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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.

rs916977

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28268218 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.42797 (53739/125568, TOPMED)
T=0.3474 (10882/31326, GnomAD)
C=0.389 (1946/5008, 1000G) (+ 5 more)
T=0.055 (245/4480, Estonian)
T=0.152 (584/3854, ALSPAC)
T=0.148 (549/3708, TWINSUK)
T=0.09 (52/600, NorthernSweden)
C=0.20 (42/210, Vietnamese)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HERC2 : Intron Variant
Publications
15 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.28268218T>C
GRCh38.p12 chr 15 NC_000015.10:g.28268218T>G
GRCh37.p13 chr 15 NC_000015.9:g.28513364T>C
GRCh37.p13 chr 15 NC_000015.9:g.28513364T>G
HERC2 RefSeqGene NG_016355.1:g.58932A>G
HERC2 RefSeqGene NG_016355.1:g.58932A>C
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.401663C>T
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.401663C>G
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.515449C>T
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.515449C>G
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: C (allele ID: 19783 )
ClinVar Accession Disease Names Clinical Significance
RCV000005010.5 Skin/hair/eye pigmentation, variation in, 1 Affects
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 T=0.42797 C=0.57203
gnomAD - Genomes Global Study-wide 31326 T=0.3474 C=0.6526
gnomAD - Genomes European Sub 18878 T=0.1110 C=0.8890
gnomAD - Genomes African Sub 8674 T=0.806 C=0.194
gnomAD - Genomes East Asian Sub 1556 T=0.738 C=0.262
gnomAD - Genomes Other Sub 1082 T=0.200 C=0.800
gnomAD - Genomes American Sub 846 T=0.41 C=0.59
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.27 C=0.73
1000Genomes Global Study-wide 5008 T=0.611 C=0.389
1000Genomes African Sub 1322 T=0.899 C=0.101
1000Genomes East Asian Sub 1008 T=0.728 C=0.272
1000Genomes Europe Sub 1006 T=0.234 C=0.766
1000Genomes South Asian Sub 978 T=0.62 C=0.38
1000Genomes American Sub 694 T=0.42 C=0.58
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.055 C=0.945
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.152 C=0.848
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.148 C=0.852
Northern Sweden ACPOP Study-wide 600 T=0.09 C=0.91
A Vietnamese Genetic Variation Database Global Study-wide 210 T=0.80 C=0.20
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 T= C G Note
GRCh38.p12 chr 15 NC_000015.10:g.28...

NC_000015.10:g.28268218=

NC_000015.10:g.28...

NC_000015.10:g.28268218T>C

NC_000015.10:g.28...

NC_000015.10:g.28268218T>G

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

NC_000015.9:g.28513364=

NC_000015.9:g.285...

NC_000015.9:g.28513364T>C

NC_000015.9:g.285...

NC_000015.9:g.28513364T>G

HERC2 RefSeqGene NG_016355.1:g.58932= NG_016355.1:g.589...

NG_016355.1:g.58932A>G

NG_016355.1:g.589...

NG_016355.1:g.58932A>C

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

NW_011332701.1:g.401663C>T

NW_011332701.1:g....

NW_011332701.1:g.401663=

NW_011332701.1:g....

NW_011332701.1:g.401663C>G

GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.515...

NT_187660.1:g.515449C>T

NT_187660.1:g.515...

NT_187660.1:g.515449=

NT_187660.1:g.515...

NT_187660.1:g.515449C>G

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#.

114 SubSNP, 8 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1352559 Oct 05, 2000 (86)
2 WI_SSAHASNP ss6820954 Feb 20, 2003 (111)
3 PERLEGEN ss23388292 Sep 20, 2004 (123)
4 ABI ss43791123 Mar 14, 2006 (126)
5 ILLUMINA ss65757427 Oct 13, 2006 (127)
6 AFFY ss66422663 Nov 29, 2006 (127)
7 PERLEGEN ss69171498 May 16, 2007 (127)
8 ILLUMINA ss75002265 Dec 07, 2007 (129)
9 AFFY ss76189315 Dec 07, 2007 (129)
10 KRIBB_YJKIM ss81444611 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss90104098 Mar 24, 2008 (129)
12 KRIBB_YJKIM ss102644582 Feb 06, 2009 (130)
13 BGI ss103224379 Dec 01, 2009 (131)
14 1000GENOMES ss108696677 Jan 23, 2009 (130)
15 ENSEMBL ss134210702 Dec 01, 2009 (131)
16 ENSEMBL ss136931700 Dec 01, 2009 (131)
17 ILLUMINA ss160967517 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss167717291 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss170885044 Jul 04, 2010 (132)
20 AFFY ss172753436 Jul 04, 2010 (132)
21 ILLUMINA ss174782821 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss207197517 Jul 04, 2010 (132)
23 1000GENOMES ss226813708 Jul 14, 2010 (132)
24 1000GENOMES ss236722879 Jul 15, 2010 (132)
25 1000GENOMES ss243120801 Jul 15, 2010 (132)
26 BL ss254862597 May 09, 2011 (134)
27 GMI ss282193275 May 04, 2012 (137)
28 GMI ss286924800 Apr 25, 2013 (138)
29 PJP ss291808413 May 09, 2011 (134)
30 ILLUMINA ss410956161 Sep 17, 2011 (135)
31 ILLUMINA ss481841317 May 04, 2012 (137)
32 ILLUMINA ss481873981 May 04, 2012 (137)
33 ILLUMINA ss482831298 Sep 08, 2015 (146)
34 ILLUMINA ss485715112 May 04, 2012 (137)
35 EXOME_CHIP ss491491443 May 04, 2012 (137)
36 ILLUMINA ss537576225 Sep 08, 2015 (146)
37 TISHKOFF ss564384300 Apr 25, 2013 (138)
38 SSMP ss660096420 Apr 25, 2013 (138)
39 ILLUMINA ss778632837 Sep 08, 2015 (146)
40 ILLUMINA ss780687198 Sep 08, 2015 (146)
41 ILLUMINA ss783303201 Sep 08, 2015 (146)
42 ILLUMINA ss783360745 Sep 08, 2015 (146)
43 ILLUMINA ss784255408 Sep 08, 2015 (146)
44 ILLUMINA ss832564572 Sep 08, 2015 (146)
45 ILLUMINA ss834090475 Sep 08, 2015 (146)
46 EVA-GONL ss991625369 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1080004190 Aug 21, 2014 (142)
48 1000GENOMES ss1352827202 Aug 21, 2014 (142)
49 HAMMER_LAB ss1397692517 Sep 08, 2015 (146)
50 DDI ss1427576144 Apr 01, 2015 (144)
51 EVA_GENOME_DK ss1577523243 Apr 01, 2015 (144)
52 EVA_UK10K_ALSPAC ss1632673333 Apr 01, 2015 (144)
53 EVA_UK10K_TWINSUK ss1675667366 Apr 01, 2015 (144)
54 EVA_DECODE ss1695637154 Apr 01, 2015 (144)
55 EVA_SVP ss1713477715 Apr 01, 2015 (144)
56 ILLUMINA ss1752154525 Sep 08, 2015 (146)
57 ILLUMINA ss1752154526 Sep 08, 2015 (146)
58 ILLUMINA ss1917893751 Feb 12, 2016 (147)
59 WEILL_CORNELL_DGM ss1935022909 Feb 12, 2016 (147)
60 ILLUMINA ss1946388556 Feb 12, 2016 (147)
61 ILLUMINA ss1959597649 Feb 12, 2016 (147)
62 GENOMED ss1968070894 Jul 19, 2016 (147)
63 JJLAB ss2028291433 Sep 14, 2016 (149)
64 ILLUMINA ss2094797605 Dec 20, 2016 (150)
65 ILLUMINA ss2095057523 Dec 20, 2016 (150)
66 USC_VALOUEV ss2156688498 Dec 20, 2016 (150)
67 HUMAN_LONGEVITY ss2205534972 Dec 20, 2016 (150)
68 TOPMED ss2370076727 Dec 20, 2016 (150)
69 SYSTEMSBIOZJU ss2628638981 Nov 08, 2017 (151)
70 ILLUMINA ss2633208817 Nov 08, 2017 (151)
71 GRF ss2701147731 Nov 08, 2017 (151)
72 GNOMAD ss2933004365 Nov 08, 2017 (151)
73 AFFY ss2985035149 Nov 08, 2017 (151)
74 AFFY ss2985667543 Nov 08, 2017 (151)
75 SWEGEN ss3013008112 Nov 08, 2017 (151)
76 ILLUMINA ss3021616418 Nov 08, 2017 (151)
77 BIOINF_KMB_FNS_UNIBA ss3027969927 Nov 08, 2017 (151)
78 TOPMED ss3223272918 Nov 08, 2017 (151)
79 TOPMED ss3223272919 Nov 08, 2017 (151)
80 CSHL ss3351042300 Nov 08, 2017 (151)
81 ILLUMINA ss3625669102 Oct 12, 2018 (152)
82 ILLUMINA ss3627323638 Oct 12, 2018 (152)
83 ILLUMINA ss3627323639 Oct 12, 2018 (152)
84 ILLUMINA ss3631203132 Oct 12, 2018 (152)
85 ILLUMINA ss3633091669 Oct 12, 2018 (152)
86 ILLUMINA ss3633796022 Oct 12, 2018 (152)
87 ILLUMINA ss3634598039 Oct 12, 2018 (152)
88 ILLUMINA ss3634598040 Oct 12, 2018 (152)
89 ILLUMINA ss3635485094 Oct 12, 2018 (152)
90 ILLUMINA ss3636288488 Oct 12, 2018 (152)
91 ILLUMINA ss3637236325 Oct 12, 2018 (152)
92 ILLUMINA ss3638075992 Oct 12, 2018 (152)
93 ILLUMINA ss3640305366 Oct 12, 2018 (152)
94 ILLUMINA ss3640305367 Oct 12, 2018 (152)
95 ILLUMINA ss3643060702 Oct 12, 2018 (152)
96 ILLUMINA ss3644641678 Oct 12, 2018 (152)
97 URBANLAB ss3650317314 Oct 12, 2018 (152)
98 ILLUMINA ss3652015764 Oct 12, 2018 (152)
99 ILLUMINA ss3652015765 Oct 12, 2018 (152)
100 ILLUMINA ss3653806877 Oct 12, 2018 (152)
101 EGCUT_WGS ss3680178688 Jul 13, 2019 (153)
102 EVA_DECODE ss3697586793 Jul 13, 2019 (153)
103 ILLUMINA ss3725484890 Jul 13, 2019 (153)
104 ACPOP ss3740788033 Jul 13, 2019 (153)
105 ILLUMINA ss3744417251 Jul 13, 2019 (153)
106 ILLUMINA ss3744898604 Jul 13, 2019 (153)
107 ILLUMINA ss3744898605 Jul 13, 2019 (153)
108 EVA ss3752892844 Jul 13, 2019 (153)
109 ILLUMINA ss3772397319 Jul 13, 2019 (153)
110 ILLUMINA ss3772397320 Jul 13, 2019 (153)
111 PACBIO ss3787801305 Jul 13, 2019 (153)
112 PACBIO ss3792820478 Jul 13, 2019 (153)
113 PACBIO ss3797704941 Jul 13, 2019 (153)
114 KHV_HUMAN_GENOMES ss3818209963 Jul 13, 2019 (153)
115 1000Genomes NC_000015.9 - 28513364 Oct 12, 2018 (152)
116 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28513364 Oct 12, 2018 (152)
117 Genetic variation in the Estonian population NC_000015.9 - 28513364 Oct 12, 2018 (152)
118 gnomAD - Genomes NC_000015.9 - 28513364 Jul 13, 2019 (153)
119 Northern Sweden NC_000015.9 - 28513364 Jul 13, 2019 (153)
120 TopMed NC_000015.10 - 28268218 Oct 12, 2018 (152)
121 UK 10K study - Twins NC_000015.9 - 28513364 Oct 12, 2018 (152)
122 A Vietnamese Genetic Variation Database NC_000015.9 - 28513364 Jul 13, 2019 (153)
123 ClinVar RCV000005010.5 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)
rs60705971 Feb 27, 2009 (130)
rs386620749 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66422663, ss76189315, ss90104098, ss108696677, ss160967517, ss167717291, ss170885044, ss172753436, ss207197517, ss254862597, ss282193275, ss286924800, ss291808413, ss481841317, ss1397692517, ss1695637154, ss1713477715, ss3643060702 NC_000015.8:26186958:T:C NC_000015.10:28268217:T:C (self)
65874562, 36577650, 25916936, 179711845, 14072898, 36577650, 8138433, ss226813708, ss236722879, ss243120801, ss481873981, ss482831298, ss485715112, ss491491443, ss537576225, ss564384300, ss660096420, ss778632837, ss780687198, ss783303201, ss783360745, ss784255408, ss832564572, ss834090475, ss991625369, ss1080004190, ss1352827202, ss1427576144, ss1577523243, ss1632673333, ss1675667366, ss1752154525, ss1752154526, ss1917893751, ss1935022909, ss1946388556, ss1959597649, ss1968070894, ss2028291433, ss2094797605, ss2095057523, ss2156688498, ss2370076727, ss2628638981, ss2633208817, ss2701147731, ss2933004365, ss2985035149, ss2985667543, ss3013008112, ss3021616418, ss3351042300, ss3625669102, ss3627323638, ss3627323639, ss3631203132, ss3633091669, ss3633796022, ss3634598039, ss3634598040, ss3635485094, ss3636288488, ss3637236325, ss3638075992, ss3640305366, ss3640305367, ss3644641678, ss3652015764, ss3652015765, ss3653806877, ss3680178688, ss3740788033, ss3744417251, ss3744898604, ss3744898605, ss3752892844, ss3772397319, ss3772397320, ss3787801305, ss3792820478, ss3797704941 NC_000015.9:28513363:T:C NC_000015.10:28268217:T:C (self)
RCV000005010.5, 125954857, ss2205534972, ss3027969927, ss3223272918, ss3650317314, ss3697586793, ss3725484890, ss3818209963 NC_000015.10:28268217:T:C NC_000015.10:28268217:T:C (self)
ss1352559, ss6820954, ss23388292, ss43791123, ss65757427, ss69171498, ss75002265, ss81444611, ss102644582, ss103224379, ss134210702, ss136931700, ss174782821, ss410956161 NT_026446.14:4948510:T:C NC_000015.10:28268217:T:C (self)
ss3223272919 NC_000015.10:28268217:T:G NC_000015.10:28268217:T:G (self)
Help

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

15 citations for rs916977
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
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
19068216 Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Anderson CA et al. 2009 Gastroenterology
19174780 Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort. Weersma RK et al. 2009 The American journal of gastroenterology
19915572 Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. UK IBD Genetics Consortium. et al. 2009 Nature genetics
20042077 Genetic determinants of hair and eye colours in the Scottish and Danish populations. Mengel-From J et al. 2009 BMC genetics
20176734 Comparative genetic analysis of inflammatory bowel disease and type 1 diabetes implicates multiple loci with opposite effects. Wang K et al. 2010 Human molecular genetics
20650992 Association of inflammatory bowel disease risk loci with sarcoidosis, and its acute and chronic subphenotypes. Fischer A et al. 2011 The European respiratory journal
21197618 Model-based prediction of human hair color using DNA variants. Branicki W et al. 2011 Human genetics
22065085 A global view of the OCA2-HERC2 region and pigmentation. Donnelly MP et al. 2012 Human genetics
23300620 Genotype/phenotype analyses for 53 Crohn's disease associated genetic polymorphisms. Jung C et al. 2012 PloS one
26547235 Crowdsourced direct-to-consumer genomic analysis of a family quartet. Corpas M et al. 2015 BMC genomics
27499155 Genetic markers of pigmentation are novel risk loci for uveal melanoma. Ferguson R et al. 2016 Scientific reports
28456133 Variants at the OCA2/HERC2 locus affect time to first cutaneous squamous cell carcinoma in solid organ transplant recipients collected using two different study designs. Wei L et al. 2017 The British journal of dermatology

Genomic regions, transcripts, and products
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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