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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.

rs2031526

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr13:94448587 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.21842 (27426/125568, TOPMED)
A=0.1973 (6099/30916, GnomAD)
A=0.329 (1647/5008, 1000G) (+ 3 more)
A=0.175 (784/4480, Estonian)
A=0.191 (737/3854, ALSPAC)
A=0.189 (702/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DCT : Intron Variant
Publications
3 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 13 NC_000013.11:g.94448587A>C
GRCh38.p12 chr 13 NC_000013.11:g.94448587A>G
GRCh38.p12 chr 13 NC_000013.11:g.94448587A>T
GRCh37.p13 chr 13 NC_000013.10:g.95100841A>C
GRCh37.p13 chr 13 NC_000013.10:g.95100841A>G
GRCh37.p13 chr 13 NC_000013.10:g.95100841A>T
Gene: DCT, dopachrome tautomerase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DCT transcript variant 2 NM_001129889.2:c. N/A Intron Variant
DCT transcript variant 3 NM_001322182.1:c. N/A Intron Variant
DCT transcript variant 4 NM_001322183.1:c. N/A Intron Variant
DCT transcript variant 5 NM_001322184.1:c. N/A Intron Variant
DCT transcript variant 6 NM_001322185.1:c. N/A Intron Variant
DCT transcript variant 7 NM_001322186.1:c. N/A Intron Variant
DCT transcript variant 1 NM_001922.4:c. N/A Intron Variant
DCT transcript variant X1 XM_011521049.2:c. N/A Intron Variant
DCT transcript variant X4 XM_017020401.2:c. N/A Intron Variant
DCT transcript variant X3 XM_024449328.1:c. N/A Intron Variant
DCT transcript variant X2 XR_002957452.1: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 A=0.21842 G=0.78158
gnomAD - Genomes Global Study-wide 30916 A=0.1973 G=0.8027
gnomAD - Genomes European Sub 18460 A=0.1880 G=0.8120
gnomAD - Genomes African Sub 8720 A=0.085 G=0.915
gnomAD - Genomes East Asian Sub 1618 A=0.756 G=0.244
gnomAD - Genomes Other Sub 980 A=0.22 G=0.78
gnomAD - Genomes American Sub 836 A=0.45 G=0.55
gnomAD - Genomes Ashkenazi Jewish Sub 302 A=0.26 G=0.74
1000Genomes Global Study-wide 5008 A=0.329 G=0.671
1000Genomes African Sub 1322 A=0.059 G=0.941
1000Genomes East Asian Sub 1008 A=0.739 G=0.261
1000Genomes Europe Sub 1006 A=0.192 G=0.808
1000Genomes South Asian Sub 978 A=0.35 G=0.65
1000Genomes American Sub 694 A=0.41 G=0.59
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.175 G=0.825
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.191 G=0.809
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.189 G=0.811
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 A= C G T Note
GRCh38.p12 chr 13 NC_000013.11:...

NC_000013.11:g.94448587A=

NC_000013.11:...

NC_000013.11:g.94448587A>C

NC_000013.11:...

NC_000013.11:g.94448587A>G

NC_000013.11:...

NC_000013.11:g.94448587A>T

GRCh37.p13 chr 13 NC_000013.10:...

NC_000013.10:g.95100841A=

NC_000013.10:...

NC_000013.10:g.95100841A>C

NC_000013.10:...

NC_000013.10:g.95100841A>G

NC_000013.10:...

NC_000013.10:g.95100841A>T

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#.

53 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2940384 Apr 12, 2001 (94)
2 WI_SSAHASNP ss12258132 Jul 11, 2003 (116)
3 SC_SNP ss13196424 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss16608687 Feb 27, 2004 (120)
5 PERLEGEN ss24216468 Sep 20, 2004 (123)
6 ABI ss40394651 Mar 14, 2006 (126)
7 HGSV ss80770313 Dec 16, 2007 (130)
8 HGSV ss84526915 Dec 16, 2007 (130)
9 BCMHGSC_JDW ss89804792 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss97183612 Feb 06, 2009 (130)
11 1000GENOMES ss108007940 Jan 22, 2009 (130)
12 1000GENOMES ss115131969 Jan 25, 2009 (130)
13 ILLUMINA-UK ss118940173 Dec 01, 2009 (131)
14 ENSEMBL ss132270724 Dec 01, 2009 (131)
15 ENSEMBL ss133767005 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss168567115 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss170487431 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss171570595 Jul 04, 2010 (132)
19 BUSHMAN ss199575805 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss208490957 Jul 04, 2010 (132)
21 1000GENOMES ss226354858 Jul 14, 2010 (132)
22 1000GENOMES ss236384165 Jul 15, 2010 (132)
23 1000GENOMES ss242850085 Jul 15, 2010 (132)
24 GMI ss281840046 May 04, 2012 (137)
25 GMI ss286766287 Apr 25, 2013 (138)
26 PJP ss291510458 May 09, 2011 (134)
27 TISHKOFF ss563849215 Apr 25, 2013 (138)
28 SSMP ss659490427 Apr 25, 2013 (138)
29 EVA-GONL ss990730594 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1079343853 Aug 21, 2014 (142)
31 1000GENOMES ss1349454847 Aug 21, 2014 (142)
32 DDI ss1427291240 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1576996467 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1630929881 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1673923914 Apr 01, 2015 (144)
36 EVA_DECODE ss1694720491 Apr 01, 2015 (144)
37 HAMMER_LAB ss1807742880 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1934091388 Feb 12, 2016 (147)
39 GENOMED ss1967866371 Jul 19, 2016 (147)
40 JJLAB ss2027818673 Sep 14, 2016 (149)
41 USC_VALOUEV ss2156185301 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2198923972 Dec 20, 2016 (150)
43 TOPMED ss2363110657 Dec 20, 2016 (150)
44 SYSTEMSBIOZJU ss2628396881 Nov 08, 2017 (151)
45 GRF ss2700578845 Nov 08, 2017 (151)
46 GNOMAD ss2923186394 Nov 08, 2017 (151)
47 SWEGEN ss3011530276 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3027730356 Nov 08, 2017 (151)
49 TOPMED ss3200891016 Nov 08, 2017 (151)
50 TOPMED ss3200891017 Nov 08, 2017 (151)
51 TOPMED ss3200891018 Nov 08, 2017 (151)
52 CSHL ss3350608495 Nov 08, 2017 (151)
53 URBANLAB ss3650108934 Oct 12, 2018 (152)
54 1000Genomes NC_000013.10 - 95100841 Oct 12, 2018 (152)
55 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 95100841 Oct 12, 2018 (152)
56 Genetic variation in the Estonian population NC_000013.10 - 95100841 Oct 12, 2018 (152)
57 gnomAD - Genomes NC_000013.10 - 95100841 Oct 12, 2018 (152)
58 TopMed NC_000013.11 - 94448587 Oct 12, 2018 (152)
59 UK 10K study - Twins NC_000013.10 - 95100841 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)
rs17181717 Oct 08, 2004 (123)
rs61524205 May 27, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss80770313, ss84526915, ss89804792, ss108007940, ss115131969, ss118940173, ss168567115, ss170487431, ss171570595, ss199575805, ss208490957, ss281840046, ss286766287, ss291510458, ss1694720491 NC_000013.9:93898841:A= NC_000013.11:94448586:A= (self)
62376228, 34656163, 24551093, 56887918, 34656163, ss226354858, ss236384165, ss242850085, ss563849215, ss659490427, ss990730594, ss1079343853, ss1349454847, ss1427291240, ss1576996467, ss1630929881, ss1673923914, ss1807742880, ss1934091388, ss1967866371, ss2027818673, ss2156185301, ss2363110657, ss2628396881, ss2700578845, ss2923186394, ss3011530276, ss3350608495 NC_000013.10:95100840:A= NC_000013.11:94448586:A= (self)
108273788, ss2198923972, ss3027730356, ss3200891016, ss3200891017, ss3200891018, ss3650108934 NC_000013.11:94448586:A= NC_000013.11:94448586:A= (self)
ss12258132, ss13196424 NT_009952.13:8190515:A= NC_000013.11:94448586:A= (self)
ss2940384, ss16608687, ss24216468, ss40394651, ss97183612, ss132270724, ss133767005 NT_009952.14:8190516:A= NC_000013.11:94448586:A= (self)
ss3200891016 NC_000013.11:94448586:A>C NC_000013.11:94448586:A>C (self)
ss80770313, ss84526915, ss89804792, ss108007940, ss115131969, ss118940173, ss168567115, ss170487431, ss171570595, ss199575805, ss208490957, ss281840046, ss286766287, ss291510458, ss1694720491 NC_000013.9:93898841:A>G NC_000013.11:94448586:A>G (self)
62376228, 34656163, 24551093, 56887918, 34656163, ss226354858, ss236384165, ss242850085, ss563849215, ss659490427, ss990730594, ss1079343853, ss1349454847, ss1427291240, ss1576996467, ss1630929881, ss1673923914, ss1807742880, ss1934091388, ss1967866371, ss2027818673, ss2156185301, ss2363110657, ss2628396881, ss2700578845, ss2923186394, ss3011530276, ss3350608495 NC_000013.10:95100840:A>G NC_000013.11:94448586:A>G (self)
108273788, ss2198923972, ss3027730356, ss3200891017, ss3650108934 NC_000013.11:94448586:A>G NC_000013.11:94448586:A>G (self)
ss12258132, ss13196424 NT_009952.13:8190515:A>G NC_000013.11:94448586:A>G (self)
ss2940384, ss16608687, ss24216468, ss40394651, ss97183612, ss132270724, ss133767005 NT_009952.14:8190516:A>G NC_000013.11:94448586:A>G (self)
ss2198923972, ss3200891018 NC_000013.11:94448586:A>T NC_000013.11:94448586:A>T (self)
Help

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

3 citations for rs2031526
PMID Title Author Year Journal
18312627 Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans. Alonso S et al. 2008 BMC evolutionary biology
20221248 Association of the OCA2 polymorphism His615Arg with melanin content in east Asian populations: further evidence of convergent evolution of skin pigmentation. Edwards M et al. 2010 PLoS genetics
23110848 Human pigmentation genes under environmental selection. Sturm RA et al. 2012 Genome biology

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.post63+3f7b20b