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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 HGVS 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.

rs3845

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:124985524 (GRCh38.p13) 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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.397941 (105331/264690, TOPMED)
T=0.379528 (53146/140032, GnomAD)
T=0.31242 (18072/57846, ALFA) (+ 15 more)
T=0.30877 (5175/16760, 8.3KJPN)
T=0.3980 (1993/5008, 1000G)
T=0.2567 (1150/4480, Estonian)
T=0.2535 (977/3854, ALSPAC)
T=0.2567 (952/3708, TWINSUK)
T=0.3294 (965/2930, KOREAN)
T=0.3111 (570/1832, Korea1K)
T=0.248 (248/998, GoNL)
T=0.205 (123/600, NorthernSweden)
T=0.277 (148/534, MGP)
T=0.251 (109/434, SGDP_PRJ)
T=0.324 (70/216, Qatari)
T=0.150 (32/214, Vietnamese)
T=0.20 (10/50, Siberian)
T=0.17 (7/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CTBP2 : 3 Prime UTR Variant
ZRANB1 : 3 Prime UTR Variant
Publications
0 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.p13 chr 10 NC_000010.11:g.124985524T>A
GRCh38.p13 chr 10 NC_000010.11:g.124985524T>C
GRCh37.p13 chr 10 NC_000010.10:g.126674093T>A
GRCh37.p13 chr 10 NC_000010.10:g.126674093T>C
Gene: CTBP2, C-terminal binding protein 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CTBP2 transcript variant 2 NM_022802.3:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant 4 NM_001290214.3:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant 3 NM_001083914.3:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant 9 NM_001363508.2:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant 7 NM_001321013.2:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant 6 NM_001321012.2:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant 8 NM_001321014.2:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant 5 NM_001290215.3:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant 1 NM_001329.4:c.*3994= N/A 3 Prime UTR Variant
CTBP2 transcript variant X2 XM_005269561.3:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X4 XM_005269564.3:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X10 XM_005269567.3:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X11 XM_005269568.5:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X13 XM_005269569.3:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X16 XM_005269571.3:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X14 XM_005269572.4:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X6 XM_006717642.3:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X7 XM_011539351.2:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X8 XM_011539353.2:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X9 XM_011539354.2:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X12 XM_011539355.2:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X17 XM_011539357.2:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X18 XM_011539358.2:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X3 XM_017015756.2:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X5 XM_017015757.2:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X15 XM_024447830.1:c. N/A Genic Downstream Transcript Variant
CTBP2 transcript variant X19 XM_024447831.1:c. N/A Genic Downstream Transcript Variant
Gene: ZRANB1, zinc finger RANBP2-type containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ZRANB1 transcript NM_017580.3:c.*532= N/A 3 Prime UTR Variant
ZRANB1 transcript variant X1 XM_006717907.2:c.*532= N/A 3 Prime UTR 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

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 57846 T=0.31242 A=0.00000, C=0.68758
European Sub 42370 T=0.25058 A=0.00000, C=0.74942
African Sub 4846 T=0.6432 A=0.0000, C=0.3568
African Others Sub 180 T=0.733 A=0.000, C=0.267
African American Sub 4666 T=0.6397 A=0.0000, C=0.3603
Asian Sub 454 T=0.271 A=0.000, C=0.729
East Asian Sub 386 T=0.264 A=0.000, C=0.736
Other Asian Sub 68 T=0.31 A=0.00, C=0.69
Latin American 1 Sub 596 T=0.411 A=0.000, C=0.589
Latin American 2 Sub 4994 T=0.5320 A=0.0000, C=0.4680
South Asian Sub 178 T=0.348 A=0.000, C=0.652
Other Sub 4408 T=0.2838 A=0.0000, C=0.7162


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 264690 T=0.397941 C=0.602059
gnomAD - Genomes Global Study-wide 140032 T=0.379528 C=0.620472
gnomAD - Genomes European Sub 75870 T=0.24987 C=0.75013
gnomAD - Genomes African Sub 41918 T=0.62157 C=0.37843
gnomAD - Genomes American Sub 13646 T=0.43603 C=0.56397
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.1835 C=0.8165
gnomAD - Genomes East Asian Sub 3132 T=0.2577 C=0.7423
gnomAD - Genomes Other Sub 2142 T=0.3576 C=0.6424
8.3KJPN JAPANESE Study-wide 16760 T=0.30877 C=0.69123
1000Genomes Global Study-wide 5008 T=0.3980 C=0.6020
1000Genomes African Sub 1322 T=0.6778 C=0.3222
1000Genomes East Asian Sub 1008 T=0.2192 C=0.7808
1000Genomes Europe Sub 1006 T=0.2545 C=0.7455
1000Genomes South Asian Sub 978 T=0.264 C=0.736
1000Genomes American Sub 694 T=0.522 C=0.478
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.2567 C=0.7433
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.2535 C=0.7465
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.2567 C=0.7433
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.3294 C=0.6706
Korean Genome Project KOREAN Study-wide 1832 T=0.3111 C=0.6889
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.248 C=0.752
Northern Sweden ACPOP Study-wide 600 T=0.205 C=0.795
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.277 C=0.723
SGDP_PRJ Global Study-wide 434 T=0.251 C=0.749
Qatari Global Study-wide 216 T=0.324 C=0.676
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.150 C=0.850
Siberian Global Study-wide 50 T=0.20 C=0.80
The Danish reference pan genome Danish Study-wide 40 T=0.17 C=0.82
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= A C
GRCh38.p13 chr 10 NC_000010.11:g.124985524= NC_000010.11:g.124985524T>A NC_000010.11:g.124985524T>C
GRCh37.p13 chr 10 NC_000010.10:g.126674093= NC_000010.10:g.126674093T>A NC_000010.10:g.126674093T>C
CTBP2 transcript variant 1 NM_001329.4:c.*3994= NM_001329.4:c.*3994A>T NM_001329.4:c.*3994A>G
CTBP2 transcript variant 2 NM_022802.3:c.*3994= NM_022802.3:c.*3994A>T NM_022802.3:c.*3994A>G
CTBP2 transcript variant 4 NM_001290214.3:c.*3994= NM_001290214.3:c.*3994A>T NM_001290214.3:c.*3994A>G
CTBP2 transcript variant 3 NM_001083914.3:c.*3994= NM_001083914.3:c.*3994A>T NM_001083914.3:c.*3994A>G
CTBP2 transcript variant 5 NM_001290215.3:c.*3994= NM_001290215.3:c.*3994A>T NM_001290215.3:c.*3994A>G
ZRANB1 transcript NM_017580.3:c.*532= NM_017580.3:c.*532T>A NM_017580.3:c.*532T>C
ZRANB1 transcript NM_017580.2:c.*532= NM_017580.2:c.*532T>A NM_017580.2:c.*532T>C
CTBP2 transcript variant 9 NM_001363508.2:c.*3994= NM_001363508.2:c.*3994A>T NM_001363508.2:c.*3994A>G
CTBP2 transcript variant 8 NM_001321014.2:c.*3994= NM_001321014.2:c.*3994A>T NM_001321014.2:c.*3994A>G
CTBP2 transcript variant 6 NM_001321012.2:c.*3994= NM_001321012.2:c.*3994A>T NM_001321012.2:c.*3994A>G
CTBP2 transcript variant 7 NM_001321013.2:c.*3994= NM_001321013.2:c.*3994A>T NM_001321013.2:c.*3994A>G
ZRANB1 transcript variant X1 XM_006717907.2:c.*532= XM_006717907.2:c.*532T>A XM_006717907.2:c.*532T>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#.

81 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss3882 Sep 19, 2000 (36)
2 CGAP-GAI ss10257 Sep 19, 2000 (52)
3 LEE ss1517423 Oct 04, 2000 (86)
4 HGBASE ss2421858 Nov 14, 2000 (89)
5 LEE ss4392637 May 29, 2002 (106)
6 LEE ss4409851 May 29, 2002 (106)
7 CGAP-GAI ss16239692 Feb 27, 2004 (120)
8 SSAHASNP ss20620208 Apr 05, 2004 (121)
9 ABI ss38630608 Mar 13, 2006 (126)
10 SI_EXO ss71648515 May 17, 2007 (127)
11 HUMANGENOME_JCVI ss97593323 Feb 04, 2009 (130)
12 1000GENOMES ss109834779 Jan 24, 2009 (130)
13 1000GENOMES ss113969552 Jan 25, 2009 (130)
14 ENSEMBL ss138777415 Dec 01, 2009 (131)
15 GMI ss155679096 Dec 01, 2009 (131)
16 ILLUMINA ss160649636 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss168794860 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss171296885 Jul 04, 2010 (132)
19 1000GENOMES ss224998282 Jul 14, 2010 (132)
20 1000GENOMES ss235374902 Jul 15, 2010 (132)
21 1000GENOMES ss242044264 Jul 15, 2010 (132)
22 BL ss254702184 May 09, 2011 (134)
23 GMI ss280814214 May 04, 2012 (137)
24 GMI ss286282573 Apr 25, 2013 (138)
25 PJP ss290954462 May 09, 2011 (134)
26 ILLUMINA ss481813198 Sep 08, 2015 (146)
27 ILLUMINA ss482503524 May 04, 2012 (137)
28 ILLUMINA ss483612277 May 04, 2012 (137)
29 ILLUMINA ss535816937 Sep 08, 2015 (146)
30 ILLUMINA ss779511825 Sep 08, 2015 (146)
31 ILLUMINA ss782249533 Sep 08, 2015 (146)
32 ILLUMINA ss834982195 Sep 08, 2015 (146)
33 EVA-GONL ss988031311 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1077378314 Aug 21, 2014 (142)
35 1000GENOMES ss1339477790 Aug 21, 2014 (142)
36 DDI ss1426476914 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1575419269 Apr 01, 2015 (144)
38 EVA_DECODE ss1597711058 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1625659981 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1668654014 Apr 01, 2015 (144)
41 EVA_MGP ss1711273536 Apr 01, 2015 (144)
42 HAMMER_LAB ss1806616470 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1931388552 Feb 12, 2016 (147)
44 GENOMED ss1967250397 Jul 19, 2016 (147)
45 JJLAB ss2026432449 Sep 14, 2016 (149)
46 USC_VALOUEV ss2154710970 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2178937077 Dec 20, 2016 (150)
48 TOPMED ss2342058723 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2627684119 Nov 08, 2017 (151)
50 ILLUMINA ss2632776766 Nov 08, 2017 (151)
51 GRF ss2698973323 Nov 08, 2017 (151)
52 GNOMAD ss2894541392 Nov 08, 2017 (151)
53 SWEGEN ss3007315102 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3027006584 Nov 08, 2017 (151)
55 TOPMED ss3133075868 Nov 08, 2017 (151)
56 TOPMED ss3133075869 Nov 08, 2017 (151)
57 CSHL ss3349360182 Nov 08, 2017 (151)
58 ILLUMINA ss3626559128 Oct 12, 2018 (152)
59 ILLUMINA ss3630798191 Oct 12, 2018 (152)
60 ILLUMINA ss3636114461 Oct 12, 2018 (152)
61 OMUKHERJEE_ADBS ss3646416737 Oct 12, 2018 (152)
62 URBANLAB ss3649490800 Oct 12, 2018 (152)
63 EGCUT_WGS ss3674735173 Jul 13, 2019 (153)
64 EVA_DECODE ss3690890067 Jul 13, 2019 (153)
65 ACPOP ss3737769851 Jul 13, 2019 (153)
66 EVA ss3748735467 Jul 13, 2019 (153)
67 PACBIO ss3786817151 Jul 13, 2019 (153)
68 PACBIO ss3791975220 Jul 13, 2019 (153)
69 PACBIO ss3796857381 Jul 13, 2019 (153)
70 KHV_HUMAN_GENOMES ss3814091723 Jul 13, 2019 (153)
71 EVA ss3825785984 Apr 26, 2020 (154)
72 EVA ss3832386914 Apr 26, 2020 (154)
73 EVA ss3839735043 Apr 26, 2020 (154)
74 EVA ss3845210365 Apr 26, 2020 (154)
75 SGDP_PRJ ss3875273042 Apr 26, 2020 (154)
76 KRGDB ss3923458592 Apr 26, 2020 (154)
77 KOGIC ss3968883734 Apr 26, 2020 (154)
78 FSA-LAB ss3983988733 Apr 26, 2021 (155)
79 EVA ss3986052220 Apr 26, 2021 (155)
80 TOPMED ss4870033245 Apr 26, 2021 (155)
81 TOMMO_GENOMICS ss5199939069 Apr 26, 2021 (155)
82 1000Genomes NC_000010.10 - 126674093 Oct 12, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 126674093 Oct 12, 2018 (152)
84 Genetic variation in the Estonian population NC_000010.10 - 126674093 Oct 12, 2018 (152)
85 The Danish reference pan genome NC_000010.10 - 126674093 Apr 26, 2020 (154)
86 gnomAD - Genomes NC_000010.11 - 124985524 Apr 26, 2021 (155)
87 Genome of the Netherlands Release 5 NC_000010.10 - 126674093 Apr 26, 2020 (154)
88 KOREAN population from KRGDB NC_000010.10 - 126674093 Apr 26, 2020 (154)
89 Korean Genome Project NC_000010.11 - 124985524 Apr 26, 2020 (154)
90 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 126674093 Apr 26, 2020 (154)
91 Northern Sweden NC_000010.10 - 126674093 Jul 13, 2019 (153)
92 Qatari NC_000010.10 - 126674093 Apr 26, 2020 (154)
93 SGDP_PRJ NC_000010.10 - 126674093 Apr 26, 2020 (154)
94 Siberian NC_000010.10 - 126674093 Apr 26, 2020 (154)
95 8.3KJPN NC_000010.10 - 126674093 Apr 26, 2021 (155)
96 TopMed NC_000010.11 - 124985524 Apr 26, 2021 (155)
97 UK 10K study - Twins NC_000010.10 - 126674093 Oct 12, 2018 (152)
98 A Vietnamese Genetic Variation Database NC_000010.10 - 126674093 Jul 13, 2019 (153)
99 ALFA NC_000010.11 - 124985524 Apr 26, 2021 (155)
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)
rs3168029 Jul 03, 2002 (106)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
11908533557, ss3133075868 NC_000010.11:124985523:T:A NC_000010.11:124985523:T:A (self)
ss109834779, ss113969552, ss168794860, ss171296885, ss254702184, ss280814214, ss286282573, ss290954462, ss482503524, ss1597711058 NC_000010.9:126664082:T:C NC_000010.11:124985523:T:C (self)
51939676, 28855885, 20473421, 2370394, 12860212, 30635986, 389296, 11054716, 13430482, 27290022, 7227324, 57908376, 28855885, 6403729, ss224998282, ss235374902, ss242044264, ss481813198, ss483612277, ss535816937, ss779511825, ss782249533, ss834982195, ss988031311, ss1077378314, ss1339477790, ss1426476914, ss1575419269, ss1625659981, ss1668654014, ss1711273536, ss1806616470, ss1931388552, ss1967250397, ss2026432449, ss2154710970, ss2342058723, ss2627684119, ss2632776766, ss2698973323, ss2894541392, ss3007315102, ss3349360182, ss3626559128, ss3630798191, ss3636114461, ss3646416737, ss3674735173, ss3737769851, ss3748735467, ss3786817151, ss3791975220, ss3796857381, ss3825785984, ss3832386914, ss3839735043, ss3875273042, ss3923458592, ss3983988733, ss3986052220, ss5199939069 NC_000010.10:126674092:T:C NC_000010.11:124985523:T:C (self)
366928660, 25261735, 53768650, 85578900, 11908533557, ss2178937077, ss3027006584, ss3133075869, ss3649490800, ss3690890067, ss3814091723, ss3845210365, ss3968883734, ss4870033245 NC_000010.11:124985523:T:C NC_000010.11:124985523:T:C (self)
ss3882, ss10257, ss1517423, ss2421858, ss4392637, ss4409851, ss16239692, ss38630608, ss71648515, ss97593323, ss138777415, ss155679096, ss160649636 NT_030059.13:77478556:T:C NC_000010.11:124985523:T:C (self)
ss20620208 NT_035040.4:754620:T:C NC_000010.11:124985523:T:C (self)
Help

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

No publications for rs3845

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post596+ae089ad