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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.

rs1129038

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28111713 (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=0.49308 (119373/242098, GnomAD_exome)
T=0.45261 (56833/125568, TOPMED)
C=0.49270 (57801/117314, ExAC) (+ 8 more)
T=0.1650 (12982/78698, PAGE_STUDY)
C=0.4403 (13800/31340, GnomAD)
C=0.4635 (6028/13006, GO-ESP)
T=0.177 (886/5008, 1000G)
C=0.090 (405/4480, Estonian)
C=0.231 (892/3854, ALSPAC)
C=0.231 (855/3708, TWINSUK)
C=0.13 (80/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HERC2 : 3 Prime UTR Variant
Publications
19 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.28111713C>T
GRCh37.p13 chr 15 NC_000015.9:g.28356859C>T
HERC2 RefSeqGene NG_016355.1:g.215437G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.245178T>C
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.245178T>C
Gene: HERC2, HECT and RLD domain containing E3 ubiquitin protein ligase 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HERC2 transcript NM_004667.5:c. N/A 3 Prime UTR Variant
HERC2 transcript variant X1 XM_006720726.3:c. N/A 3 Prime UTR Variant
HERC2 transcript variant X2 XM_017022695.1:c. N/A 3 Prime UTR Variant
HERC2 transcript variant X4 XM_017022696.1:c. N/A 3 Prime UTR Variant
HERC2 transcript variant X5 XM_006720727.3:c. N/A 3 Prime UTR Variant
HERC2 transcript variant X8 XM_017022697.1:c. N/A 3 Prime UTR Variant
HERC2 transcript variant X9 XM_017022698.1:c. N/A 3 Prime UTR Variant
HERC2 transcript variant X3 XM_005268276.5:c. N/A 3 Prime UTR Variant
HERC2 transcript variant X7 XR_001751410.1:n. N/A Genic Downstream Transcript Variant
HERC2 transcript variant X6 XR_931930.2:n. N/A Genic Downstream Transcript 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
gnomAD - Exomes Global Study-wide 242098 C=0.50692 T=0.49308
gnomAD - Exomes European Sub 130904 C=0.22921 T=0.77079
gnomAD - Exomes Asian Sub 46314 C=0.9410 T=0.0590
gnomAD - Exomes American Sub 33874 C=0.8328 T=0.1672
gnomAD - Exomes African Sub 16142 C=0.8836 T=0.1164
gnomAD - Exomes Ashkenazi Jewish Sub 8982 C=0.414 T=0.586
gnomAD - Exomes Other Sub 5882 C=0.501 T=0.499
TopMed Global Study-wide 125568 C=0.54739 T=0.45261
ExAC Global Study-wide 117314 C=0.49270 T=0.50730
ExAC Europe Sub 72116 C=0.2402 T=0.7598
ExAC Asian Sub 22598 C=0.9387 T=0.0613
ExAC American Sub 11464 C=0.8535 T=0.1465
ExAC African Sub 10270 C=0.8787 T=0.1213
ExAC Other Sub 866 C=0.53 T=0.47
The PAGE Study Global Study-wide 78698 C=0.8350 T=0.1650
The PAGE Study AfricanAmerican Sub 32514 C=0.8540 T=0.1460
The PAGE Study Mexican Sub 10810 C=0.8074 T=0.1926
The PAGE Study Asian Sub 8318 C=0.997 T=0.003
The PAGE Study PuertoRican Sub 7918 C=0.761 T=0.239
The PAGE Study NativeHawaiian Sub 4534 C=0.835 T=0.165
The PAGE Study Cuban Sub 4228 C=0.711 T=0.289
The PAGE Study Dominican Sub 3828 C=0.814 T=0.186
The PAGE Study CentralAmerican Sub 2450 C=0.823 T=0.177
The PAGE Study SouthAmerican Sub 1982 C=0.787 T=0.213
The PAGE Study NativeAmerican Sub 1260 C=0.523 T=0.477
The PAGE Study SouthAsian Sub 856 C=0.89 T=0.11
gnomAD - Genomes Global Study-wide 31340 C=0.4403 T=0.5597
gnomAD - Genomes European Sub 18874 C=0.1858 T=0.8142
gnomAD - Genomes African Sub 8690 C=0.875 T=0.125
gnomAD - Genomes East Asian Sub 1556 C=0.999 T=0.001
gnomAD - Genomes Other Sub 1086 C=0.323 T=0.677
gnomAD - Genomes American Sub 844 C=0.77 T=0.23
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.45 T=0.55
GO Exome Sequencing Project Global Study-wide 13006 C=0.4635 T=0.5365
GO Exome Sequencing Project European American Sub 8600 C=0.261 T=0.739
GO Exome Sequencing Project African American Sub 4406 C=0.858 T=0.142
1000Genomes Global Study-wide 5008 C=0.823 T=0.177
1000Genomes African Sub 1322 C=0.972 T=0.028
1000Genomes East Asian Sub 1008 C=0.999 T=0.001
1000Genomes Europe Sub 1006 C=0.365 T=0.635
1000Genomes South Asian Sub 978 C=0.93 T=0.07
1000Genomes American Sub 694 C=0.80 T=0.20
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.090 T=0.910
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.231 T=0.769
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.231 T=0.769
Northern Sweden ACPOP Study-wide 600 C=0.13 T=0.87
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.28111713= NC_000015.10:g.28111713C>T
GRCh37.p13 chr 15 NC_000015.9:g.28356859= NC_000015.9:g.28356859C>T
HERC2 RefSeqGene NG_016355.1:g.215437= NG_016355.1:g.215437G>A
HERC2 transcript NM_004667.5:c.*50= NM_004667.5:c.*50G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.245178T>C NW_011332701.1:g.245178=
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.245178T>C NT_187660.1:g.245178=
HERC2 transcript variant X3 XM_005268276.5:c.*50= XM_005268276.5:c.*50G>A
HERC2 transcript variant X2 XM_005268276.1:c.*50= XM_005268276.1:c.*50G>A
HERC2 transcript variant X1 XM_006720726.3:c.*50= XM_006720726.3:c.*50G>A
HERC2 transcript variant X5 XM_006720727.3:c.*50= XM_006720727.3:c.*50G>A
HERC2 transcript variant X2 XM_017022695.1:c.*50= XM_017022695.1:c.*50G>A
HERC2 transcript variant X4 XM_017022696.1:c.*50= XM_017022696.1:c.*50G>A
HERC2 transcript variant X8 XM_017022697.1:c.*50= XM_017022697.1:c.*50G>A
HERC2 transcript variant X9 XM_017022698.1:c.*50= XM_017022698.1:c.*50G>A
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#.

94 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 LEE ss1517796 Oct 13, 2000 (86)
2 CGAP-GAI ss4321391 Jan 05, 2002 (103)
3 LEE ss4410160 May 29, 2002 (108)
4 CGAP-GAI ss16260531 Feb 27, 2004 (120)
5 SSAHASNP ss21255932 Apr 05, 2004 (121)
6 ABI ss43730882 Mar 13, 2006 (126)
7 AFFY ss74814846 Aug 16, 2007 (128)
8 BCMHGSC_JDW ss90103929 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss96746318 Feb 06, 2009 (130)
10 1000GENOMES ss108696351 Jan 23, 2009 (130)
11 ENSEMBL ss134210332 Dec 01, 2009 (131)
12 ENSEMBL ss136931838 Dec 01, 2009 (131)
13 ILLUMINA ss159976973 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss167716237 Jul 04, 2010 (132)
15 ILLUMINA ss168959279 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss170884452 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss207371954 Jul 04, 2010 (132)
18 1000GENOMES ss236722724 Jul 15, 2010 (132)
19 ILLUMINA ss244272347 Jul 04, 2010 (132)
20 BL ss254862162 May 09, 2011 (134)
21 GMI ss286924715 Apr 25, 2013 (138)
22 PJP ss291808311 May 09, 2011 (134)
23 ILLUMINA ss479517459 May 04, 2012 (137)
24 ILLUMINA ss479521362 May 04, 2012 (137)
25 ILLUMINA ss479973661 Sep 08, 2015 (146)
26 ILLUMINA ss484557895 May 04, 2012 (137)
27 1000GENOMES ss491078406 May 04, 2012 (137)
28 ILLUMINA ss535289487 Sep 08, 2015 (146)
29 SSMP ss660095885 Apr 25, 2013 (138)
30 NHLBI-ESP ss713214169 Apr 25, 2013 (138)
31 ILLUMINA ss778382864 Aug 21, 2014 (142)
32 ILLUMINA ss782725609 Aug 21, 2014 (142)
33 ILLUMINA ss783693030 Aug 21, 2014 (142)
34 ILLUMINA ss831977271 Apr 01, 2015 (144)
35 ILLUMINA ss833837863 Aug 21, 2014 (142)
36 EVA-GONL ss991624564 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1080003544 Aug 21, 2014 (142)
38 1000GENOMES ss1352822469 Aug 21, 2014 (142)
39 EVA_GENOME_DK ss1577523061 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1632671702 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1675665735 Apr 01, 2015 (144)
42 EVA_EXAC ss1691717641 Apr 01, 2015 (144)
43 EVA_DECODE ss1695636210 Apr 01, 2015 (144)
44 EVA_MGP ss1711390109 Apr 01, 2015 (144)
45 ILLUMINA ss1752154469 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1935021729 Feb 12, 2016 (147)
47 ILLUMINA ss1946388509 Feb 12, 2016 (147)
48 ILLUMINA ss1959597524 Feb 12, 2016 (147)
49 GENOMED ss1968070783 Jul 19, 2016 (147)
50 JJLAB ss2028291136 Sep 14, 2016 (149)
51 ILLUMINA ss2095057520 Dec 20, 2016 (150)
52 USC_VALOUEV ss2156688166 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2205531181 Dec 20, 2016 (150)
54 TOPMED ss2370066846 Dec 20, 2016 (150)
55 ILLUMINA ss2633208751 Nov 08, 2017 (151)
56 ILLUMINA ss2633208752 Nov 08, 2017 (151)
57 ILLUMINA ss2635056530 Nov 08, 2017 (151)
58 GRF ss2701147181 Nov 08, 2017 (151)
59 GNOMAD ss2741066596 Nov 08, 2017 (151)
60 GNOMAD ss2749249785 Nov 08, 2017 (151)
61 GNOMAD ss2932990844 Nov 08, 2017 (151)
62 AFFY ss2985667529 Nov 08, 2017 (151)
63 SWEGEN ss3013006529 Nov 08, 2017 (151)
64 ILLUMINA ss3021616281 Nov 08, 2017 (151)
65 BIOINF_KMB_FNS_UNIBA ss3027969838 Nov 08, 2017 (151)
66 TOPMED ss3223242771 Nov 08, 2017 (151)
67 CSHL ss3351042076 Nov 08, 2017 (151)
68 ILLUMINA ss3625669091 Oct 12, 2018 (152)
69 ILLUMINA ss3627323420 Oct 12, 2018 (152)
70 ILLUMINA ss3631203071 Oct 12, 2018 (152)
71 ILLUMINA ss3633091654 Oct 12, 2018 (152)
72 ILLUMINA ss3633796005 Oct 12, 2018 (152)
73 ILLUMINA ss3634597982 Oct 12, 2018 (152)
74 ILLUMINA ss3635485077 Oct 12, 2018 (152)
75 ILLUMINA ss3636288261 Oct 12, 2018 (152)
76 ILLUMINA ss3637236308 Oct 12, 2018 (152)
77 ILLUMINA ss3638075914 Oct 12, 2018 (152)
78 ILLUMINA ss3640305309 Oct 12, 2018 (152)
79 ILLUMINA ss3644641631 Oct 12, 2018 (152)
80 URBANLAB ss3650317205 Oct 12, 2018 (152)
81 ILLUMINA ss3652015625 Oct 12, 2018 (152)
82 EGCUT_WGS ss3680178099 Jul 13, 2019 (153)
83 EVA_DECODE ss3697585124 Jul 13, 2019 (153)
84 ILLUMINA ss3725484789 Jul 13, 2019 (153)
85 ACPOP ss3740787447 Jul 13, 2019 (153)
86 ILLUMINA ss3744128674 Jul 13, 2019 (153)
87 ILLUMINA ss3744898547 Jul 13, 2019 (153)
88 EVA ss3752891708 Jul 13, 2019 (153)
89 PAGE_CC ss3771818497 Jul 13, 2019 (153)
90 ILLUMINA ss3772397263 Jul 13, 2019 (153)
91 PACBIO ss3787801144 Jul 13, 2019 (153)
92 PACBIO ss3792820374 Jul 13, 2019 (153)
93 PACBIO ss3797704835 Jul 13, 2019 (153)
94 KHV_HUMAN_GENOMES ss3818208906 Jul 13, 2019 (153)
95 1000Genomes NC_000015.9 - 28356859 Oct 12, 2018 (152)
96 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28356859 Oct 12, 2018 (152)
97 Genetic variation in the Estonian population NC_000015.9 - 28356859 Oct 12, 2018 (152)
98 ExAC NC_000015.9 - 28356859 Oct 12, 2018 (152)
99 gnomAD - Genomes NC_000015.9 - 28356859 Jul 13, 2019 (153)
100 gnomAD - Exomes NC_000015.9 - 28356859 Jul 13, 2019 (153)
101 GO Exome Sequencing Project NC_000015.9 - 28356859 Oct 12, 2018 (152)
102 Northern Sweden NC_000015.9 - 28356859 Jul 13, 2019 (153)
103 The PAGE Study NC_000015.10 - 28111713 Jul 13, 2019 (153)
104 TopMed NC_000015.10 - 28111713 Oct 12, 2018 (152)
105 UK 10K study - Twins NC_000015.9 - 28356859 Oct 12, 2018 (152)
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)
rs3087778 Mar 26, 2002 (103)
rs3186511 Oct 09, 2002 (108)
rs52789316 Sep 21, 2007 (128)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss90103929, ss108696351, ss167716237, ss170884452, ss207371954, ss254862162, ss286924715, ss291808311, ss479517459, ss1695636210, ss2635056530 NC_000015.8:26030453:C:T NC_000015.10:28111712:C:T (self)
65869683, 36575857, 25916347, 2082432, 179698958, 10329962, 1354368, 14072312, 36575857, ss236722724, ss479521362, ss479973661, ss484557895, ss491078406, ss535289487, ss660095885, ss713214169, ss778382864, ss782725609, ss783693030, ss831977271, ss833837863, ss991624564, ss1080003544, ss1352822469, ss1577523061, ss1632671702, ss1675665735, ss1691717641, ss1711390109, ss1752154469, ss1935021729, ss1946388509, ss1959597524, ss1968070783, ss2028291136, ss2095057520, ss2156688166, ss2370066846, ss2633208751, ss2633208752, ss2701147181, ss2741066596, ss2749249785, ss2932990844, ss2985667529, ss3013006529, ss3021616281, ss3351042076, ss3625669091, ss3627323420, ss3631203071, ss3633091654, ss3633796005, ss3634597982, ss3635485077, ss3636288261, ss3637236308, ss3638075914, ss3640305309, ss3644641631, ss3652015625, ss3680178099, ss3740787447, ss3744128674, ss3744898547, ss3752891708, ss3772397263, ss3787801144, ss3792820374, ss3797704835 NC_000015.9:28356858:C:T NC_000015.10:28111712:C:T (self)
1039966, 125930099, ss2205531181, ss3027969838, ss3223242771, ss3650317205, ss3697585124, ss3725484789, ss3771818497, ss3818208906 NC_000015.10:28111712:C:T NC_000015.10:28111712:C:T (self)
ss21255932 NT_010280.16:722349:C:T NC_000015.10:28111712:C:T (self)
ss1517796, ss4321391, ss4410160, ss16260531, ss43730882, ss74814846, ss96746318, ss134210332, ss136931838, ss159976973, ss168959279, ss244272347 NT_026446.14:4792005:C:T NC_000015.10:28111712: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.

19 citations for rs1129038
PMID Title Author Year Journal
18172690 Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. Eiberg H et al. 2008 Human genetics
18252222 A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. Sturm RA et al. 2008 American journal of human genetics
18853455 Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease. Srinivasan BS et al. 2009 Human mutation
19472299 Genotyping of five single nucleotide polymorphisms in the OCA2 and HERC2 genes associated with blue-brown eye color in the Japanese population. Iida R et al. 2009 Cell biochemistry and function
20042077 Genetic determinants of hair and eye colours in the Scottish and Danish populations. Mengel-From J et al. 2009 BMC genetics
20457063 Human eye colour and HERC2, OCA2 and MATP. Mengel-From J et al. 2010 Forensic science international. Genetics
20463881 Digital quantification of human eye color highlights genetic association of three new loci. Liu F et al. 2010 PLoS genetics
21498954 Genetic heterogeneity of self-reported ancestry groups in an admixed Brazilian population. Lins TC et al. 2011 Journal of epidemiology
21926416 Genome-wide association study identifies novel loci predisposing to cutaneous melanoma. Amos CI et al. 2011 Human molecular genetics
22065085 A global view of the OCA2-HERC2 region and pigmentation. Donnelly MP et al. 2012 Human genetics
22073278 Genomic ancestry, self-reported "color" and quantitative measures of skin pigmentation in Brazilian admixed siblings. Leite TK et al. 2011 PloS one
22709892 Further development of forensic eye color predictive tests. Ruiz Y et al. 2013 Forensic science international. Genetics
23907626 Influence of seasonal sunlight intensity and iris color on the anti-VEGF therapy for neovascular age-related macular degeneration. Brockmann C et al. 2013 Eye (London, England)
24809478 Implications of the admixture process in skin color molecular assessment. Cerqueira CC et al. 2014 PloS one
25077817 Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions. Barrett JH et al. 2015 International journal of cancer
25376095 Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa. Alkan C et al. 2014 BMC genomics
26870082 Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci. Shen C et al. 2016 Frontiers in genetics
27468418 Importance of nonsynonymous OCA2 variants in human eye color prediction. Andersen JD et al. 2016 Molecular genetics & genomic medicine
27499155 Genetic markers of pigmentation are novel risk loci for uveal melanoma. Ferguson R et al. 2016 Scientific reports

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