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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 Aliases 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.

rs1667394

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28285036 (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
C=0.43752 (54938/125568, TOPMED)
C=0.3531 (10943/30992, GnomAD)
T=0.380 (1901/5008, 1000G) (+ 3 more)
C=0.162 (623/3854, ALSPAC)
C=0.157 (583/3708, TWINSUK)
C=0.09 (53/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HERC2 : Intron Variant
Publications
12 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.28285036C>A
GRCh38.p12 chr 15 NC_000015.10:g.28285036C>T
GRCh37.p13 chr 15 NC_000015.9:g.28530182C>A
GRCh37.p13 chr 15 NC_000015.9:g.28530182C>T
HERC2 RefSeqGene NG_016355.1:g.42114G>T
HERC2 RefSeqGene NG_016355.1:g.42114G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.418481T>C
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.418481T>A
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.532267T>C
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.532267T>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.

Allele: T (allele ID: 19782 )
ClinVar Accession Disease Names Clinical Significance
RCV000005009.4 Skin/hair/eye pigmentation, variation in, 1 Association
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=0.43752 T=0.56248
gnomAD - Genomes Global Study-wide 30992 C=0.3531 T=0.6469
gnomAD - Genomes European Sub 18736 C=0.1159 T=0.8841
gnomAD - Genomes African Sub 8544 C=0.819 T=0.181
gnomAD - Genomes East Asian Sub 1528 C=0.735 T=0.265
gnomAD - Genomes Other Sub 1068 C=0.211 T=0.789
gnomAD - Genomes American Sub 826 C=0.42 T=0.58
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.27 T=0.73
1000Genomes Global Study-wide 5008 C=0.620 T=0.380
1000Genomes African Sub 1322 C=0.913 T=0.087
1000Genomes East Asian Sub 1008 C=0.729 T=0.271
1000Genomes Europe Sub 1006 C=0.244 T=0.756
1000Genomes South Asian Sub 978 C=0.63 T=0.37
1000Genomes American Sub 694 C=0.44 T=0.56
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.162 T=0.838
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.157 T=0.843
Northern Sweden ACPOP Study-wide 600 C=0.09 T=0.91
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.28285036=

NC_000015.10:g.28...

NC_000015.10:g.28285036C>A

NC_000015.10:g.28...

NC_000015.10:g.28285036C>T

GRCh37.p13 chr 15 NC_000015.9:g.285...

NC_000015.9:g.28530182=

NC_000015.9:g.285...

NC_000015.9:g.28530182C>A

NC_000015.9:g.285...

NC_000015.9:g.28530182C>T

HERC2 RefSeqGene NG_016355.1:g.42114= NG_016355.1:g.421...

NG_016355.1:g.42114G>T

NG_016355.1:g.421...

NG_016355.1:g.42114G>A

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

NW_011332701.1:g.418481T>C

NW_011332701.1:g....

NW_011332701.1:g.418481T>A

NW_011332701.1:g....

NW_011332701.1:g.418481=

GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.532...

NT_187660.1:g.532267T>C

NT_187660.1:g.532...

NT_187660.1:g.532267T>A

NT_187660.1:g.532...

NT_187660.1:g.532267=

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#.

123 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss2493439 Nov 09, 2000 (89)
2 SSAHASNP ss21262991 Apr 05, 2004 (121)
3 ABI ss40534750 Mar 13, 2006 (126)
4 ILLUMINA ss66831117 Dec 01, 2006 (127)
5 ILLUMINA ss67145528 Dec 01, 2006 (127)
6 ILLUMINA ss67487245 Dec 01, 2006 (127)
7 PERLEGEN ss69171501 May 18, 2007 (127)
8 ILLUMINA ss70447661 May 18, 2007 (127)
9 ILLUMINA ss70638736 May 25, 2008 (130)
10 ILLUMINA ss71189767 May 18, 2007 (127)
11 ILLUMINA ss75886860 Dec 06, 2007 (129)
12 KRIBB_YJKIM ss83858907 Dec 15, 2007 (130)
13 BCMHGSC_JDW ss90104113 Mar 24, 2008 (129)
14 HUMANGENOME_JCVI ss96746400 Feb 05, 2009 (130)
15 BGI ss103224383 Dec 01, 2009 (131)
16 1000GENOMES ss108696694 Jan 23, 2009 (130)
17 ILLUMINA ss121772795 Dec 01, 2009 (131)
18 ENSEMBL ss136931692 Dec 01, 2009 (131)
19 ILLUMINA ss153547499 Dec 01, 2009 (131)
20 ILLUMINA ss159291394 Dec 01, 2009 (131)
21 ILLUMINA ss160382025 Dec 01, 2009 (131)
22 ILLUMINA ss170704821 Jul 04, 2010 (132)
23 ILLUMINA ss172613222 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss207156077 Jul 04, 2010 (132)
25 1000GENOMES ss226813753 Jul 14, 2010 (132)
26 1000GENOMES ss236722894 Jul 15, 2010 (132)
27 1000GENOMES ss243120816 Jul 15, 2010 (132)
28 GMI ss282193312 May 04, 2012 (137)
29 GMI ss286924812 Apr 25, 2013 (138)
30 PJP ss291808428 May 09, 2011 (134)
31 ILLUMINA ss410908960 Sep 17, 2011 (135)
32 ILLUMINA ss480062333 May 04, 2012 (137)
33 ILLUMINA ss480071052 May 04, 2012 (137)
34 ILLUMINA ss480745335 Sep 08, 2015 (146)
35 ILLUMINA ss484829059 May 04, 2012 (137)
36 EXOME_CHIP ss491491456 May 04, 2012 (137)
37 ILLUMINA ss536904980 Sep 08, 2015 (146)
38 TISHKOFF ss564384359 Apr 25, 2013 (138)
39 SSMP ss660096472 Apr 25, 2013 (138)
40 ILLUMINA ss778816195 Sep 08, 2015 (146)
41 ILLUMINA ss780682209 Sep 08, 2015 (146)
42 ILLUMINA ss782861105 Aug 21, 2014 (142)
43 ILLUMINA ss783355552 Sep 08, 2015 (146)
44 ILLUMINA ss783825433 Sep 08, 2015 (146)
45 ILLUMINA ss825416394 Jul 19, 2016 (147)
46 ILLUMINA ss832115128 Apr 01, 2015 (144)
47 ILLUMINA ss832803503 Aug 21, 2014 (142)
48 ILLUMINA ss833394333 Aug 21, 2014 (142)
49 ILLUMINA ss834276502 Sep 08, 2015 (146)
50 EVA-GONL ss991625436 Aug 21, 2014 (142)
51 JMKIDD_LAB ss1080004263 Aug 21, 2014 (142)
52 1000GENOMES ss1352827675 Aug 21, 2014 (142)
53 HAMMER_LAB ss1397692518 Sep 08, 2015 (146)
54 DDI ss1427576175 Apr 01, 2015 (144)
55 OMIM-CURATED-RECORDS ss1505810803 Dec 08, 2014 (142)
56 EVA_GENOME_DK ss1577523254 Apr 01, 2015 (144)
57 EVA_UK10K_ALSPAC ss1632673531 Apr 01, 2015 (144)
58 EVA_UK10K_TWINSUK ss1675667564 Apr 01, 2015 (144)
59 EVA_DECODE ss1695637239 Apr 01, 2015 (144)
60 EVA_SVP ss1713477725 Apr 01, 2015 (144)
61 ILLUMINA ss1752154535 Sep 08, 2015 (146)
62 ILLUMINA ss1752154536 Sep 08, 2015 (146)
63 ILLUMINA ss1917893760 Feb 12, 2016 (147)
64 WEILL_CORNELL_DGM ss1935023014 Feb 12, 2016 (147)
65 ILLUMINA ss1946388565 Feb 12, 2016 (147)
66 ILLUMINA ss1959597666 Feb 12, 2016 (147)
67 GENOMED ss1968070905 Jul 19, 2016 (147)
68 JJLAB ss2028291460 Sep 14, 2016 (149)
69 ILLUMINA ss2094797606 Dec 20, 2016 (150)
70 ILLUMINA ss2095057524 Dec 20, 2016 (150)
71 USC_VALOUEV ss2156688545 Dec 20, 2016 (150)
72 TOPMED ss2370077749 Dec 20, 2016 (150)
73 SYSTEMSBIOZJU ss2628638998 Nov 08, 2017 (151)
74 ILLUMINA ss2633208829 Nov 08, 2017 (151)
75 ILLUMINA ss2633208830 Nov 08, 2017 (151)
76 ILLUMINA ss2633208831 Nov 08, 2017 (151)
77 ILLUMINA ss2635056534 Nov 08, 2017 (151)
78 GRF ss2701147811 Nov 08, 2017 (151)
79 GNOMAD ss2933005848 Nov 08, 2017 (151)
80 AFFY ss2985035159 Nov 08, 2017 (151)
81 AFFY ss2985667545 Nov 08, 2017 (151)
82 SWEGEN ss3013008343 Nov 08, 2017 (151)
83 ILLUMINA ss3021616434 Nov 08, 2017 (151)
84 BIOINF_KMB_FNS_UNIBA ss3027969935 Nov 08, 2017 (151)
85 TOPMED ss3223276086 Nov 08, 2017 (151)
86 TOPMED ss3223276087 Nov 08, 2017 (151)
87 CSHL ss3351042335 Nov 08, 2017 (151)
88 ILLUMINA ss3627323681 Oct 12, 2018 (152)
89 ILLUMINA ss3627323682 Oct 12, 2018 (152)
90 ILLUMINA ss3631203144 Oct 12, 2018 (152)
91 ILLUMINA ss3633091670 Oct 12, 2018 (152)
92 ILLUMINA ss3633796023 Oct 12, 2018 (152)
93 ILLUMINA ss3634598049 Oct 12, 2018 (152)
94 ILLUMINA ss3634598050 Oct 12, 2018 (152)
95 ILLUMINA ss3635485095 Oct 12, 2018 (152)
96 ILLUMINA ss3636288512 Oct 12, 2018 (152)
97 ILLUMINA ss3637236326 Oct 12, 2018 (152)
98 ILLUMINA ss3638076004 Oct 12, 2018 (152)
99 ILLUMINA ss3639051398 Oct 12, 2018 (152)
100 ILLUMINA ss3639530795 Oct 12, 2018 (152)
101 ILLUMINA ss3640305376 Oct 12, 2018 (152)
102 ILLUMINA ss3640305377 Oct 12, 2018 (152)
103 ILLUMINA ss3641057898 Oct 12, 2018 (152)
104 ILLUMINA ss3641353161 Oct 12, 2018 (152)
105 ILLUMINA ss3643060713 Oct 12, 2018 (152)
106 ILLUMINA ss3644641687 Oct 12, 2018 (152)
107 URBANLAB ss3650317321 Oct 12, 2018 (152)
108 ILLUMINA ss3652015781 Oct 12, 2018 (152)
109 ILLUMINA ss3652015782 Oct 12, 2018 (152)
110 ILLUMINA ss3653806888 Oct 12, 2018 (152)
111 EVA_DECODE ss3697586976 Jul 13, 2019 (153)
112 ILLUMINA ss3725484899 Jul 13, 2019 (153)
113 ACPOP ss3740788094 Jul 13, 2019 (153)
114 ILLUMINA ss3744417260 Jul 13, 2019 (153)
115 ILLUMINA ss3744898614 Jul 13, 2019 (153)
116 ILLUMINA ss3744898615 Jul 13, 2019 (153)
117 EVA ss3752892957 Jul 13, 2019 (153)
118 ILLUMINA ss3772397329 Jul 13, 2019 (153)
119 ILLUMINA ss3772397330 Jul 13, 2019 (153)
120 PACBIO ss3787801318 Jul 13, 2019 (153)
121 PACBIO ss3792820484 Jul 13, 2019 (153)
122 PACBIO ss3797704950 Jul 13, 2019 (153)
123 KHV_HUMAN_GENOMES ss3818210059 Jul 13, 2019 (153)
124 1000Genomes NC_000015.9 - 28530182 Oct 12, 2018 (152)
125 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28530182 Oct 12, 2018 (152)
126 gnomAD - Genomes NC_000015.9 - 28530182 Jul 13, 2019 (153)
127 Northern Sweden NC_000015.9 - 28530182 Jul 13, 2019 (153)
128 TopMed NC_000015.10 - 28285036 Oct 12, 2018 (152)
129 UK 10K study - Twins NC_000015.9 - 28530182 Oct 12, 2018 (152)
130 ClinVar RCV000005009.4 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)
rs58956823 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3223276086 NC_000015.10:28285035:C:A NC_000015.10:28285035:C:A (self)
ss90104113, ss108696694, ss207156077, ss282193312, ss286924812, ss291808428, ss410908960, ss480062333, ss825416394, ss1397692518, ss1695637239, ss1713477725, ss2635056534, ss3639051398, ss3639530795, ss3643060713 NC_000015.8:26203776:C:T NC_000015.10:28285035:C:T (self)
65875053, 36577869, 179713156, 14072959, 36577869, ss226813753, ss236722894, ss243120816, ss480071052, ss480745335, ss484829059, ss491491456, ss536904980, ss564384359, ss660096472, ss778816195, ss780682209, ss782861105, ss783355552, ss783825433, ss832115128, ss832803503, ss833394333, ss834276502, ss991625436, ss1080004263, ss1352827675, ss1427576175, ss1577523254, ss1632673531, ss1675667564, ss1752154535, ss1752154536, ss1917893760, ss1935023014, ss1946388565, ss1959597666, ss1968070905, ss2028291460, ss2094797606, ss2095057524, ss2156688545, ss2370077749, ss2628638998, ss2633208829, ss2633208830, ss2633208831, ss2701147811, ss2933005848, ss2985035159, ss2985667545, ss3013008343, ss3021616434, ss3351042335, ss3627323681, ss3627323682, ss3631203144, ss3633091670, ss3633796023, ss3634598049, ss3634598050, ss3635485095, ss3636288512, ss3637236326, ss3638076004, ss3640305376, ss3640305377, ss3641057898, ss3641353161, ss3644641687, ss3652015781, ss3652015782, ss3653806888, ss3740788094, ss3744417260, ss3744898614, ss3744898615, ss3752892957, ss3772397329, ss3772397330, ss3787801318, ss3792820484, ss3797704950 NC_000015.9:28530181:C:T NC_000015.10:28285035:C:T (self)
RCV000005009.4, 125957522, ss1505810803, ss3027969935, ss3223276087, ss3650317321, ss3697586976, ss3725484899, ss3818210059 NC_000015.10:28285035:C:T NC_000015.10:28285035:C:T (self)
ss21262991 NT_010280.16:895672:C:T NC_000015.10:28285035:C:T (self)
ss2493439, ss40534750, ss66831117, ss67145528, ss67487245, ss69171501, ss70447661, ss70638736, ss71189767, ss75886860, ss83858907, ss96746400, ss103224383, ss121772795, ss136931692, ss153547499, ss159291394, ss160382025, ss170704821, ss172613222 NT_026446.14:4965328:C:T NC_000015.10:28285035: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.

12 citations for rs1667394
PMID Title Author Year Journal
17952075 Genetic determinants of hair, eye and skin pigmentation in Europeans. Sulem P et al. 2007 Nature genetics
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
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
18483556 A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Han J et al. 2008 PLoS genetics
19863770 Moderate- to low-risk variant alleles of cutaneous malignancies and nevi: lessons from genome-wide association studies. Udayakumar D et al. 2009 Genome medicine
20546537 Genome-wide association studies of pigmentation and skin cancer: a review and meta-analysis. Gerstenblith MR et al. 2010 Pigment cell & melanoma research
20585627 Web-based, participant-driven studies yield novel genetic associations for common traits. Eriksson N et al. 2010 PLoS genetics
20876667 Genome-wide significant associations for variants with minor allele frequency of 5% or less--an overview: A HuGE review. Panagiotou OA et al. 2010 American journal of epidemiology
21533023 Adaptations to climate-mediated selective pressures in humans. Hancock AM et al. 2011 PLoS genetics
22065085 A global view of the OCA2-HERC2 region and pigmentation. Donnelly MP et al. 2012 Human 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
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.post308+0fe9b3b