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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.

rs11636232

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28141480 (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=0.24877 (62555/251456, GnomAD_exome)
T=0.23067 (28965/125568, TOPMED)
T=0.25423 (30858/121378, ExAC) (+ 6 more)
T=0.2957 (9255/31296, GnomAD)
T=0.2793 (3632/13006, GO-ESP)
T=0.086 (429/5008, 1000G)
T=0.391 (1506/3854, ALSPAC)
T=0.404 (1498/3708, TWINSUK)
T=0.48 (290/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HERC2 : Synonymous Variant
Publications
5 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.28141480C>T
GRCh37.p13 chr 15 NC_000015.9:g.28386626C>T
HERC2 RefSeqGene NG_016355.1:g.185670G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.274922C>T
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.274922C>T
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.11967G>A Q [CAG] > Q [CAA] Coding Sequence Variant
E3 ubiquitin-protein ligase HERC2 NP_004658.3:p.Gln3989= Q (Gln) > Q (Gln) Synonymous Variant
HERC2 transcript variant X1 XM_006720726.3:c.11952G>A Q [CAG] > Q [CAA] Coding Sequence Variant
E3 ubiquitin-protein ligase HERC2 isoform X1 XP_006720789.1:p.Gln3984= Q (Gln) > Q (Gln) Synonymous Variant
HERC2 transcript variant X2 XM_017022695.1:c.11853G>A Q [CAG] > Q [CAA] Coding Sequence Variant
E3 ubiquitin-protein ligase HERC2 isoform X2 XP_016878184.1:p.Gln3951= Q (Gln) > Q (Gln) Synonymous Variant
HERC2 transcript variant X4 XM_017022696.1:c.11853G>A Q [CAG] > Q [CAA] Coding Sequence Variant
E3 ubiquitin-protein ligase HERC2 isoform X2 XP_016878185.1:p.Gln3951= Q (Gln) > Q (Gln) Synonymous Variant
HERC2 transcript variant X5 XM_006720727.3:c.11709G>A Q [CAG] > Q [CAA] Coding Sequence Variant
E3 ubiquitin-protein ligase HERC2 isoform X3 XP_006720790.1:p.Gln3903= Q (Gln) > Q (Gln) Synonymous Variant
HERC2 transcript variant X8 XM_017022697.1:c.5133G>A Q [CAG] > Q [CAA] Coding Sequence Variant
E3 ubiquitin-protein ligase HERC2 isoform X4 XP_016878186.1:p.Gln1711= Q (Gln) > Q (Gln) Synonymous Variant
HERC2 transcript variant X9 XM_017022698.1:c.5133G>A Q [CAG] > Q [CAA] Coding Sequence Variant
E3 ubiquitin-protein ligase HERC2 isoform X4 XP_016878187.1:p.Gln1711= Q (Gln) > Q (Gln) Synonymous Variant
HERC2 transcript variant X3 XM_005268276.5:c.11853G>A Q [CAG] > Q [CAA] Coding Sequence Variant
E3 ubiquitin-protein ligase HERC2 isoform X2 XP_005268333.1:p.Gln3951= Q (Gln) > Q (Gln) Synonymous 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251456 C=0.75123 T=0.24877
gnomAD - Exomes European Sub 135384 C=0.59336 T=0.40664
gnomAD - Exomes Asian Sub 49010 C=0.9835 T=0.0165
gnomAD - Exomes American Sub 34592 C=0.9304 T=0.0696
gnomAD - Exomes African Sub 16256 C=0.9376 T=0.0624
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=0.8262 T=0.1738
gnomAD - Exomes Other Sub 6134 C=0.753 T=0.247
TopMed Global Study-wide 125568 C=0.76933 T=0.23067
ExAC Global Study-wide 121378 C=0.74577 T=0.25423
ExAC Europe Sub 73326 C=0.6065 T=0.3935
ExAC Asian Sub 25166 C=0.9827 T=0.0173
ExAC American Sub 11572 C=0.9421 T=0.0579
ExAC African Sub 10406 C=0.9336 T=0.0664
ExAC Other Sub 908 C=0.77 T=0.23
gnomAD - Genomes Global Study-wide 31296 C=0.7043 T=0.2957
gnomAD - Genomes European Sub 18822 C=0.5678 T=0.4322
gnomAD - Genomes African Sub 8700 C=0.934 T=0.066
gnomAD - Genomes East Asian Sub 1552 C=1.000 T=0.000
gnomAD - Genomes Other Sub 1086 C=0.619 T=0.381
gnomAD - Genomes American Sub 846 C=0.90 T=0.10
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.83 T=0.17
GO Exome Sequencing Project Global Study-wide 13006 C=0.7207 T=0.2793
GO Exome Sequencing Project European American Sub 8600 C=0.618 T=0.382
GO Exome Sequencing Project African American Sub 4406 C=0.922 T=0.078
1000Genomes Global Study-wide 5008 C=0.914 T=0.086
1000Genomes African Sub 1322 C=0.985 T=0.015
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.678 T=0.322
1000Genomes South Asian Sub 978 C=0.98 T=0.02
1000Genomes American Sub 694 C=0.91 T=0.09
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.609 T=0.391
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.596 T=0.404
Northern Sweden ACPOP Study-wide 600 C=0.52 T=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 C= T Note
GRCh38.p12 chr 15 NC_000015.10:g.28141480= NC_000015.10:g.28141480C>T
GRCh37.p13 chr 15 NC_000015.9:g.28386626= NC_000015.9:g.28386626C>T
HERC2 RefSeqGene NG_016355.1:g.185670= NG_016355.1:g.185670G>A
HERC2 transcript NM_004667.5:c.11967= NM_004667.5:c.11967G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.274922= NW_011332701.1:g.274922C>T
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.274922= NT_187660.1:g.274922C>T
HERC2 transcript variant X3 XM_005268276.5:c.11853= XM_005268276.5:c.11853G>A
HERC2 transcript variant X2 XM_005268276.1:c.11853= XM_005268276.1:c.11853G>A
HERC2 transcript variant X1 XM_006720726.3:c.11952= XM_006720726.3:c.11952G>A
HERC2 transcript variant X5 XM_006720727.3:c.11709= XM_006720727.3:c.11709G>A
HERC2 transcript variant X2 XM_017022695.1:c.11853= XM_017022695.1:c.11853G>A
HERC2 transcript variant X4 XM_017022696.1:c.11853= XM_017022696.1:c.11853G>A
HERC2 transcript variant X8 XM_017022697.1:c.5133= XM_017022697.1:c.5133G>A
HERC2 transcript variant X9 XM_017022698.1:c.5133= XM_017022698.1:c.5133G>A
E3 ubiquitin-protein ligase HERC2 NP_004658.3:p.Gln3989= NP_004658.3:p.Gln3989=
E3 ubiquitin-protein ligase HERC2 isoform X2 XP_005268333.1:p.Gln3951= XP_005268333.1:p.Gln3951=
E3 ubiquitin-protein ligase HERC2 isoform X1 XP_006720789.1:p.Gln3984= XP_006720789.1:p.Gln3984=
E3 ubiquitin-protein ligase HERC2 isoform X3 XP_006720790.1:p.Gln3903= XP_006720790.1:p.Gln3903=
E3 ubiquitin-protein ligase HERC2 isoform X2 XP_016878184.1:p.Gln3951= XP_016878184.1:p.Gln3951=
E3 ubiquitin-protein ligase HERC2 isoform X2 XP_016878185.1:p.Gln3951= XP_016878185.1:p.Gln3951=
E3 ubiquitin-protein ligase HERC2 isoform X4 XP_016878186.1:p.Gln1711= XP_016878186.1:p.Gln1711=
E3 ubiquitin-protein ligase HERC2 isoform X4 XP_016878187.1:p.Gln1711= XP_016878187.1:p.Gln1711=
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#.

92 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16684473 Feb 28, 2004 (120)
2 ILLUMINA ss66939019 Nov 30, 2006 (127)
3 ILLUMINA ss67100009 Nov 30, 2006 (127)
4 ILLUMINA ss68108492 Dec 12, 2006 (127)
5 PERLEGEN ss69171493 May 17, 2007 (127)
6 ILLUMINA ss70533579 May 26, 2008 (130)
7 ILLUMINA ss71064629 May 17, 2007 (127)
8 ILLUMINA ss75638073 Dec 06, 2007 (129)
9 KRIBB_YJKIM ss85110528 Dec 16, 2007 (130)
10 CANCER-GENOME ss86348004 Mar 23, 2008 (129)
11 BCMHGSC_JDW ss90104047 Mar 24, 2008 (129)
12 1000GENOMES ss108696554 Jan 23, 2009 (130)
13 ENSEMBL ss134210515 Dec 01, 2009 (131)
14 ILLUMINA ss153014396 Dec 01, 2009 (131)
15 ILLUMINA ss159180288 Dec 01, 2009 (131)
16 SEATTLESEQ ss159730256 Dec 01, 2009 (131)
17 ILLUMINA ss159988197 Dec 01, 2009 (131)
18 ENSEMBL ss161704167 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167716939 Jul 04, 2010 (132)
20 ILLUMINA ss171369417 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss207366471 Jul 04, 2010 (132)
22 1000GENOMES ss236722789 Jul 15, 2010 (132)
23 BL ss254862460 May 09, 2011 (134)
24 GMI ss286924772 Apr 25, 2013 (138)
25 NHLBI-ESP ss342398493 May 09, 2011 (134)
26 ILLUMINA ss410894210 Sep 17, 2011 (135)
27 ILLUMINA ss479548078 May 04, 2012 (137)
28 ILLUMINA ss479552115 May 04, 2012 (137)
29 ILLUMINA ss480018686 Sep 08, 2015 (146)
30 ILLUMINA ss484572876 May 04, 2012 (137)
31 1000GENOMES ss491078439 May 04, 2012 (137)
32 CLINSEQ_SNP ss491696484 May 04, 2012 (137)
33 ILLUMINA ss536706460 Sep 08, 2015 (146)
34 SSMP ss660096010 Apr 25, 2013 (138)
35 ILLUMINA ss778761269 Sep 08, 2015 (146)
36 ILLUMINA ss782733217 Sep 08, 2015 (146)
37 ILLUMINA ss783700396 Sep 08, 2015 (146)
38 ILLUMINA ss831985007 Sep 08, 2015 (146)
39 ILLUMINA ss832692799 Jul 13, 2019 (153)
40 ILLUMINA ss834221035 Sep 08, 2015 (146)
41 JMKIDD_LAB ss974490408 Aug 21, 2014 (142)
42 EVA-GONL ss991624704 Aug 21, 2014 (142)
43 JMKIDD_LAB ss1067550326 Aug 21, 2014 (142)
44 JMKIDD_LAB ss1080003682 Aug 21, 2014 (142)
45 1000GENOMES ss1352823367 Aug 21, 2014 (142)
46 EVA_GENOME_DK ss1577523170 Apr 01, 2015 (144)
47 EVA_FINRISK ss1584092721 Apr 01, 2015 (144)
48 EVA_UK10K_ALSPAC ss1632672082 Apr 01, 2015 (144)
49 EVA_UK10K_TWINSUK ss1675666115 Apr 01, 2015 (144)
50 EVA_EXAC ss1691718392 Apr 01, 2015 (144)
51 EVA_DECODE ss1695636422 Apr 01, 2015 (144)
52 EVA_MGP ss1711390137 Apr 01, 2015 (144)
53 EVA_SVP ss1713477682 Apr 01, 2015 (144)
54 ILLUMINA ss1752154489 Sep 08, 2015 (146)
55 WEILL_CORNELL_DGM ss1935021929 Feb 12, 2016 (147)
56 JJLAB ss2028291219 Sep 14, 2016 (149)
57 USC_VALOUEV ss2156688259 Dec 20, 2016 (150)
58 TOPMED ss2370068700 Dec 20, 2016 (150)
59 ILLUMINA ss2633208782 Nov 08, 2017 (151)
60 ILLUMINA ss2635056532 Nov 08, 2017 (151)
61 GRF ss2701147293 Nov 08, 2017 (151)
62 GNOMAD ss2741067633 Nov 08, 2017 (151)
63 GNOMAD ss2749250094 Nov 08, 2017 (151)
64 GNOMAD ss2932993282 Nov 08, 2017 (151)
65 SWEGEN ss3013006819 Nov 08, 2017 (151)
66 EVA_SAMSUNG_MC ss3023068939 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3027969887 Nov 08, 2017 (151)
68 TOPMED ss3223248304 Nov 08, 2017 (151)
69 CSHL ss3351042153 Nov 08, 2017 (151)
70 ILLUMINA ss3625669094 Oct 12, 2018 (152)
71 ILLUMINA ss3627323488 Oct 12, 2018 (152)
72 ILLUMINA ss3631203099 Oct 12, 2018 (152)
73 ILLUMINA ss3633091662 Oct 12, 2018 (152)
74 ILLUMINA ss3633796013 Oct 12, 2018 (152)
75 ILLUMINA ss3634598002 Oct 12, 2018 (152)
76 ILLUMINA ss3635485085 Oct 12, 2018 (152)
77 ILLUMINA ss3636288327 Oct 12, 2018 (152)
78 ILLUMINA ss3637236316 Oct 12, 2018 (152)
79 ILLUMINA ss3638075944 Oct 12, 2018 (152)
80 ILLUMINA ss3639051388 Oct 12, 2018 (152)
81 ILLUMINA ss3639835017 Oct 12, 2018 (152)
82 ILLUMINA ss3640305329 Oct 12, 2018 (152)
83 ILLUMINA ss3641057880 Oct 12, 2018 (152)
84 ILLUMINA ss3641353146 Oct 12, 2018 (152)
85 ILLUMINA ss3643060651 Oct 12, 2018 (152)
86 ILLUMINA ss3643885261 Oct 12, 2018 (152)
87 EVA_DECODE ss3697585478 Jul 13, 2019 (153)
88 ACPOP ss3740787576 Jul 13, 2019 (153)
89 ILLUMINA ss3744898567 Jul 13, 2019 (153)
90 EVA ss3752891961 Jul 13, 2019 (153)
91 ILLUMINA ss3772397283 Jul 13, 2019 (153)
92 KHV_HUMAN_GENOMES ss3818209083 Jul 13, 2019 (153)
93 1000Genomes NC_000015.9 - 28386626 Oct 12, 2018 (152)
94 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28386626 Oct 12, 2018 (152)
95 ExAC NC_000015.9 - 28386626 Oct 12, 2018 (152)
96 gnomAD - Genomes NC_000015.9 - 28386626 Jul 13, 2019 (153)
97 gnomAD - Exomes NC_000015.9 - 28386626 Jul 13, 2019 (153)
98 GO Exome Sequencing Project NC_000015.9 - 28386626 Oct 12, 2018 (152)
99 Northern Sweden NC_000015.9 - 28386626 Jul 13, 2019 (153)
100 TopMed NC_000015.10 - 28141480 Oct 12, 2018 (152)
101 UK 10K study - Twins NC_000015.9 - 28386626 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)
rs61223686 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss90104047, ss108696554, ss167716939, ss207366471, ss254862460, ss286924772, ss479548078, ss491696484, ss1695636422, ss1713477682, ss2635056532, ss3639051388, ss3639835017, ss3643060651, ss3643885261 NC_000015.8:26060220:C:T NC_000015.10:28141479:C:T (self)
65870602, 36576275, 2083225, 179701344, 10331083, 1354538, 14072441, 36576275, ss236722789, ss342398493, ss479552115, ss480018686, ss484572876, ss491078439, ss536706460, ss660096010, ss778761269, ss782733217, ss783700396, ss831985007, ss832692799, ss834221035, ss974490408, ss991624704, ss1067550326, ss1080003682, ss1352823367, ss1577523170, ss1584092721, ss1632672082, ss1675666115, ss1691718392, ss1711390137, ss1752154489, ss1935021929, ss2028291219, ss2156688259, ss2370068700, ss2633208782, ss2701147293, ss2741067633, ss2749250094, ss2932993282, ss3013006819, ss3023068939, ss3351042153, ss3625669094, ss3627323488, ss3631203099, ss3633091662, ss3633796013, ss3634598002, ss3635485085, ss3636288327, ss3637236316, ss3638075944, ss3640305329, ss3641057880, ss3641353146, ss3740787576, ss3744898567, ss3752891961, ss3772397283 NC_000015.9:28386625:C:T NC_000015.10:28141479:C:T (self)
125934932, ss3027969887, ss3223248304, ss3697585478, ss3818209083 NC_000015.10:28141479:C:T NC_000015.10:28141479:C:T (self)
ss16684473 NT_010280.16:752116:C:T NC_000015.10:28141479:C:T (self)
ss66939019, ss67100009, ss68108492, ss69171493, ss70533579, ss71064629, ss75638073, ss85110528, ss86348004, ss134210515, ss153014396, ss159180288, ss159730256, ss159988197, ss161704167, ss171369417, ss410894210 NT_026446.14:4821772:C:T NC_000015.10:28141479: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.

5 citations for rs11636232
PMID Title Author Year Journal
18483556 A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Han J et al. 2008 PLoS genetics
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
20546537 Genome-wide association studies of pigmentation and skin cancer: a review and meta-analysis. Gerstenblith MR et al. 2010 Pigment cell & melanoma research
27468418 Importance of nonsynonymous OCA2 variants in human eye color prediction. Andersen JD et al. 2016 Molecular genetics & genomic medicine

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