.28036619= NC_000015.10:g.28036619C>T
GRCh37.p13 chr 15 NC_000015.9:g.28281765= NC_000015.9:g.28281765C>T
OCA2 RefSeqGene NG_009846.1:g.67694= NG_009846.1:g.67694G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.170917= NW_011332701.1:g.170917C>T
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.170917= NT_187660.1:g.170917C>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#.

105 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6592615 Feb 20, 2003 (111)
2 PERLEGEN ss23752744 Sep 20, 2004 (123)
3 ABI ss43700222 Mar 14, 2006 (126)
4 ILLUMINA ss66684642 Nov 30, 2006 (127)
5 ILLUMINA ss67374931 Nov 30, 2006 (127)
6 ILLUMINA ss67755783 Nov 30, 2006 (127)
7 ILLUMINA ss70824110 May 25, 2008 (130)
8 ILLUMINA ss71406022 May 17, 2007 (127)
9 ILLUMINA ss75573302 Dec 06, 2007 (129)
10 AFFY ss76685052 Dec 06, 2007 (129)
11 ILLUMINA ss79194784 Dec 15, 2007 (130)
12 HGSV ss81072419 Dec 15, 2007 (130)
13 HGSV ss81588282 Dec 15, 2007 (130)
14 HGSV ss81630765 Dec 15, 2007 (130)
15 KRIBB_YJKIM ss84349623 Dec 15, 2007 (130)
16 BGI ss106418877 Feb 05, 2009 (130)
17 1000GENOMES ss108695957 Jan 23, 2009 (130)
18 1000GENOMES ss113953383 Jan 25, 2009 (130)
19 ILLUMINA-UK ss118171821 Feb 14, 2009 (130)
20 ILLUMINA ss122384872 Dec 01, 2009 (131)
21 ILLUMINA ss154316422 Dec 01, 2009 (131)
22 GMI ss156360089 Dec 01, 2009 (131)
23 ILLUMINA ss159493095 Dec 01, 2009 (131)
24 ILLUMINA ss160710485 Dec 01, 2009 (131)
25 COMPLETE_GENOMICS ss168984727 Jul 04, 2010 (132)
26 ILLUMINA ss171912673 Jul 04, 2010 (132)
27 ILLUMINA ss173808857 Jul 04, 2010 (132)
28 BUSHMAN ss200653900 Jul 04, 2010 (132)
29 1000GENOMES ss226813038 Jul 14, 2010 (132)
30 1000GENOMES ss236722535 Jul 15, 2010 (132)
31 1000GENOMES ss243120539 Jul 15, 2010 (132)
32 GMI ss282192817 May 04, 2012 (137)
33 GMI ss286924622 Apr 25, 2013 (138)
34 PJP ss291808263 May 09, 2011 (134)
35 ILLUMINA ss481043870 May 04, 2012 (137)
36 ILLUMINA ss481065263 May 04, 2012 (137)
37 ILLUMINA ss482056136 Sep 08, 2015 (146)
38 ILLUMINA ss485316898 May 04, 2012 (137)
39 ILLUMINA ss537272845 Sep 08, 2015 (146)
40 TISHKOFF ss564383447 Apr 25, 2013 (138)
41 SSMP ss660095546 Apr 25, 2013 (138)
42 ILLUMINA ss778546796 Sep 08, 2015 (146)
43 ILLUMINA ss783104276 Sep 08, 2015 (146)
44 ILLUMINA ss784061459 Sep 08, 2015 (146)
45 ILLUMINA ss825525302 Apr 01, 2015 (144)
46 ILLUMINA ss832362883 Sep 08, 2015 (146)
47 ILLUMINA ss833004486 Jul 13, 2019 (153)
48 ILLUMINA ss834003475 Sep 08, 2015 (146)
49 EVA-GONL ss991624130 Aug 21, 2014 (142)
50 JMKIDD_LAB ss1080003148 Aug 21, 2014 (142)
51 1000GENOMES ss1352820481 Aug 21, 2014 (142)
52 DDI ss1427575842 Apr 01, 2015 (144)
53 EVA_GENOME_DK ss1577522832 Apr 01, 2015 (144)
54 EVA_UK10K_ALSPAC ss1632670784 Apr 01, 2015 (144)
55 EVA_UK10K_TWINSUK ss1675664817 Apr 01, 2015 (144)
56 EVA_DECODE ss1695635744 Apr 01, 2015 (144)
57 EVA_SVP ss1713477620 Apr 01, 2015 (144)
58 ILLUMINA ss1752154444 Sep 08, 2015 (146)
59 HAMMER_LAB ss1808131218 Sep 08, 2015 (146)
60 WEILL_CORNELL_DGM ss1935021165 Feb 12, 2016 (147)
61 ILLUMINA ss1946388494 Feb 12, 2016 (147)
62 ILLUMINA ss1959597478 Feb 12, 2016 (147)
63 GENOMED ss1968070709 Jul 19, 2016 (147)
64 JJLAB ss2028290906 Sep 14, 2016 (149)
65 USC_VALOUEV ss2156687903 Dec 20, 2016 (150)
66 HUMAN_LONGEVITY ss2205526939 Dec 20, 2016 (150)
67 TOPMED ss2370062342 Dec 20, 2016 (150)
68 SYSTEMSBIOZJU ss2628638621 Nov 08, 2017 (151)
69 ILLUMINA ss2633208688 Nov 08, 2017 (151)
70 GRF ss2701146930 Nov 08, 2017 (151)
71 ILLUMINA ss2710811769 Nov 08, 2017 (151)
72 GNOMAD ss2932984561 Nov 08, 2017 (151)
73 SWEGEN ss3013005734 Nov 08, 2017 (151)
74 ILLUMINA ss3021616227 Nov 08, 2017 (151)
75 BIOINF_KMB_FNS_UNIBA ss3027969704 Nov 08, 2017 (151)
76 TOPMED ss3223228551 Nov 08, 2017 (151)
77 CSHL ss3351041895 Nov 08, 2017 (151)
78 ILLUMINA ss3625669077 Oct 12, 2018 (152)
79 ILLUMINA ss3627323324 Oct 12, 2018 (152)
80 ILLUMINA ss3631203012 Oct 12, 2018 (152)
81 ILLUMINA ss3633091634 Oct 12, 2018 (152)
82 ILLUMINA ss3633795985 Oct 12, 2018 (152)
83 ILLUMINA ss3634597957 Oct 12, 2018 (152)
84 ILLUMINA ss3635485057 Oct 12, 2018 (152)
85 ILLUMINA ss3636288188 Oct 12, 2018 (152)
86 ILLUMINA ss3637236288 Oct 12, 2018 (152)
87 ILLUMINA ss3638075887 Oct 12, 2018 (152)
88 ILLUMINA ss3639051369 Oct 12, 2018 (152)
89 ILLUMINA ss3639530778 Oct 12, 2018 (152)
90 ILLUMINA ss3640305284 Oct 12, 2018 (152)
91 ILLUMINA ss3641057863 Oct 12, 2018 (152)
92 ILLUMINA ss3641353129 Oct 12, 2018 (152)
93 ILLUMINA ss3643060598 Oct 12, 2018 (152)
94 ILLUMINA ss3644641617 Oct 12, 2018 (152)
95 ILLUMINA ss3652015565 Oct 12, 2018 (152)
96 EGCUT_WGS ss3680177288 Jul 13, 2019 (153)
97 EVA_DECODE ss3697584139 Jul 13, 2019 (153)
98 ILLUMINA ss3725484742 Jul 13, 2019 (153)
99 ACPOP ss3740787050 Jul 13, 2019 (153)
100 ILLUMINA ss3744128665 Jul 13, 2019 (153)
101 ILLUMINA ss3744898523 Jul 13, 2019 (153)
102 EVA ss3752891098 Jul 13, 2019 (153)
103 PAGE_CC ss3771818460 Jul 13, 2019 (153)
104 ILLUMINA ss3772397239 Jul 13, 2019 (153)
105 KHV_HUMAN_GENOMES ss3818208314 Jul 13, 2019 (153)
106 1000Genomes NC_000015.9 - 28281765 Oct 12, 2018 (152)
107 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28281765 Oct 12, 2018 (152)
108 Genetic variation in the Estonian population NC_000015.9 - 28281765 Oct 12, 2018 (152)
109 gnomAD - Genomes NC_000015.9 - 28281765 Jul 13, 2019 (153)
110 Northern Sweden NC_000015.9 - 28281765 Jul 13, 2019 (153)
111 The PAGE Study NC_000015.10 - 28036619 Jul 13, 2019 (153)
112 TopMed NC_000015.10 - 28036619 Oct 12, 2018 (152)
113 UK 10K study - Twins NC_000015.9 - 28281765 Oct 12, 2018 (152)
114 A Vietnamese Genetic Variation Database NC_000015.9 - 28281765 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)
rs59222536 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss81072419, ss81588282, ss81630765, ss108695957, ss113953383, ss118171821, ss168984727, ss200653900, ss282192817, ss286924622, ss291808263, ss481043870, ss825525302, ss1695635744, ss1713477620, ss3639051369, ss3639530778, ss3643060598 NC_000015.8:25955359:C:T NC_000015.10:28036618:C:T (self)
65867575, 36574801, 25915536, 179692760, 14071915, 36574801, 8137800, ss226813038, ss236722535, ss243120539, ss481065263, ss482056136, ss485316898, ss537272845, ss564383447, ss660095546, ss778546796, ss783104276, ss784061459, ss832362883, ss833004486, ss834003475, ss991624130, ss1080003148, ss1352820481, ss1427575842, ss1577522832, ss1632670784, ss1675664817, ss1752154444, ss1808131218, ss1935021165, ss1946388494, ss1959597478, ss1968070709, ss2028290906, ss2156687903, ss2370062342, ss2628638621, ss2633208688, ss2701146930, ss2710811769, ss2932984561, ss3013005734, ss3021616227, ss3351041895, ss3625669077, ss3627323324, ss3631203012, ss3633091634, ss3633795985, ss3634597957, ss3635485057, ss3636288188, ss3637236288, ss3638075887, ss3640305284, ss3641057863, ss3641353129, ss3644641617, ss3652015565, ss3680177288, ss3740787050, ss3744128665, ss3744898523, ss3752891098, ss3772397239 NC_000015.9:28281764:C:T NC_000015.10:28036618:C:T (self)
1039929, 125918816, ss2205526939, ss3027969704, ss3223228551, ss3697584139, ss3725484742, ss3771818460, ss3818208314 NC_000015.10:28036618:C:T NC_000015.10:28036618:C:T (self)
ss6592615, ss23752744, ss43700222, ss66684642, ss67374931, ss67755783, ss70824110, ss71406022, ss75573302, ss76685052, ss79194784, ss84349623, ss106418877, ss122384872, ss154316422, ss156360089, ss159493095, ss160710485, ss171912673, ss173808857 NT_026446.14:4716911:C:T NC_000015.10:28036618: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.

2 citations for rs4778232
PMID Title Author Year Journal
18252221 Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene. Kayser M et al. 2008 American journal of human genetics
20585627 Web-based, participant-driven studies yield novel genetic associations for common traits. Eriksson N et al. 2010 PLoS 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