dbSNP Short Genetic Variations
Welcome to the Reference SNP (rs) Report
All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.
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 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr15:28111713 (GRCh38.p14) 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=0.422438 (111815/264690, TOPMED)T=0.493077 (119373/242098, GnomAD_exome)C=0.371554 (59942/161328, ALFA) (+ 21 more)
- Clinical Significance
- Not Reported in ClinVar
- Gene : Consequence
- HERC2 : 3 Prime UTR Variant
- Publications
- 22 citations
- Genomic View
- See rs on genome
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").
DownloadStudy | Population | Group | Sample Size | Ref Allele | Alt Allele |
---|---|---|---|---|---|
TopMed | Global | Study-wide | 264690 | C=0.577562 | T=0.422438 |
gnomAD - Exomes | Global | Study-wide | 242098 | C=0.506923 | T=0.493077 |
gnomAD - Exomes | European | Sub | 130904 | C=0.229206 | T=0.770794 |
gnomAD - Exomes | Asian | Sub | 46314 | C=0.94101 | T=0.05899 |
gnomAD - Exomes | American | Sub | 33874 | C=0.83282 | T=0.16718 |
gnomAD - Exomes | African | Sub | 16142 | C=0.88360 | T=0.11640 |
gnomAD - Exomes | Ashkenazi Jewish | Sub | 8982 | C=0.4137 | T=0.5863 |
gnomAD - Exomes | Other | Sub | 5882 | C=0.5014 | T=0.4986 |
Allele Frequency Aggregator | Total | Global | 161328 | C=0.371554 | T=0.628446 |
Allele Frequency Aggregator | European | Sub | 135802 | C=0.308125 | T=0.691875 |
Allele Frequency Aggregator | Other | Sub | 9318 | C=0.4957 | T=0.5043 |
Allele Frequency Aggregator | African | Sub | 8862 | C=0.8617 | T=0.1383 |
Allele Frequency Aggregator | Latin American 2 | Sub | 6064 | C=0.7991 | T=0.2009 |
Allele Frequency Aggregator | Latin American 1 | Sub | 692 | C=0.618 | T=0.382 |
Allele Frequency Aggregator | Asian | Sub | 418 | C=0.995 | T=0.005 |
Allele Frequency Aggregator | South Asian | Sub | 172 | C=0.890 | T=0.110 |
gnomAD - Genomes | Global | Study-wide | 140132 | C=0.495676 | T=0.504324 |
gnomAD - Genomes | European | Sub | 75904 | C=0.22117 | T=0.77883 |
gnomAD - Genomes | African | Sub | 41988 | C=0.86925 | T=0.13075 |
gnomAD - Genomes | American | Sub | 13638 | C=0.75216 | T=0.24784 |
gnomAD - Genomes | Ashkenazi Jewish | Sub | 3324 | C=0.4281 | T=0.5719 |
gnomAD - Genomes | East Asian | Sub | 3126 | C=0.9987 | T=0.0013 |
gnomAD - Genomes | Other | Sub | 2152 | C=0.6371 | T=0.3629 |
ExAC | Global | Study-wide | 117314 | C=0.492703 | T=0.507297 |
ExAC | Europe | Sub | 72116 | C=0.24021 | T=0.75979 |
ExAC | Asian | Sub | 22598 | C=0.93867 | T=0.06133 |
ExAC | American | Sub | 11464 | C=0.85354 | T=0.14646 |
ExAC | African | Sub | 10270 | C=0.87868 | T=0.12132 |
ExAC | Other | Sub | 866 | C=0.528 | T=0.472 |
The PAGE Study | Global | Study-wide | 78698 | C=0.83504 | T=0.16496 |
The PAGE Study | AfricanAmerican | Sub | 32514 | C=0.85403 | T=0.14597 |
The PAGE Study | Mexican | Sub | 10810 | C=0.80740 | T=0.19260 |
The PAGE Study | Asian | Sub | 8318 | C=0.9969 | T=0.0031 |
The PAGE Study | PuertoRican | Sub | 7918 | C=0.7605 | T=0.2395 |
The PAGE Study | NativeHawaiian | Sub | 4534 | C=0.8348 | T=0.1652 |
The PAGE Study | Cuban | Sub | 4228 | C=0.7105 | T=0.2895 |
The PAGE Study | Dominican | Sub | 3828 | C=0.8143 | T=0.1857 |
The PAGE Study | CentralAmerican | Sub | 2450 | C=0.8233 | T=0.1767 |
The PAGE Study | SouthAmerican | Sub | 1982 | C=0.7866 | T=0.2134 |
The PAGE Study | NativeAmerican | Sub | 1260 | C=0.5230 | T=0.4770 |
The PAGE Study | SouthAsian | Sub | 856 | C=0.894 | T=0.106 |
14KJPN | JAPANESE | Study-wide | 28258 | C=0.99996 | T=0.00004 |
8.3KJPN | JAPANESE | Study-wide | 16760 | C=0.99994 | T=0.00006 |
GO Exome Sequencing Project | Global | Study-wide | 13006 | C=0.46348 | T=0.53652 |
GO Exome Sequencing Project | European American | Sub | 8600 | C=0.2612 | T=0.7388 |
GO Exome Sequencing Project | African American | Sub | 4406 | C=0.8584 | T=0.1416 |
1000Genomes_30x | Global | Study-wide | 6404 | C=0.8212 | T=0.1788 |
1000Genomes_30x | African | Sub | 1786 | C=0.9720 | T=0.0280 |
1000Genomes_30x | Europe | Sub | 1266 | C=0.3673 | T=0.6327 |
1000Genomes_30x | South Asian | Sub | 1202 | C=0.9218 | T=0.0782 |
1000Genomes_30x | East Asian | Sub | 1170 | C=0.9991 | T=0.0009 |
1000Genomes_30x | American | Sub | 980 | C=0.797 | T=0.203 |
1000Genomes | Global | Study-wide | 5008 | C=0.8231 | T=0.1769 |
1000Genomes | African | Sub | 1322 | C=0.9720 | T=0.0280 |
1000Genomes | East Asian | Sub | 1008 | C=0.9990 | T=0.0010 |
1000Genomes | Europe | Sub | 1006 | C=0.3648 | T=0.6352 |
1000Genomes | South Asian | Sub | 978 | C=0.930 | T=0.070 |
1000Genomes | American | Sub | 694 | C=0.797 | T=0.203 |
Genetic variation in the Estonian population | Estonian | Study-wide | 4480 | C=0.0904 | T=0.9096 |
The Avon Longitudinal Study of Parents and Children | PARENT AND CHILD COHORT | Study-wide | 3854 | C=0.2314 | T=0.7686 |
UK 10K study - Twins | TWIN COHORT | Study-wide | 3708 | C=0.2306 | T=0.7694 |
KOREAN population from KRGDB | KOREAN | Study-wide | 2922 | C=0.9983 | T=0.0017 |
Genome of the Netherlands Release 5 | Genome of the Netherlands | Study-wide | 998 | C=0.120 | T=0.880 |
CNV burdens in cranial meningiomas | Global | Study-wide | 792 | C=0.994 | T=0.006 |
CNV burdens in cranial meningiomas | CRM | Sub | 792 | C=0.994 | T=0.006 |
Northern Sweden | ACPOP | Study-wide | 600 | C=0.133 | T=0.867 |
Medical Genome Project healthy controls from Spanish population | Spanish controls | Study-wide | 534 | C=0.670 | T=0.330 |
Qatari | Global | Study-wide | 216 | C=0.972 | T=0.028 |
SGDP_PRJ | Global | Study-wide | 128 | C=0.336 | T=0.664 |
Ancient Sardinia genome-wide 1240k capture data generation and analysis | Global | Study-wide | 50 | C=0.80 | T=0.20 |
Siberian | Global | Study-wide | 42 | C=0.14 | T=0.86 |
The Danish reference pan genome | Danish | Study-wide | 40 | C=0.10 | T=0.90 |
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.
Sequence name | Change |
---|---|
GRCh38.p14 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 |
GRCh38.p14 chr 15 fix patch HG2139_PATCH | NW_011332701.1:g.245178T>C |
GRCh38.p14 chr 15 alt locus HSCHR15_4_CTG8 | NT_187660.1:g.245178T>C |
Molecule type | Change | Amino acid[Codon] | SO Term |
---|---|---|---|
HERC2 transcript | NM_004667.6:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X3 | XM_017022695.1:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X1 | XM_006720726.4:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X2 | XM_047433206.1:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X4 | XM_017022696.2:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X5 | XM_005268276.6:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X6 | XM_006720727.4:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X7 | XM_047433207.1:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X10 | XM_017022697.2:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X11 | XM_017022698.2:c.*50= | N/A | 3 Prime UTR Variant |
HERC2 transcript variant X8 | XM_047433208.1:c. | N/A | Genic Downstream Transcript Variant |
HERC2 transcript variant X9 | XM_047433209.1:c. | N/A | Genic Downstream Transcript Variant |
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.
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 |
---|---|---|
GRCh38.p14 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_004667.6:c.*50= | NM_004667.6:c.*50G>A |
HERC2 transcript | NM_004667.5:c.*50= | NM_004667.5:c.*50G>A |
GRCh38.p14 chr 15 fix patch HG2139_PATCH | NW_011332701.1:g.245178T>C | NW_011332701.1:g.245178= |
GRCh38.p14 chr 15 alt locus HSCHR15_4_CTG8 | NT_187660.1:g.245178T>C | NT_187660.1:g.245178= |
HERC2 transcript variant X5 | XM_005268276.6:c.*50= | XM_005268276.6:c.*50G>A |
HERC2 transcript variant X3 | XM_005268276.5:c.*50= | XM_005268276.5:c.*50G>A |
HERC2 transcript variant X3 | XM_005268276.4:c.*50= | XM_005268276.4:c.*50G>A |
HERC2 transcript variant X5 | XM_005268276.3:c.*50= | XM_005268276.3:c.*50G>A |
HERC2 transcript variant X2 | XM_005268276.2:c.*50= | XM_005268276.2:c.*50G>A |
HERC2 transcript variant X2 | XM_005268276.1:c.*50= | XM_005268276.1:c.*50G>A |
HERC2 transcript variant X1 | XM_006720726.4:c.*50= | XM_006720726.4:c.*50G>A |
HERC2 transcript variant X1 | XM_006720726.3:c.*50= | XM_006720726.3:c.*50G>A |
HERC2 transcript variant X3 | XM_006720726.2:c.*50= | XM_006720726.2:c.*50G>A |
HERC2 transcript variant X4 | XM_006720726.1:c.*50= | XM_006720726.1:c.*50G>A |
HERC2 transcript variant X6 | XM_006720727.4:c.*50= | XM_006720727.4:c.*50G>A |
HERC2 transcript variant X5 | XM_006720727.3:c.*50= | XM_006720727.3:c.*50G>A |
HERC2 transcript variant X6 | XM_006720727.2:c.*50= | XM_006720727.2:c.*50G>A |
HERC2 transcript variant X5 | XM_006720727.1:c.*50= | XM_006720727.1:c.*50G>A |
HERC2 transcript variant X11 | XM_017022698.2:c.*50= | XM_017022698.2:c.*50G>A |
HERC2 transcript variant X9 | XM_017022698.1:c.*50= | XM_017022698.1:c.*50G>A |
HERC2 transcript variant X10 | XM_017022697.2:c.*50= | XM_017022697.2:c.*50G>A |
HERC2 transcript variant X8 | XM_017022697.1:c.*50= | XM_017022697.1:c.*50G>A |
HERC2 transcript variant X4 | XM_017022696.2:c.*50= | XM_017022696.2:c.*50G>A |
HERC2 transcript variant X4 | XM_017022696.1:c.*50= | XM_017022696.1:c.*50G>A |
HERC2 transcript variant X3 | XM_017022695.1:c.*50= | XM_017022695.1:c.*50G>A |
HERC2 transcript variant X2 | XM_047433206.1:c.*50= | XM_047433206.1:c.*50G>A |
HERC2 transcript variant X7 | XM_047433207.1:c.*50= | XM_047433207.1:c.*50G>A |
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#.
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 | ILLUMINA | ss2633208751 | Nov 08, 2017 (151) |
55 | ILLUMINA | ss2633208752 | Nov 08, 2017 (151) |
56 | ILLUMINA | ss2635056530 | Nov 08, 2017 (151) |
57 | GRF | ss2701147181 | Nov 08, 2017 (151) |
58 | GNOMAD | ss2741066596 | Nov 08, 2017 (151) |
59 | GNOMAD | ss2749249785 | Nov 08, 2017 (151) |
60 | AFFY | ss2985667529 | Nov 08, 2017 (151) |
61 | SWEGEN | ss3013006529 | Nov 08, 2017 (151) |
62 | ILLUMINA | ss3021616281 | Nov 08, 2017 (151) |
63 | BIOINF_KMB_FNS_UNIBA | ss3027969838 | Nov 08, 2017 (151) |
64 | CSHL | ss3351042076 | Nov 08, 2017 (151) |
65 | ILLUMINA | ss3625669091 | Oct 12, 2018 (152) |
66 | ILLUMINA | ss3627323420 | Oct 12, 2018 (152) |
67 | ILLUMINA | ss3631203071 | Oct 12, 2018 (152) |
68 | ILLUMINA | ss3633091654 | Oct 12, 2018 (152) |
69 | ILLUMINA | ss3633796005 | Oct 12, 2018 (152) |
70 | ILLUMINA | ss3634597982 | Oct 12, 2018 (152) |
71 | ILLUMINA | ss3635485077 | Oct 12, 2018 (152) |
72 | ILLUMINA | ss3636288261 | Oct 12, 2018 (152) |
73 | ILLUMINA | ss3637236308 | Oct 12, 2018 (152) |
74 | ILLUMINA | ss3638075914 | Oct 12, 2018 (152) |
75 | ILLUMINA | ss3640305309 | Oct 12, 2018 (152) |
76 | ILLUMINA | ss3644641631 | Oct 12, 2018 (152) |
77 | URBANLAB | ss3650317205 | Oct 12, 2018 (152) |
78 | ILLUMINA | ss3652015625 | Oct 12, 2018 (152) |
79 | EGCUT_WGS | ss3680178099 | Jul 13, 2019 (153) |
80 | EVA_DECODE | ss3697585124 | Jul 13, 2019 (153) |
81 | ILLUMINA | ss3725484789 | Jul 13, 2019 (153) |
82 | ACPOP | ss3740787447 | Jul 13, 2019 (153) |
83 | ILLUMINA | ss3744128674 | Jul 13, 2019 (153) |
84 | ILLUMINA | ss3744898547 | Jul 13, 2019 (153) |
85 | EVA | ss3752891708 | Jul 13, 2019 (153) |
86 | PAGE_CC | ss3771818497 | Jul 13, 2019 (153) |
87 | ILLUMINA | ss3772397263 | Jul 13, 2019 (153) |
88 | PACBIO | ss3787801144 | Jul 13, 2019 (153) |
89 | PACBIO | ss3792820374 | Jul 13, 2019 (153) |
90 | PACBIO | ss3797704835 | Jul 13, 2019 (153) |
91 | KHV_HUMAN_GENOMES | ss3818208906 | Jul 13, 2019 (153) |
92 | EVA | ss3824897077 | Apr 27, 2020 (154) |
93 | EVA | ss3825854761 | Apr 27, 2020 (154) |
94 | EVA | ss3834156877 | Apr 27, 2020 (154) |
95 | EVA | ss3840675178 | Apr 27, 2020 (154) |
96 | EVA | ss3846163960 | Apr 27, 2020 (154) |
97 | SGDP_PRJ | ss3882552837 | Apr 27, 2020 (154) |
98 | KRGDB | ss3931676982 | Apr 27, 2020 (154) |
99 | FSA-LAB | ss3984068275 | Apr 26, 2021 (155) |
100 | EVA | ss3984698658 | Apr 26, 2021 (155) |
101 | EVA | ss3985707114 | Apr 26, 2021 (155) |
102 | EVA | ss3986639176 | Apr 26, 2021 (155) |
103 | EVA | ss4017693132 | Apr 26, 2021 (155) |
104 | VINODS | ss4031999367 | Apr 26, 2021 (155) |
105 | TOPMED | ss4985731834 | Apr 26, 2021 (155) |
106 | TOMMO_GENOMICS | ss5215406657 | Apr 26, 2021 (155) |
107 | 1000G_HIGH_COVERAGE | ss5297861669 | Oct 16, 2022 (156) |
108 | EVA | ss5418197496 | Oct 16, 2022 (156) |
109 | HUGCELL_USP | ss5491677608 | Oct 16, 2022 (156) |
110 | EVA | ss5511382807 | Oct 16, 2022 (156) |
111 | 1000G_HIGH_COVERAGE | ss5598973479 | Oct 16, 2022 (156) |
112 | EVA | ss5624050714 | Oct 16, 2022 (156) |
113 | SANFORD_IMAGENETICS | ss5624356241 | Oct 16, 2022 (156) |
114 | SANFORD_IMAGENETICS | ss5657176093 | Oct 16, 2022 (156) |
115 | TOMMO_GENOMICS | ss5768982633 | Oct 16, 2022 (156) |
116 | EVA | ss5799933050 | Oct 16, 2022 (156) |
117 | EVA | ss5800191633 | Oct 16, 2022 (156) |
118 | YY_MCH | ss5815188601 | Oct 16, 2022 (156) |
119 | EVA | ss5827983806 | Oct 16, 2022 (156) |
120 | EVA | ss5847445866 | Oct 16, 2022 (156) |
121 | EVA | ss5847736189 | Oct 16, 2022 (156) |
122 | EVA | ss5848396513 | Oct 16, 2022 (156) |
123 | EVA | ss5875251401 | Oct 16, 2022 (156) |
124 | EVA | ss5936559600 | Oct 16, 2022 (156) |
125 | EVA | ss5948586582 | Oct 16, 2022 (156) |
126 | EVA | ss5979455539 | Oct 16, 2022 (156) |
127 | EVA | ss5980859189 | Oct 16, 2022 (156) |
128 | 1000Genomes | NC_000015.9 - 28356859 | Oct 12, 2018 (152) |
129 | 1000Genomes_30x | NC_000015.10 - 28111713 | Oct 16, 2022 (156) |
130 | The Avon Longitudinal Study of Parents and Children | NC_000015.9 - 28356859 | Oct 12, 2018 (152) |
131 | Genetic variation in the Estonian population | NC_000015.9 - 28356859 | Oct 12, 2018 (152) |
132 | ExAC | NC_000015.9 - 28356859 | Oct 12, 2018 (152) |
133 | The Danish reference pan genome | NC_000015.9 - 28356859 | Apr 27, 2020 (154) |
134 | gnomAD - Genomes | NC_000015.10 - 28111713 | Apr 26, 2021 (155) |
135 | gnomAD - Exomes | NC_000015.9 - 28356859 | Jul 13, 2019 (153) |
136 | GO Exome Sequencing Project | NC_000015.9 - 28356859 | Oct 12, 2018 (152) |
137 | Genome of the Netherlands Release 5 | NC_000015.9 - 28356859 | Apr 27, 2020 (154) |
138 | KOREAN population from KRGDB | NC_000015.9 - 28356859 | Apr 27, 2020 (154) |
139 | Medical Genome Project healthy controls from Spanish population | NC_000015.9 - 28356859 | Apr 27, 2020 (154) |
140 | Northern Sweden | NC_000015.9 - 28356859 | Jul 13, 2019 (153) |
141 | The PAGE Study | NC_000015.10 - 28111713 | Jul 13, 2019 (153) |
142 | Ancient Sardinia genome-wide 1240k capture data generation and analysis | NC_000015.9 - 28356859 | Apr 26, 2021 (155) |
143 | CNV burdens in cranial meningiomas | NC_000015.9 - 28356859 | Apr 26, 2021 (155) |
144 | Qatari | NC_000015.9 - 28356859 | Apr 27, 2020 (154) |
145 | SGDP_PRJ | NC_000015.9 - 28356859 | Apr 27, 2020 (154) |
146 | Siberian | NC_000015.9 - 28356859 | Apr 27, 2020 (154) |
147 | 8.3KJPN | NC_000015.9 - 28356859 | Apr 26, 2021 (155) |
148 | 14KJPN | NC_000015.10 - 28111713 | Oct 16, 2022 (156) |
149 | TopMed | NC_000015.10 - 28111713 | Apr 26, 2021 (155) |
150 | UK 10K study - Twins | NC_000015.9 - 28356859 | Oct 12, 2018 (152) |
151 | ALFA | NC_000015.10 - 28111713 | Apr 26, 2021 (155) |
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) |
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, 3792747, 10329962, 1354368, 16338483, 38854376, 505869, 14072312, 933041, 248179, 17063659, 34569817, 9204520, 73375964, 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, ss2633208751, ss2633208752, ss2701147181, ss2741066596, ss2749249785, 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, ss3824897077, ss3825854761, ss3834156877, ss3840675178, ss3882552837, ss3931676982, ss3984068275, ss3984698658, ss3985707114, ss3986639176, ss4017693132, ss5215406657, ss5418197496, ss5511382807, ss5624050714, ss5624356241, ss5657176093, ss5799933050, ss5800191633, ss5827983806, ss5847445866, ss5847736189, ss5848396513, ss5936559600, ss5948586582, ss5979455539, ss5980859189 | NC_000015.9:28356858:C:T | NC_000015.10:28111712:C:T | (self) |
86499414, 464287067, 1039966, 102819737, 201277494, 6705876281, ss2205531181, ss3027969838, ss3650317205, ss3697585124, ss3725484789, ss3771818497, ss3818208906, ss3846163960, ss4985731834, ss5297861669, ss5491677608, ss5598973479, ss5768982633, ss5815188601, ss5875251401 | 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) |
ss4031999367 | NT_187660.1:245177:T:T | NC_000015.10:28111712:C:T | (self) |
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
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 |
30306274 | Genome-wide association studies for corneal and refractive astigmatism in UK Biobank demonstrate a shared role for myopia susceptibility loci. | Shah RL et al. | 2018 | Human genetics |
33167923 | Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil. | Reis LB et al. | 2020 | BMC cancer |
33692100 | Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color. | Simcoe M et al. | 2021 | Science advances |
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genomic regions, transcripts, and products
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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.
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.