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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.

rs16950987

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28281082 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.25516 (32040/125568, TOPMED)
A=0.2122 (6649/31328, GnomAD)
A=0.333 (1666/5008, 1000G) (+ 5 more)
A=0.012 (53/4480, Estonian)
A=0.057 (218/3854, ALSPAC)
A=0.051 (188/3708, TWINSUK)
A=0.03 (16/600, NorthernSweden)
A=0.48 (100/210, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HERC2 : Intron Variant
Publications
4 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.28281082G>A
GRCh37.p13 chr 15 NC_000015.9:g.28526228G>A
HERC2 RefSeqGene NG_016355.1:g.46068C>T
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.414527G>A
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.528313G>A
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 Intron Variant
HERC2 transcript variant X3 XM_005268276.5:c. N/A Intron Variant
HERC2 transcript variant X1 XM_006720726.3:c. N/A Intron Variant
HERC2 transcript variant X5 XM_006720727.3:c. N/A Intron Variant
HERC2 transcript variant X2 XM_017022695.1:c. N/A Intron Variant
HERC2 transcript variant X4 XM_017022696.1:c. N/A Intron Variant
HERC2 transcript variant X8 XM_017022697.1:c. N/A Genic Upstream Transcript Variant
HERC2 transcript variant X9 XM_017022698.1:c. N/A Genic Upstream Transcript Variant
HERC2 transcript variant X7 XR_001751410.1:n. N/A Intron Variant
HERC2 transcript variant X6 XR_931930.2: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 G=0.74484 A=0.25516
gnomAD - Genomes Global Study-wide 31328 G=0.7878 A=0.2122
gnomAD - Genomes European Sub 18882 G=0.9586 A=0.0414
gnomAD - Genomes African Sub 8682 G=0.422 A=0.578
gnomAD - Genomes East Asian Sub 1544 G=0.588 A=0.412
gnomAD - Genomes Other Sub 1084 G=0.905 A=0.095
gnomAD - Genomes American Sub 846 G=0.89 A=0.11
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.93 A=0.07
1000Genomes Global Study-wide 5008 G=0.667 A=0.333
1000Genomes African Sub 1322 G=0.343 A=0.657
1000Genomes East Asian Sub 1008 G=0.612 A=0.388
1000Genomes Europe Sub 1006 G=0.910 A=0.090
1000Genomes South Asian Sub 978 G=0.77 A=0.23
1000Genomes American Sub 694 G=0.87 A=0.13
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.988 A=0.012
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.943 A=0.057
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.949 A=0.051
Northern Sweden ACPOP Study-wide 600 G=0.97 A=0.03
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.52 A=0.48
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= A Note
GRCh38.p12 chr 15 NC_000015.10:g.28281082= NC_000015.10:g.28281082G>A
GRCh37.p13 chr 15 NC_000015.9:g.28526228= NC_000015.9:g.28526228G>A
HERC2 RefSeqGene NG_016355.1:g.46068= NG_016355.1:g.46068C>T
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.414527= NW_011332701.1:g.414527G>A
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.528313= NT_187660.1:g.528313G>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#.

63 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23973309 Sep 20, 2004 (123)
2 ILLUMINA ss66831565 Nov 29, 2006 (127)
3 ILLUMINA ss67160528 Nov 29, 2006 (127)
4 ILLUMINA ss67509784 Nov 29, 2006 (127)
5 PERLEGEN ss69171500 May 16, 2007 (127)
6 ILLUMINA ss70449213 May 16, 2007 (127)
7 ILLUMINA ss70646301 May 26, 2008 (130)
8 ILLUMINA ss71201004 May 16, 2007 (127)
9 ILLUMINA ss75867652 Dec 06, 2007 (129)
10 HGSV ss82395713 Dec 15, 2007 (130)
11 HGSV ss84707232 Dec 15, 2007 (130)
12 KRIBB_YJKIM ss85340978 Dec 15, 2007 (130)
13 1000GENOMES ss113955455 Jan 25, 2009 (130)
14 ILLUMINA-UK ss118172310 Feb 14, 2009 (130)
15 ILLUMINA ss121779822 Dec 01, 2009 (131)
16 ILLUMINA ss153583384 Dec 01, 2009 (131)
17 GMI ss156361723 Dec 01, 2009 (131)
18 ILLUMINA ss159299416 Dec 01, 2009 (131)
19 ILLUMINA ss161050666 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss168988415 Jul 04, 2010 (132)
21 ILLUMINA ss170727314 Jul 04, 2010 (132)
22 ILLUMINA ss172676153 Jul 04, 2010 (132)
23 BUSHMAN ss200656023 Jul 04, 2010 (132)
24 1000GENOMES ss226813738 Jul 14, 2010 (132)
25 1000GENOMES ss236722891 Jul 15, 2010 (132)
26 1000GENOMES ss243120813 Jul 15, 2010 (132)
27 GMI ss282193309 May 04, 2012 (137)
28 PJP ss291808426 May 09, 2011 (134)
29 ILLUMINA ss479401694 Sep 08, 2015 (146)
30 TISHKOFF ss564384341 Apr 25, 2013 (138)
31 SSMP ss660096461 Apr 25, 2013 (138)
32 ILLUMINA ss825417946 Apr 01, 2015 (144)
33 ILLUMINA ss832811502 Jul 13, 2019 (153)
34 EVA-GONL ss991625415 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1080004243 Aug 21, 2014 (142)
36 1000GENOMES ss1352827566 Aug 21, 2014 (142)
37 DDI ss1427576171 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1632673483 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1675667516 Apr 01, 2015 (144)
40 EVA_DECODE ss1695637214 Apr 01, 2015 (144)
41 EVA_SVP ss1713477724 Apr 01, 2015 (144)
42 HAMMER_LAB ss1808131864 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1935022984 Feb 12, 2016 (147)
44 JJLAB ss2028291452 Sep 14, 2016 (149)
45 USC_VALOUEV ss2156688542 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2205535514 Dec 20, 2016 (150)
47 TOPMED ss2370077501 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2628638994 Nov 08, 2017 (151)
49 GRF ss2701147803 Nov 08, 2017 (151)
50 GNOMAD ss2933005498 Nov 08, 2017 (151)
51 SWEGEN ss3013008303 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3027969933 Nov 08, 2017 (151)
53 TOPMED ss3223275269 Nov 08, 2017 (151)
54 ILLUMINA ss3636288506 Oct 12, 2018 (152)
55 ILLUMINA ss3638076003 Oct 12, 2018 (152)
56 ILLUMINA ss3639051397 Oct 12, 2018 (152)
57 ILLUMINA ss3639530794 Oct 12, 2018 (152)
58 ILLUMINA ss3643060712 Oct 12, 2018 (152)
59 EGCUT_WGS ss3680178786 Jul 13, 2019 (153)
60 EVA_DECODE ss3697586920 Jul 13, 2019 (153)
61 ACPOP ss3740788080 Jul 13, 2019 (153)
62 EVA ss3752892936 Jul 13, 2019 (153)
63 KHV_HUMAN_GENOMES ss3818210034 Jul 13, 2019 (153)
64 1000Genomes NC_000015.9 - 28526228 Oct 12, 2018 (152)
65 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28526228 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000015.9 - 28526228 Oct 12, 2018 (152)
67 gnomAD - Genomes NC_000015.9 - 28526228 Jul 13, 2019 (153)
68 Northern Sweden NC_000015.9 - 28526228 Jul 13, 2019 (153)
69 TopMed NC_000015.10 - 28281082 Oct 12, 2018 (152)
70 UK 10K study - Twins NC_000015.9 - 28526228 Oct 12, 2018 (152)
71 A Vietnamese Genetic Variation Database NC_000015.9 - 28526228 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)
rs60588104 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss82395713, ss84707232, ss113955455, ss118172310, ss168988415, ss200656023, ss282193309, ss291808426, ss825417946, ss1695637214, ss1713477724, ss3639051397, ss3639530794, ss3643060712 NC_000015.8:26199822:G:A NC_000015.10:28281081:G:A (self)
65874938, 36577816, 25917034, 179712812, 14072945, 36577816, 8138467, ss226813738, ss236722891, ss243120813, ss479401694, ss564384341, ss660096461, ss832811502, ss991625415, ss1080004243, ss1352827566, ss1427576171, ss1632673483, ss1675667516, ss1808131864, ss1935022984, ss2028291452, ss2156688542, ss2370077501, ss2628638994, ss2701147803, ss2933005498, ss3013008303, ss3636288506, ss3638076003, ss3680178786, ss3740788080, ss3752892936 NC_000015.9:28526227:G:A NC_000015.10:28281081:G:A (self)
125956888, ss2205535514, ss3027969933, ss3223275269, ss3697586920, ss3818210034 NC_000015.10:28281081:G:A NC_000015.10:28281081:G:A (self)
ss23973309, ss66831565, ss67160528, ss67509784, ss69171500, ss70449213, ss70646301, ss71201004, ss75867652, ss85340978, ss121779822, ss153583384, ss156361723, ss159299416, ss161050666, ss170727314, ss172676153 NT_026446.14:4961374:G:A NC_000015.10:28281081:G:A (self)
Help

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

4 citations for rs16950987
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
18483556 A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Han J et al. 2008 PLoS genetics
20585627 Web-based, participant-driven studies yield novel genetic associations for common traits. Eriksson N et al. 2010 PLoS genetics
23118974 Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four European populations. Candille SI et al. 2012 PloS one

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