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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.

rs12826

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr10:99852563 (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
T=0.30473 (38264/125568, TOPMED)
T=0.3076 (9504/30902, GnomAD)
T=0.272 (1363/5008, 1000G) (+ 1 more)
T=0.363 (1626/4480, Estonian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ABCC2 : 3 Prime UTR Variant
Publications
1 citation
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 10 NC_000010.11:g.99852563C>A
GRCh38.p12 chr 10 NC_000010.11:g.99852563C>T
GRCh37.p13 chr 10 NC_000010.10:g.101612320C>A
GRCh37.p13 chr 10 NC_000010.10:g.101612320C>T
ABCC2 RefSeqGene NG_011798.1:g.74858C>A
ABCC2 RefSeqGene NG_011798.1:g.74858C>T
Gene: ABCC2, ATP binding cassette subfamily C member 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCC2 transcript NM_000392.4:c. N/A Genic Downstream Transcript Variant
ABCC2 transcript variant X2 XM_006717630.3:c. N/A 3 Prime UTR Variant
ABCC2 transcript variant X5 XM_006717631.4:c. N/A Genic Downstream Transcript Variant
ABCC2 transcript variant X4 XM_011539291.3:c. N/A Genic Downstream Transcript Variant
ABCC2 transcript variant X6 XM_017015675.2:c. N/A Genic Downstream Transcript Variant
ABCC2 transcript variant X1 XR_945604.3:n. N/A Genic Downstream Transcript Variant
ABCC2 transcript variant X3 XR_945605.3: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
TopMed Global Study-wide 125568 C=0.69527 T=0.30473
gnomAD - Genomes Global Study-wide 30902 C=0.6924 T=0.3076
gnomAD - Genomes European Sub 18466 C=0.6326 T=0.3674
gnomAD - Genomes African Sub 8704 C=0.810 T=0.190
gnomAD - Genomes East Asian Sub 1616 C=0.787 T=0.213
gnomAD - Genomes Other Sub 976 C=0.67 T=0.33
gnomAD - Genomes American Sub 838 C=0.65 T=0.35
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.66 T=0.34
1000Genomes Global Study-wide 5008 C=0.728 T=0.272
1000Genomes African Sub 1322 C=0.852 T=0.148
1000Genomes East Asian Sub 1008 C=0.752 T=0.248
1000Genomes Europe Sub 1006 C=0.622 T=0.378
1000Genomes South Asian Sub 978 C=0.69 T=0.31
1000Genomes American Sub 694 C=0.66 T=0.34
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.637 T=0.363
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 10 NC_000010.11:g.99...

NC_000010.11:g.99852563C=

NC_000010.11:g.99...

NC_000010.11:g.99852563C>A

NC_000010.11:g.99...

NC_000010.11:g.99852563C>T

GRCh37.p13 chr 10 NC_000010.10:g.10...

NC_000010.10:g.101612320C=

NC_000010.10:g.10...

NC_000010.10:g.101612320C>A

NC_000010.10:g.10...

NC_000010.10:g.101612320C>T

ABCC2 RefSeqGene NG_011798.1:g.748...

NG_011798.1:g.74858C=

NG_011798.1:g.748...

NG_011798.1:g.74858C>A

NG_011798.1:g.748...

NG_011798.1:g.74858C>T

ABCC2 transcript variant X2 XM_006717630.3:c....

XM_006717630.3:c.*932C=

XM_006717630.3:c....

XM_006717630.3:c.*932C>A

XM_006717630.3:c....

XM_006717630.3:c.*932C>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#.

82 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss15125 Sep 19, 2000 (52)
2 RIKENSNPRC ss5602246 Dec 12, 2002 (110)
3 BCM_SSAHASNP ss10602919 Jul 11, 2003 (116)
4 SSAHASNP ss20683266 Apr 05, 2004 (121)
5 ABI ss39806394 Mar 14, 2006 (126)
6 ILLUMINA ss67366230 Dec 01, 2006 (127)
7 ILLUMINA ss71128868 May 18, 2007 (127)
8 ILLUMINA ss75342884 Dec 06, 2007 (129)
9 AFFY ss76511438 Dec 06, 2007 (129)
10 HGSV ss85935722 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss88330828 Mar 23, 2008 (129)
12 HUMANGENOME_JCVI ss97578913 Feb 06, 2009 (130)
13 BGI ss102905812 Dec 01, 2009 (131)
14 1000GENOMES ss109695530 Jan 24, 2009 (130)
15 1000GENOMES ss113721821 Jan 25, 2009 (130)
16 KRIBB_YJKIM ss119339203 Dec 01, 2009 (131)
17 ENSEMBL ss138837539 Dec 01, 2009 (131)
18 ILLUMINA ss153285309 Dec 01, 2009 (131)
19 GMI ss155453134 Dec 01, 2009 (131)
20 ILLUMINA ss159235985 Dec 01, 2009 (131)
21 ILLUMINA ss160301754 Dec 01, 2009 (131)
22 COMPLETE_GENOMICS ss168710360 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss170942397 Jul 04, 2010 (132)
24 ILLUMINA ss172252506 Jul 04, 2010 (132)
25 1000GENOMES ss224901609 Jul 14, 2010 (132)
26 1000GENOMES ss235305936 Jul 15, 2010 (132)
27 1000GENOMES ss241986549 Jul 15, 2010 (132)
28 BL ss254564563 May 09, 2011 (134)
29 GMI ss280745537 May 04, 2012 (137)
30 PJP ss290916874 May 09, 2011 (134)
31 ILLUMINA ss479826633 May 04, 2012 (137)
32 ILLUMINA ss479833819 May 04, 2012 (137)
33 ILLUMINA ss480423849 Sep 08, 2015 (146)
34 ILLUMINA ss484711771 May 04, 2012 (137)
35 ILLUMINA ss536815620 Sep 08, 2015 (146)
36 SSMP ss657232792 Apr 25, 2013 (138)
37 ILLUMINA ss778416364 Sep 08, 2015 (146)
38 ILLUMINA ss782802646 Sep 08, 2015 (146)
39 ILLUMINA ss783768098 Sep 08, 2015 (146)
40 ILLUMINA ss832055662 Sep 08, 2015 (146)
41 ILLUMINA ss833871687 Sep 08, 2015 (146)
42 EVA-GONL ss987841975 Aug 21, 2014 (142)
43 JMKIDD_LAB ss1077241268 Aug 21, 2014 (142)
44 1000GENOMES ss1338761893 Aug 21, 2014 (142)
45 DDI ss1426422775 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1575315611 Apr 01, 2015 (144)
47 EVA_DECODE ss1597515597 Apr 01, 2015 (144)
48 EVA_UK10K_ALSPAC ss1625270983 Apr 01, 2015 (144)
49 EVA_UK10K_ALSPAC ss1625270984 Apr 01, 2015 (144)
50 EVA_UK10K_TWINSUK ss1668265016 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1668265017 Apr 01, 2015 (144)
52 EVA_SVP ss1713205602 Apr 01, 2015 (144)
53 ILLUMINA ss1751942668 Sep 08, 2015 (146)
54 WEILL_CORNELL_DGM ss1931206585 Feb 12, 2016 (147)
55 GENOMED ss1967207835 Jul 19, 2016 (147)
56 JJLAB ss2026333198 Sep 14, 2016 (149)
57 ILLUMINA ss2095016896 Dec 20, 2016 (150)
58 USC_VALOUEV ss2154610554 Nov 08, 2017 (151)
59 HUMAN_LONGEVITY ss2177432182 Dec 20, 2016 (150)
60 TOPMED ss2340553626 Dec 20, 2016 (150)
61 SYSTEMSBIOZJU ss2627634788 Nov 08, 2017 (151)
62 ILLUMINA ss2632753162 Nov 08, 2017 (151)
63 ILLUMINA ss2635018323 Nov 08, 2017 (151)
64 GRF ss2698864070 Nov 08, 2017 (151)
65 GNOMAD ss2892525392 Nov 08, 2017 (151)
66 SWEGEN ss3007024645 Nov 08, 2017 (151)
67 TOPMED ss3128429969 Nov 08, 2017 (151)
68 CSHL ss3349277178 Nov 08, 2017 (151)
69 ILLUMINA ss3626518161 Oct 12, 2018 (152)
70 ILLUMINA ss3630776016 Oct 12, 2018 (152)
71 ILLUMINA ss3632961878 Oct 12, 2018 (152)
72 ILLUMINA ss3633659596 Oct 12, 2018 (152)
73 ILLUMINA ss3634420185 Oct 12, 2018 (152)
74 ILLUMINA ss3635351823 Oct 12, 2018 (152)
75 ILLUMINA ss3636104868 Oct 12, 2018 (152)
76 ILLUMINA ss3637102543 Oct 12, 2018 (152)
77 ILLUMINA ss3637869621 Oct 12, 2018 (152)
78 ILLUMINA ss3640127526 Oct 12, 2018 (152)
79 ILLUMINA ss3642871508 Oct 12, 2018 (152)
80 BIOINF_KMB_FNS_UNIBA ss3645158494 Oct 12, 2018 (152)
81 URBANLAB ss3649449896 Oct 12, 2018 (152)
82 ILLUMINA ss3651627196 Oct 12, 2018 (152)
83 1000Genomes NC_000010.10 - 101612320 Oct 12, 2018 (152)
84 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 28428200 (NC_000010.10:101612319:C:C 2384/3854, NC_000010.10:101612319:C:T 1470/3854)
Row 28428201 (NC_000010.10:101612319:C:C 3852/3854, NC_000010.10:101612319:C:A 2/3854)

- Oct 12, 2018 (152)
85 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 28428200 (NC_000010.10:101612319:C:C 2384/3854, NC_000010.10:101612319:C:T 1470/3854)
Row 28428201 (NC_000010.10:101612319:C:C 3852/3854, NC_000010.10:101612319:C:A 2/3854)

- Oct 12, 2018 (152)
86 Genetic variation in the Estonian population NC_000010.10 - 101612320 Oct 12, 2018 (152)
87 gnomAD - Genomes NC_000010.10 - 101612320 Oct 12, 2018 (152)
88 TopMed NC_000010.11 - 99852563 Oct 12, 2018 (152)
89 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 28428200 (NC_000010.10:101612319:C:C 2254/3708, NC_000010.10:101612319:C:T 1454/3708)
Row 28428201 (NC_000010.10:101612319:C:C 3708/3708, NC_000010.10:101612319:C:A 0/3708)

- Oct 12, 2018 (152)
90 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 28428200 (NC_000010.10:101612319:C:C 2254/3708, NC_000010.10:101612319:C:T 1454/3708)
Row 28428201 (NC_000010.10:101612319:C:C 3708/3708, NC_000010.10:101612319:C:A 0/3708)

- 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)
rs60993883 May 26, 2008 (130)
rs386526149 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss1625270984, ss1668265017 NC_000010.10:101612319:C:A NC_000010.11:99852562:C:A (self)
ss85935722 NC_000010.8:101602309:C:T NC_000010.11:99852562:C:T (self)
ss88330828, ss109695530, ss113721821, ss168710360, ss170942397, ss254564563, ss280745537, ss290916874, ss479826633, ss1597515597, ss1713205602, ss2635018323, ss3642871508 NC_000010.9:101602309:C:T NC_000010.11:99852562:C:T (self)
51198199, 20174327, 26226913, ss224901609, ss235305936, ss241986549, ss479833819, ss480423849, ss484711771, ss536815620, ss657232792, ss778416364, ss782802646, ss783768098, ss832055662, ss833871687, ss987841975, ss1077241268, ss1338761893, ss1426422775, ss1575315611, ss1625270983, ss1668265016, ss1751942668, ss1931206585, ss1967207835, ss2026333198, ss2095016896, ss2154610554, ss2340553626, ss2627634788, ss2632753162, ss2698864070, ss2892525392, ss3007024645, ss3349277178, ss3626518161, ss3630776016, ss3632961878, ss3633659596, ss3634420185, ss3635351823, ss3636104868, ss3637102543, ss3637869621, ss3640127526, ss3651627196 NC_000010.10:101612319:C:T NC_000010.11:99852562:C:T (self)
49906062, ss2177432182, ss3128429969, ss3645158494, ss3649449896 NC_000010.11:99852562:C:T NC_000010.11:99852562:C:T (self)
ss10602919 NT_030059.10:20050877:C:T NC_000010.11:99852562:C:T (self)
ss20683266 NT_030059.11:20360845:C:T NC_000010.11:99852562:C:T (self)
ss15125, ss5602246, ss39806394, ss67366230, ss71128868, ss75342884, ss76511438, ss97578913, ss102905812, ss119339203, ss138837539, ss153285309, ss155453134, ss159235985, ss160301754, ss172252506 NT_030059.13:52416783:C:T NC_000010.11:99852562: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.

1 citation for rs12826
PMID Title Author Year Journal
27180762 Vincristine pharmacokinetics pathway and neurotoxicity during early phases of treatment in pediatric acute lymphoblastic leukemia. Lopez-Lopez E et al. 2016 Pharmacogenomics

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