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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.

rs10513137

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr3:141424588 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.16992 (21336/125568, TOPMED)
A=0.1582 (4895/30940, GnomAD)
A=0.198 (992/5008, 1000G) (+ 3 more)
A=0.079 (353/4480, Estonian)
A=0.086 (333/3854, ALSPAC)
A=0.084 (310/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZBTB38 : Intron 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 3 NC_000003.12:g.141424588G>A
GRCh38.p12 chr 3 NC_000003.12:g.141424588G>C
GRCh37.p13 chr 3 NC_000003.11:g.141143430G>A
GRCh37.p13 chr 3 NC_000003.11:g.141143430G>C
ZBTB38 RefSeqGene NG_021426.1:g.105376G>A
ZBTB38 RefSeqGene NG_021426.1:g.105376G>C
Gene: ZBTB38, zinc finger and BTB domain containing 38 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ZBTB38 transcript variant 1 NM_001080412.2:c. N/A Intron Variant
ZBTB38 transcript variant 2 NM_001350099.1:c. N/A Intron Variant
ZBTB38 transcript variant 3 NM_001350100.1:c. N/A Intron Variant
ZBTB38 transcript variant X10 XM_005247257.2:c. N/A Intron Variant
ZBTB38 transcript variant X3 XM_005247258.1:c. N/A Intron Variant
ZBTB38 transcript variant X9 XM_005247261.3:c. N/A Intron Variant
ZBTB38 transcript variant X1 XM_017006050.2:c. N/A Intron Variant
ZBTB38 transcript variant X6 XM_017006057.1:c. N/A Intron Variant
ZBTB38 transcript variant X7 XM_017006058.1:c. N/A Intron Variant
ZBTB38 transcript variant X4 XM_024453431.1:c. N/A Intron Variant
ZBTB38 transcript variant X5 XM_024453432.1:c. N/A Intron Variant
ZBTB38 transcript variant X8 XM_024453433.1:c. N/A Intron Variant
ZBTB38 transcript variant X11 XM_024453434.1:c. N/A Intron Variant
ZBTB38 transcript variant X2 XM_005247256.5:c. N/A Genic Upstream 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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 G=0.83007 A=0.16992, C=0.00002
gnomAD - Genomes Global Study-wide 30940 G=0.8418 A=0.1582
gnomAD - Genomes European Sub 18484 G=0.9178 A=0.0822
gnomAD - Genomes African Sub 8716 G=0.679 A=0.321
gnomAD - Genomes East Asian Sub 1620 G=0.779 A=0.221
gnomAD - Genomes Other Sub 980 G=0.90 A=0.10
gnomAD - Genomes American Sub 838 G=0.87 A=0.13
gnomAD - Genomes Ashkenazi Jewish Sub 302 G=0.95 A=0.05
1000Genomes Global Study-wide 5008 G=0.802 A=0.198
1000Genomes African Sub 1322 G=0.644 A=0.356
1000Genomes East Asian Sub 1008 G=0.756 A=0.244
1000Genomes Europe Sub 1006 G=0.911 A=0.089
1000Genomes South Asian Sub 978 G=0.90 A=0.10
1000Genomes American Sub 694 G=0.87 A=0.13
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.921 A=0.079
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.914 A=0.086
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.916 A=0.084
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 G= A C Note
GRCh38.p12 chr 3 NC_000003.12:g.14...

NC_000003.12:g.141424588G=

NC_000003.12:g.14...

NC_000003.12:g.141424588G>A

NC_000003.12:g.14...

NC_000003.12:g.141424588G>C

GRCh37.p13 chr 3 NC_000003.11:g.14...

NC_000003.11:g.141143430G=

NC_000003.11:g.14...

NC_000003.11:g.141143430G>A

NC_000003.11:g.14...

NC_000003.11:g.141143430G>C

ZBTB38 RefSeqGene NG_021426.1:g.105...

NG_021426.1:g.105376G=

NG_021426.1:g.105...

NG_021426.1:g.105376G>A

NG_021426.1:g.105...

NG_021426.1:g.105376G>C

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#.

75 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14912173 Dec 05, 2003 (119)
2 PERLEGEN ss23656601 Sep 20, 2004 (123)
3 AFFY ss66505805 Nov 29, 2006 (127)
4 PERLEGEN ss68877198 May 17, 2007 (127)
5 AFFY ss76328531 Dec 08, 2007 (130)
6 KRIBB_YJKIM ss82742407 Dec 14, 2007 (131)
7 ILLUMINA-UK ss117298202 Dec 01, 2009 (131)
8 ILLUMINA ss161077905 Dec 01, 2009 (131)
9 AFFY ss173277971 Jun 24, 2010 (142)
10 BUSHMAN ss203268691 Jul 04, 2010 (132)
11 1000GENOMES ss211279086 Jul 14, 2010 (132)
12 1000GENOMES ss220463832 Jul 14, 2010 (132)
13 1000GENOMES ss232058519 Jul 14, 2010 (132)
14 1000GENOMES ss239424771 Jul 15, 2010 (132)
15 BL ss253552370 May 09, 2011 (134)
16 GMI ss277376626 May 04, 2012 (137)
17 ILLUMINA ss479179076 Sep 08, 2015 (146)
18 ILLUMINA ss479798671 May 04, 2012 (137)
19 ILLUMINA ss484472437 May 04, 2012 (137)
20 EXOME_CHIP ss491347261 May 04, 2012 (137)
21 ILLUMINA ss536620423 Sep 08, 2015 (146)
22 TISHKOFF ss556987356 Apr 25, 2013 (138)
23 SSMP ss650714705 Apr 25, 2013 (138)
24 ILLUMINA ss778687403 Sep 08, 2015 (146)
25 ILLUMINA ss779653928 Sep 08, 2015 (146)
26 ILLUMINA ss780680580 Sep 08, 2015 (146)
27 ILLUMINA ss781071326 Sep 08, 2015 (146)
28 ILLUMINA ss783353860 Sep 08, 2015 (146)
29 ILLUMINA ss834146079 Sep 08, 2015 (146)
30 ILLUMINA ss835127045 Sep 08, 2015 (146)
31 EVA-GONL ss979233625 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1070883698 Aug 21, 2014 (142)
33 1000GENOMES ss1306443615 Aug 21, 2014 (142)
34 EVA_GENOME_DK ss1580209226 Apr 01, 2015 (144)
35 EVA_DECODE ss1588721798 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1608363746 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1651357779 Apr 01, 2015 (144)
38 EVA_SVP ss1712617606 Apr 01, 2015 (144)
39 ILLUMINA ss1752443316 Sep 08, 2015 (146)
40 HAMMER_LAB ss1800131188 Sep 08, 2015 (146)
41 ILLUMINA ss1917773592 Feb 12, 2016 (147)
42 WEILL_CORNELL_DGM ss1922457518 Feb 12, 2016 (147)
43 ILLUMINA ss1946097889 Feb 12, 2016 (147)
44 ILLUMINA ss1958611284 Feb 12, 2016 (147)
45 JJLAB ss2021798647 Sep 14, 2016 (149)
46 ILLUMINA ss2094813546 Dec 20, 2016 (150)
47 ILLUMINA ss2095138379 Dec 20, 2016 (150)
48 USC_VALOUEV ss2149894610 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2256415190 Dec 20, 2016 (150)
50 TOPMED ss2423794274 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2625401427 Nov 08, 2017 (151)
52 ILLUMINA ss2634020607 Nov 08, 2017 (151)
53 ILLUMINA ss2634020608 Nov 08, 2017 (151)
54 ILLUMINA ss2634020609 Nov 08, 2017 (151)
55 ILLUMINA ss2634020610 Nov 08, 2017 (151)
56 GRF ss2705306764 Nov 08, 2017 (151)
57 GNOMAD ss2799946417 Nov 08, 2017 (151)
58 AFFY ss2985272026 Nov 08, 2017 (151)
59 AFFY ss2985896242 Nov 08, 2017 (151)
60 SWEGEN ss2993310719 Nov 08, 2017 (151)
61 ILLUMINA ss3022293222 Nov 08, 2017 (151)
62 TOPMED ss3407403553 Nov 08, 2017 (151)
63 TOPMED ss3407403554 Nov 08, 2017 (151)
64 ILLUMINA ss3628792090 Oct 12, 2018 (152)
65 ILLUMINA ss3628792091 Oct 12, 2018 (152)
66 ILLUMINA ss3631962846 Oct 12, 2018 (152)
67 ILLUMINA ss3631962847 Oct 12, 2018 (152)
68 ILLUMINA ss3634920523 Oct 12, 2018 (152)
69 ILLUMINA ss3636617319 Oct 12, 2018 (152)
70 ILLUMINA ss3640627821 Oct 12, 2018 (152)
71 ILLUMINA ss3642286073 Oct 12, 2018 (152)
72 ILLUMINA ss3644830543 Oct 12, 2018 (152)
73 ILLUMINA ss3652772600 Oct 12, 2018 (152)
74 ILLUMINA ss3652772601 Oct 12, 2018 (152)
75 ILLUMINA ss3654041483 Oct 12, 2018 (152)
76 1000Genomes NC_000003.11 - 141143430 Oct 12, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 141143430 Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000003.11 - 141143430 Oct 12, 2018 (152)
79 gnomAD - Genomes NC_000003.11 - 141143430 Oct 12, 2018 (152)
80 TopMed NC_000003.12 - 141424588 Oct 12, 2018 (152)
81 UK 10K study - Twins NC_000003.11 - 141143430 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)
rs56500515 May 24, 2008 (130)
rs56696880 Dec 02, 2009 (131)
rs111193285 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss66505805, ss76328531, ss117298202, ss173277971, ss203268691, ss211279086, ss253552370, ss277376626, ss484472437, ss1588721798, ss1712617606 NC_000003.10:142626119:G= NC_000003.12:141424587:G= (self)
17716302, 9866337, 6972734, 140574171, 9866337, ss220463832, ss232058519, ss239424771, ss479179076, ss479798671, ss491347261, ss536620423, ss556987356, ss650714705, ss778687403, ss779653928, ss780680580, ss781071326, ss783353860, ss834146079, ss835127045, ss979233625, ss1070883698, ss1306443615, ss1580209226, ss1608363746, ss1651357779, ss1752443316, ss1800131188, ss1917773592, ss1922457518, ss1946097889, ss1958611284, ss2021798647, ss2094813546, ss2095138379, ss2149894610, ss2423794274, ss2625401427, ss2634020607, ss2634020608, ss2634020609, ss2634020610, ss2705306764, ss2799946417, ss2985272026, ss2985896242, ss2993310719, ss3022293222, ss3628792090, ss3628792091, ss3631962846, ss3631962847, ss3634920523, ss3636617319, ss3640627821, ss3642286073, ss3644830543, ss3652772600, ss3652772601, ss3654041483 NC_000003.11:141143429:G= NC_000003.12:141424587:G= (self)
264663521, ss2256415190, ss3407403553, ss3407403554 NC_000003.12:141424587:G= NC_000003.12:141424587:G= (self)
ss14912173, ss23656601, ss68877198, ss82742407, ss161077905 NT_005612.16:47638575:G= NC_000003.12:141424587:G= (self)
ss66505805, ss76328531, ss117298202, ss173277971, ss203268691, ss211279086, ss253552370, ss277376626, ss484472437, ss1588721798, ss1712617606 NC_000003.10:142626119:G>A NC_000003.12:141424587:G>A (self)
17716302, 9866337, 6972734, 140574171, 9866337, ss220463832, ss232058519, ss239424771, ss479179076, ss479798671, ss491347261, ss536620423, ss556987356, ss650714705, ss778687403, ss779653928, ss780680580, ss781071326, ss783353860, ss834146079, ss835127045, ss979233625, ss1070883698, ss1306443615, ss1580209226, ss1608363746, ss1651357779, ss1752443316, ss1800131188, ss1917773592, ss1922457518, ss1946097889, ss1958611284, ss2021798647, ss2094813546, ss2095138379, ss2149894610, ss2423794274, ss2625401427, ss2634020607, ss2634020608, ss2634020609, ss2634020610, ss2705306764, ss2799946417, ss2985272026, ss2985896242, ss2993310719, ss3022293222, ss3628792090, ss3628792091, ss3631962846, ss3631962847, ss3634920523, ss3636617319, ss3640627821, ss3642286073, ss3644830543, ss3652772600, ss3652772601, ss3654041483 NC_000003.11:141143429:G>A NC_000003.12:141424587:G>A (self)
264663521, ss2256415190, ss3407403553 NC_000003.12:141424587:G>A NC_000003.12:141424587:G>A (self)
ss14912173, ss23656601, ss68877198, ss82742407, ss161077905 NT_005612.16:47638575:G>A NC_000003.12:141424587:G>A (self)
264663521, ss3407403554 NC_000003.12:141424587:G>C NC_000003.12:141424587:G>C (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 rs10513137
PMID Title Author Year Journal
25464127 On the analysis of a repeated measure design in genome-wide association analysis. Lee Y et al. 2014 International journal of environmental research and public health

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