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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.

rs6667923

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1270963 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.101526 (26873/264690, TOPMED)
A=0.03468 (1183/34116, ALFA)
A=0.00024 (4/16760, 8.3KJPN) (+ 16 more)
A=0.1004 (503/5008, 1000G)
A=0.0312 (140/4480, Estonian)
A=0.0330 (127/3854, ALSPAC)
A=0.0372 (138/3708, TWINSUK)
A=0.0003 (1/2918, KOREAN)
A=0.0691 (144/2084, HGDP_Stanford)
A=0.0005 (1/1832, Korea1K)
A=0.1521 (237/1558, HapMap)
A=0.028 (28/998, GoNL)
A=0.037 (22/600, NorthernSweden)
A=0.079 (17/216, Qatari)
A=0.00 (0/80, Ancient Sardinia)
C=0.37 (28/76, SGDP_PRJ)
A=0.05 (2/40, GENOME_DK)
C=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
UBE2J2 : Intron 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 1 NC_000001.11:g.1270963C>A
GRCh38.p13 chr 1 NC_000001.11:g.1270963C>G
GRCh38.p13 chr 1 NC_000001.11:g.1270963C>T
GRCh37.p13 chr 1 NC_000001.10:g.1206343C>A
GRCh37.p13 chr 1 NC_000001.10:g.1206343C>G
GRCh37.p13 chr 1 NC_000001.10:g.1206343C>T
Gene: UBE2J2, ubiquitin conjugating enzyme E2 J2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
UBE2J2 transcript variant 2 NM_058167.3:c.-1+2703G>T N/A Intron Variant
UBE2J2 transcript variant 1 NM_194315.2:c.-1+2703G>T N/A Intron Variant
UBE2J2 transcript variant 4 NM_194457.2:c.-26+2703G>T N/A Intron Variant
UBE2J2 transcript variant 3 NM_194458.2:c.-286+2703G>T N/A Intron Variant
UBE2J2 transcript variant X2 XM_005244718.3:c.-1+2414G…

XM_005244718.3:c.-1+2414G>T

N/A Intron Variant
UBE2J2 transcript variant X4 XM_005244719.4:c.-1+2536G…

XM_005244719.4:c.-1+2536G>T

N/A Intron Variant
UBE2J2 transcript variant X3 XM_006710333.3:c.-1+1890G…

XM_006710333.3:c.-1+1890G>T

N/A Intron Variant
UBE2J2 transcript variant X5 XM_011540614.2:c.-1+2088G…

XM_011540614.2:c.-1+2088G>T

N/A Intron Variant
UBE2J2 transcript variant X9 XM_011540616.2:c.-408+270…

XM_011540616.2:c.-408+2703G>T

N/A Intron Variant
UBE2J2 transcript variant X7 XM_017000238.1:c.-279+270…

XM_017000238.1:c.-279+2703G>T

N/A Intron Variant
UBE2J2 transcript variant X1 XM_024453022.1:c.-224+270…

XM_024453022.1:c.-224+2703G>T

N/A Intron Variant
UBE2J2 transcript variant X6 XM_011540613.3:c. N/A Genic Upstream Transcript Variant
UBE2J2 transcript variant X10 XM_011540617.3:c. N/A Genic Upstream Transcript Variant
UBE2J2 transcript variant X8 XM_017000239.2: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

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 34116 C=0.96532 A=0.03468, G=0.00000, T=0.00000
European Sub 28062 C=0.97352 A=0.02648, G=0.00000, T=0.00000
African Sub 3040 C=0.8783 A=0.1217, G=0.0000, T=0.0000
African Others Sub 106 C=0.840 A=0.160, G=0.000, T=0.000
African American Sub 2934 C=0.8797 A=0.1203, G=0.0000, T=0.0000
Asian Sub 134 C=1.000 A=0.000, G=0.000, T=0.000
East Asian Sub 108 C=1.000 A=0.000, G=0.000, T=0.000
Other Asian Sub 26 C=1.00 A=0.00, G=0.00, T=0.00
Latin American 1 Sub 154 C=0.974 A=0.026, G=0.000, T=0.000
Latin American 2 Sub 736 C=1.000 A=0.000, G=0.000, T=0.000
South Asian Sub 110 C=1.000 A=0.000, G=0.000, T=0.000
Other Sub 1880 C=0.9649 A=0.0351, G=0.0000, T=0.0000


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 C=0.898474 A=0.101526
8.3KJPN JAPANESE Study-wide 16760 C=0.99976 A=0.00024
1000Genomes Global Study-wide 5008 C=0.8996 A=0.1004
1000Genomes African Sub 1322 C=0.7027 A=0.2973
1000Genomes East Asian Sub 1008 C=0.9990 A=0.0010
1000Genomes Europe Sub 1006 C=0.9682 A=0.0318
1000Genomes South Asian Sub 978 C=0.951 A=0.049
1000Genomes American Sub 694 C=0.958 A=0.042
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9688 A=0.0312
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9670 A=0.0330
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9628 A=0.0372
KOREAN population from KRGDB KOREAN Study-wide 2918 C=0.9997 A=0.0003
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.9309 A=0.0691
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.994 A=0.006
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.947 A=0.053
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.969 A=0.031
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.956 A=0.044
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.624 A=0.376
HGDP-CEPH-db Supplement 1 America Sub 216 C=1.000 A=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.96 A=0.04
Korean Genome Project KOREAN Study-wide 1832 C=0.9995 A=0.0005
HapMap Global Study-wide 1558 C=0.8479 A=0.1521
HapMap African Sub 692 C=0.727 A=0.273
HapMap American Sub 600 C=0.925 A=0.075
HapMap Europe Sub 176 C=0.983 A=0.017
HapMap Asian Sub 90 C=1.00 A=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.972 A=0.028
Northern Sweden ACPOP Study-wide 600 C=0.963 A=0.037
Qatari Global Study-wide 216 C=0.921 A=0.079
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 80 C=1.00 A=0.00
SGDP_PRJ Global Study-wide 76 C=0.37 A=0.63
The Danish reference pan genome Danish Study-wide 40 C=0.95 A=0.05
Siberian Global Study-wide 12 C=0.50 A=0.50
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 G T
GRCh38.p13 chr 1 NC_000001.11:g.1270963= NC_000001.11:g.1270963C>A NC_000001.11:g.1270963C>G NC_000001.11:g.1270963C>T
GRCh37.p13 chr 1 NC_000001.10:g.1206343= NC_000001.10:g.1206343C>A NC_000001.10:g.1206343C>G NC_000001.10:g.1206343C>T
UBE2J2 transcript variant 2 NM_058167.2:c.-1+2703= NM_058167.2:c.-1+2703G>T NM_058167.2:c.-1+2703G>C NM_058167.2:c.-1+2703G>A
UBE2J2 transcript variant 2 NM_058167.3:c.-1+2703= NM_058167.3:c.-1+2703G>T NM_058167.3:c.-1+2703G>C NM_058167.3:c.-1+2703G>A
UBE2J2 transcript variant 1 NM_194315.1:c.-1+2703= NM_194315.1:c.-1+2703G>T NM_194315.1:c.-1+2703G>C NM_194315.1:c.-1+2703G>A
UBE2J2 transcript variant 1 NM_194315.2:c.-1+2703= NM_194315.2:c.-1+2703G>T NM_194315.2:c.-1+2703G>C NM_194315.2:c.-1+2703G>A
UBE2J2 transcript variant 4 NM_194457.1:c.-26+2703= NM_194457.1:c.-26+2703G>T NM_194457.1:c.-26+2703G>C NM_194457.1:c.-26+2703G>A
UBE2J2 transcript variant 4 NM_194457.2:c.-26+2703= NM_194457.2:c.-26+2703G>T NM_194457.2:c.-26+2703G>C NM_194457.2:c.-26+2703G>A
UBE2J2 transcript variant 3 NM_194458.1:c.-286+2703= NM_194458.1:c.-286+2703G>T NM_194458.1:c.-286+2703G>C NM_194458.1:c.-286+2703G>A
UBE2J2 transcript variant 3 NM_194458.2:c.-286+2703= NM_194458.2:c.-286+2703G>T NM_194458.2:c.-286+2703G>C NM_194458.2:c.-286+2703G>A
UBE2J2 transcript variant X1 XM_005244718.1:c.-1+2414= XM_005244718.1:c.-1+2414G>T XM_005244718.1:c.-1+2414G>C XM_005244718.1:c.-1+2414G>A
UBE2J2 transcript variant X2 XM_005244718.3:c.-1+2414= XM_005244718.3:c.-1+2414G>T XM_005244718.3:c.-1+2414G>C XM_005244718.3:c.-1+2414G>A
UBE2J2 transcript variant X2 XM_005244719.1:c.-1+2536= XM_005244719.1:c.-1+2536G>T XM_005244719.1:c.-1+2536G>C XM_005244719.1:c.-1+2536G>A
UBE2J2 transcript variant X4 XM_005244719.4:c.-1+2536= XM_005244719.4:c.-1+2536G>T XM_005244719.4:c.-1+2536G>C XM_005244719.4:c.-1+2536G>A
UBE2J2 transcript variant X3 XM_006710333.3:c.-1+1890= XM_006710333.3:c.-1+1890G>T XM_006710333.3:c.-1+1890G>C XM_006710333.3:c.-1+1890G>A
UBE2J2 transcript variant X5 XM_011540614.2:c.-1+2088= XM_011540614.2:c.-1+2088G>T XM_011540614.2:c.-1+2088G>C XM_011540614.2:c.-1+2088G>A
UBE2J2 transcript variant X9 XM_011540616.2:c.-408+2703= XM_011540616.2:c.-408+2703G>T XM_011540616.2:c.-408+2703G>C XM_011540616.2:c.-408+2703G>A
UBE2J2 transcript variant X7 XM_017000238.1:c.-279+2703= XM_017000238.1:c.-279+2703G>T XM_017000238.1:c.-279+2703G>C XM_017000238.1:c.-279+2703G>A
UBE2J2 transcript variant X1 XM_024453022.1:c.-224+2703= XM_024453022.1:c.-224+2703G>T XM_024453022.1:c.-224+2703G>C XM_024453022.1:c.-224+2703G>A
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#.

61 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9831628 Jul 11, 2003 (116)
2 ILLUMINA ss67840061 Nov 29, 2006 (127)
3 PERLEGEN ss68756330 May 16, 2007 (127)
4 ILLUMINA ss71468781 May 16, 2007 (127)
5 ILLUMINA ss75406251 Dec 07, 2007 (129)
6 HGSV ss84928518 Dec 14, 2007 (130)
7 1000GENOMES ss109942456 Jan 24, 2009 (130)
8 KRIBB_YJKIM ss119519920 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss162984523 Jul 04, 2010 (132)
10 ILLUMINA ss174061991 Jul 04, 2010 (132)
11 BUSHMAN ss197890934 Jul 04, 2010 (132)
12 1000GENOMES ss218192711 Jul 14, 2010 (132)
13 1000GENOMES ss230396975 Jul 14, 2010 (132)
14 ILLUMINA ss244305837 Jul 04, 2010 (132)
15 ILLUMINA ss482087949 May 04, 2012 (137)
16 ILLUMINA ss484209910 May 04, 2012 (137)
17 ILLUMINA ss536397059 Sep 08, 2015 (146)
18 TISHKOFF ss553715523 Apr 25, 2013 (138)
19 SSMP ss647519524 Apr 25, 2013 (138)
20 ILLUMINA ss780568072 Sep 08, 2015 (146)
21 ILLUMINA ss782550937 Sep 08, 2015 (146)
22 ILLUMINA ss836060497 Sep 08, 2015 (146)
23 EVA-GONL ss974773551 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1067614531 Aug 21, 2014 (142)
25 1000GENOMES ss1289356690 Aug 21, 2014 (142)
26 EVA_GENOME_DK ss1573852591 Apr 01, 2015 (144)
27 EVA_DECODE ss1584133484 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1599385421 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1642379454 Apr 01, 2015 (144)
30 EVA_SVP ss1712305615 Apr 01, 2015 (144)
31 HAMMER_LAB ss1793720439 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1917965818 Feb 12, 2016 (147)
33 JJLAB ss2019500677 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147487699 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2159399081 Dec 20, 2016 (150)
36 TOPMED ss2321538553 Dec 20, 2016 (150)
37 TOPMED ss2321538554 Dec 20, 2016 (150)
38 ILLUMINA ss2632465923 Nov 08, 2017 (151)
39 GNOMAD ss2750689757 Nov 08, 2017 (151)
40 SWEGEN ss2986156989 Nov 08, 2017 (151)
41 TOPMED ss3066510855 Nov 08, 2017 (151)
42 TOPMED ss3066510856 Nov 08, 2017 (151)
43 CSHL ss3343275183 Nov 08, 2017 (151)
44 ILLUMINA ss3626007415 Oct 11, 2018 (152)
45 ILLUMINA ss3630505908 Oct 11, 2018 (152)
46 ILLUMINA ss3637732594 Oct 11, 2018 (152)
47 ILLUMINA ss3641566437 Oct 11, 2018 (152)
48 ILLUMINA ss3642746867 Oct 11, 2018 (152)
49 EGCUT_WGS ss3654268127 Jul 12, 2019 (153)
50 EVA_DECODE ss3686001263 Jul 12, 2019 (153)
51 ACPOP ss3726720107 Jul 12, 2019 (153)
52 EVA ss3745726174 Jul 12, 2019 (153)
53 KHV_HUMAN_GENOMES ss3798748892 Jul 12, 2019 (153)
54 EVA ss3825983395 Apr 25, 2020 (154)
55 HGDP ss3847322144 Apr 25, 2020 (154)
56 SGDP_PRJ ss3848008157 Apr 25, 2020 (154)
57 KRGDB ss3892851394 Apr 25, 2020 (154)
58 KOGIC ss3943639855 Apr 25, 2020 (154)
59 EVA ss3984774133 Apr 25, 2021 (155)
60 TOPMED ss4436568623 Apr 25, 2021 (155)
61 TOMMO_GENOMICS ss5142074631 Apr 25, 2021 (155)
62 1000Genomes NC_000001.10 - 1206343 Oct 11, 2018 (152)
63 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1206343 Oct 11, 2018 (152)
64 Genetic variation in the Estonian population NC_000001.10 - 1206343 Oct 11, 2018 (152)
65 The Danish reference pan genome NC_000001.10 - 1206343 Apr 25, 2020 (154)
66 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 183424 (NC_000001.11:1270962:C:A 13964/140174)
Row 183425 (NC_000001.11:1270962:C:T 3/140200)

- Apr 25, 2021 (155)
67 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 183424 (NC_000001.11:1270962:C:A 13964/140174)
Row 183425 (NC_000001.11:1270962:C:T 3/140200)

- Apr 25, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000001.10 - 1206343 Apr 25, 2020 (154)
69 HGDP-CEPH-db Supplement 1 NC_000001.9 - 1196206 Apr 25, 2020 (154)
70 HapMap NC_000001.11 - 1270963 Apr 25, 2020 (154)
71 KOREAN population from KRGDB NC_000001.10 - 1206343 Apr 25, 2020 (154)
72 Korean Genome Project NC_000001.11 - 1270963 Apr 25, 2020 (154)
73 Northern Sweden NC_000001.10 - 1206343 Jul 12, 2019 (153)
74 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 1206343 Apr 25, 2021 (155)
75 Qatari NC_000001.10 - 1206343 Apr 25, 2020 (154)
76 SGDP_PRJ NC_000001.10 - 1206343 Apr 25, 2020 (154)
77 Siberian NC_000001.10 - 1206343 Apr 25, 2020 (154)
78 8.3KJPN NC_000001.10 - 1206343 Apr 25, 2021 (155)
79 TopMed NC_000001.11 - 1270963 Apr 25, 2021 (155)
80 UK 10K study - Twins NC_000001.10 - 1206343 Oct 11, 2018 (152)
81 ALFA NC_000001.11 - 1270963 Apr 25, 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)
rs58099348 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84928518 NC_000001.8:1246265:C:A NC_000001.11:1270962:C:A (self)
36, ss109942456, ss162984523, ss197890934, ss482087949, ss1584133484, ss1712305615, ss3642746867, ss3847322144 NC_000001.9:1196205:C:A NC_000001.11:1270962:C:A (self)
21989, 7995, 6375, 1359825, 3369, 28788, 4972, 60, 7748, 25137, 4053, 43938, 7995, ss218192711, ss230396975, ss484209910, ss536397059, ss553715523, ss647519524, ss780568072, ss782550937, ss836060497, ss974773551, ss1067614531, ss1289356690, ss1573852591, ss1599385421, ss1642379454, ss1793720439, ss1917965818, ss2019500677, ss2147487699, ss2321538553, ss2632465923, ss2750689757, ss2986156989, ss3343275183, ss3626007415, ss3630505908, ss3637732594, ss3641566437, ss3654268127, ss3726720107, ss3745726174, ss3825983395, ss3848008157, ss3892851394, ss3984774133, ss5142074631 NC_000001.10:1206342:C:A NC_000001.11:1270962:C:A (self)
350, 17856, 102280, 174958, 3014551607, ss2159399081, ss3066510855, ss3686001263, ss3798748892, ss3943639855, ss4436568623 NC_000001.11:1270962:C:A NC_000001.11:1270962:C:A (self)
ss67840061, ss68756330, ss71468781, ss75406251, ss119519920, ss174061991, ss244305837 NT_004350.19:684974:C:A NC_000001.11:1270962:C:A (self)
ss9831628 NT_077913.1:81076:C:A NC_000001.11:1270962:C:A (self)
3014551607 NC_000001.11:1270962:C:G NC_000001.11:1270962:C:G
ss2321538554 NC_000001.10:1206342:C:T NC_000001.11:1270962:C:T (self)
3014551607, ss3066510856 NC_000001.11:1270962:C:T NC_000001.11:1270962: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.

No publications for rs6667923

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