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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs12029362

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:67158548 (GRCh38.p14) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.285621 (75601/264690, TOPMED)
A=0.278612 (39004/139994, GnomAD)
A=0.33123 (9360/28258, 14KJPN) (+ 16 more)
A=0.33258 (5574/16760, 8.3KJPN)
A=0.18300 (2514/13738, ALFA)
A=0.2861 (1832/6404, 1000G_30x)
A=0.2883 (1444/5008, 1000G)
A=0.3357 (1504/4480, Estonian)
A=0.3207 (1236/3854, ALSPAC)
A=0.3064 (1136/3708, TWINSUK)
A=0.3225 (945/2930, KOREAN)
A=0.3302 (605/1832, Korea1K)
A=0.297 (296/998, GoNL)
A=0.345 (207/600, NorthernSweden)
G=0.365 (108/296, SGDP_PRJ)
A=0.273 (59/216, Qatari)
A=0.290 (61/210, Vietnamese)
G=0.34 (15/44, Siberian)
A=0.25 (10/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IL23R : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 13738 G=0.81700 A=0.18300, T=0.00000
European Sub 10756 G=0.78366 A=0.21634, T=0.00000
African Sub 2170 G=0.9438 A=0.0562, T=0.0000
African Others Sub 92 G=0.93 A=0.07, T=0.00
African American Sub 2078 G=0.9442 A=0.0558, T=0.0000
Asian Sub 48 G=0.98 A=0.02, T=0.00
East Asian Sub 42 G=1.00 A=0.00, T=0.00
Other Asian Sub 6 G=0.8 A=0.2, T=0.0
Latin American 1 Sub 76 G=1.00 A=0.00, T=0.00
Latin American 2 Sub 166 G=1.000 A=0.000, T=0.000
South Asian Sub 58 G=0.98 A=0.02, T=0.00
Other Sub 464 G=0.864 A=0.136, T=0.000


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 G=0.714379 A=0.285621
gnomAD - Genomes Global Study-wide 139994 G=0.721388 A=0.278612
gnomAD - Genomes European Sub 75820 G=0.68846 A=0.31154
gnomAD - Genomes African Sub 41946 G=0.81817 A=0.18183
gnomAD - Genomes American Sub 13642 G=0.59251 A=0.40749
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.8234 A=0.1766
gnomAD - Genomes East Asian Sub 3120 G=0.6929 A=0.3071
gnomAD - Genomes Other Sub 2148 G=0.6960 A=0.3040
14KJPN JAPANESE Study-wide 28258 G=0.66877 A=0.33123
8.3KJPN JAPANESE Study-wide 16760 G=0.66742 A=0.33258
Allele Frequency Aggregator Total Global 13738 G=0.81700 A=0.18300, T=0.00000
Allele Frequency Aggregator European Sub 10756 G=0.78366 A=0.21634, T=0.00000
Allele Frequency Aggregator African Sub 2170 G=0.9438 A=0.0562, T=0.0000
Allele Frequency Aggregator Other Sub 464 G=0.864 A=0.136, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 166 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 76 G=1.00 A=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 58 G=0.98 A=0.02, T=0.00
Allele Frequency Aggregator Asian Sub 48 G=0.98 A=0.02, T=0.00
1000Genomes_30x Global Study-wide 6404 G=0.7139 A=0.2861
1000Genomes_30x African Sub 1786 G=0.8337 A=0.1663
1000Genomes_30x Europe Sub 1266 G=0.7148 A=0.2852
1000Genomes_30x South Asian Sub 1202 G=0.7030 A=0.2970
1000Genomes_30x East Asian Sub 1170 G=0.6906 A=0.3094
1000Genomes_30x American Sub 980 G=0.536 A=0.464
1000Genomes Global Study-wide 5008 G=0.7117 A=0.2883
1000Genomes African Sub 1322 G=0.8222 A=0.1778
1000Genomes East Asian Sub 1008 G=0.6905 A=0.3095
1000Genomes Europe Sub 1006 G=0.7167 A=0.2833
1000Genomes South Asian Sub 978 G=0.693 A=0.307
1000Genomes American Sub 694 G=0.550 A=0.450
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6643 A=0.3357
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6793 A=0.3207
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6936 A=0.3064
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6775 A=0.3225
Korean Genome Project KOREAN Study-wide 1832 G=0.6698 A=0.3302
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.703 A=0.297
Northern Sweden ACPOP Study-wide 600 G=0.655 A=0.345
SGDP_PRJ Global Study-wide 296 G=0.365 A=0.635
Qatari Global Study-wide 216 G=0.727 A=0.273
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.710 A=0.290
Siberian Global Study-wide 44 G=0.34 A=0.66
The Danish reference pan genome Danish Study-wide 40 G=0.75 A=0.25
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.p14 chr 1 NC_000001.11:g.67158548G>A
GRCh38.p14 chr 1 NC_000001.11:g.67158548G>T
GRCh37.p13 chr 1 NC_000001.10:g.67624231G>A
GRCh37.p13 chr 1 NC_000001.10:g.67624231G>T
Gene: IL23R, interleukin 23 receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
IL23R transcript NM_144701.3:c. N/A Genic Upstream Transcript Variant
IL23R transcript variant X1 XM_011540790.4:c.-29-9544…

XM_011540790.4:c.-29-9544G>A

 		N/A Intron Variant
IL23R transcript variant X2 XM_011540791.4:c. N/A Genic Upstream Transcript Variant
IL23R transcript variant X3 XM_047447227.1: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

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 T
GRCh38.p14 chr 1 NC_000001.11:g.67158548= NC_000001.11:g.67158548G>A NC_000001.11:g.67158548G>T
GRCh37.p13 chr 1 NC_000001.10:g.67624231= NC_000001.10:g.67624231G>A NC_000001.10:g.67624231G>T
IL23R transcript variant X1 XM_005270512.1:c.-633-9544= XM_005270512.1:c.-633-9544G>A XM_005270512.1:c.-633-9544G>T
IL23R transcript variant X1 XM_011540790.4:c.-29-9544= XM_011540790.4:c.-29-9544G>A XM_011540790.4:c.-29-9544G>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#.

57 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18084627 Feb 28, 2004 (120)
2 BGI ss102749440 Dec 01, 2009 (131)
3 1000GENOMES ss108276679 Jan 23, 2009 (130)
4 ILLUMINA-UK ss118769594 Feb 14, 2009 (130)
5 BUSHMAN ss198568874 Jul 04, 2010 (132)
6 BCM-HGSC-SUB ss205321318 Jul 04, 2010 (132)
7 1000GENOMES ss218431952 Jul 14, 2010 (132)
8 1000GENOMES ss230569143 Jul 14, 2010 (132)
9 1000GENOMES ss238257037 Jul 15, 2010 (132)
10 GMI ss275860407 May 04, 2012 (137)
11 GMI ss284065308 Apr 25, 2013 (138)
12 TISHKOFF ss554208453 Apr 25, 2013 (138)
13 SSMP ss648083231 Apr 25, 2013 (138)
14 EVA-GONL ss975248890 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1067955324 Aug 21, 2014 (142)
16 1000GENOMES ss1291229261 Aug 21, 2014 (142)
17 DDI ss1425838132 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1574121765 Apr 01, 2015 (144)
19 EVA_DECODE ss1584618402 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1600353438 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1643347471 Apr 01, 2015 (144)
22 HAMMER_LAB ss1794498300 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1918456765 Feb 12, 2016 (147)
24 GENOMED ss1966767010 Jul 19, 2016 (147)
25 JJLAB ss2019745789 Sep 14, 2016 (149)
26 USC_VALOUEV ss2147761706 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2163206738 Dec 20, 2016 (150)
28 SYSTEMSBIOZJU ss2624386608 Nov 08, 2017 (151)
29 GRF ss2697679369 Nov 08, 2017 (151)
30 GNOMAD ss2756098424 Nov 08, 2017 (151)
31 AFFY ss2984862492 Nov 08, 2017 (151)
32 SWEGEN ss2986951854 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3023634697 Nov 08, 2017 (151)
34 CSHL ss3343493865 Nov 08, 2017 (151)
35 EGCUT_WGS ss3655022043 Jul 12, 2019 (153)
36 EVA_DECODE ss3686937477 Jul 12, 2019 (153)
37 ACPOP ss3727121301 Jul 12, 2019 (153)
38 EVA ss3746308891 Jul 12, 2019 (153)
39 KHV_HUMAN_GENOMES ss3799315634 Jul 12, 2019 (153)
40 EVA ss3826215754 Apr 25, 2020 (154)
41 SGDP_PRJ ss3849023537 Apr 25, 2020 (154)
42 KRGDB ss3894051679 Apr 25, 2020 (154)
43 KOGIC ss3944677143 Apr 25, 2020 (154)
44 TOPMED ss4452709319 Apr 25, 2021 (155)
45 TOMMO_GENOMICS ss5144327598 Apr 25, 2021 (155)
46 1000G_HIGH_COVERAGE ss5242561404 Oct 12, 2022 (156)
47 EVA ss5319265724 Oct 12, 2022 (156)
48 HUGCELL_USP ss5443595618 Oct 12, 2022 (156)
49 EVA ss5505880771 Oct 12, 2022 (156)
50 1000G_HIGH_COVERAGE ss5514985087 Oct 12, 2022 (156)
51 SANFORD_IMAGENETICS ss5625696746 Oct 12, 2022 (156)
52 TOMMO_GENOMICS ss5669207782 Oct 12, 2022 (156)
53 YY_MCH ss5800670071 Oct 12, 2022 (156)
54 EVA ss5832073420 Oct 12, 2022 (156)
55 EVA ss5848942628 Oct 12, 2022 (156)
56 EVA ss5908598480 Oct 12, 2022 (156)
57 EVA ss5937535409 Oct 12, 2022 (156)
58 1000Genomes NC_000001.10 - 67624231 Oct 11, 2018 (152)
59 1000Genomes_30x NC_000001.11 - 67158548 Oct 12, 2022 (156)
60 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 67624231 Oct 11, 2018 (152)
61 Genetic variation in the Estonian population NC_000001.10 - 67624231 Oct 11, 2018 (152)
62 The Danish reference pan genome NC_000001.10 - 67624231 Apr 25, 2020 (154)
63 gnomAD - Genomes NC_000001.11 - 67158548 Apr 25, 2021 (155)
64 Genome of the Netherlands Release 5 NC_000001.10 - 67624231 Apr 25, 2020 (154)
65 KOREAN population from KRGDB NC_000001.10 - 67624231 Apr 25, 2020 (154)
66 Korean Genome Project NC_000001.11 - 67158548 Apr 25, 2020 (154)
67 Northern Sweden NC_000001.10 - 67624231 Jul 12, 2019 (153)
68 Qatari NC_000001.10 - 67624231 Apr 25, 2020 (154)
69 SGDP_PRJ NC_000001.10 - 67624231 Apr 25, 2020 (154)
70 Siberian NC_000001.10 - 67624231 Apr 25, 2020 (154)
71 8.3KJPN NC_000001.10 - 67624231 Apr 25, 2021 (155)
72 14KJPN NC_000001.11 - 67158548 Oct 12, 2022 (156)
73 TopMed NC_000001.11 - 67158548 Apr 25, 2021 (155)
74 UK 10K study - Twins NC_000001.10 - 67624231 Oct 11, 2018 (152)
75 A Vietnamese Genetic Variation Database NC_000001.10 - 67624231 Jul 12, 2019 (153)
76 ALFA NC_000001.11 - 67158548 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108276679, ss118769594, ss198568874, ss205321318, ss275860407, ss284065308, ss1584618402 NC_000001.9:67396818:G:A NC_000001.11:67158547:G:A (self)
1959701, 1073712, 760291, 1537054, 458330, 1229073, 406166, 498695, 1040517, 278060, 2296905, 1073712, 225058, ss218431952, ss230569143, ss238257037, ss554208453, ss648083231, ss975248890, ss1067955324, ss1291229261, ss1425838132, ss1574121765, ss1600353438, ss1643347471, ss1794498300, ss1918456765, ss1966767010, ss2019745789, ss2147761706, ss2624386608, ss2697679369, ss2756098424, ss2984862492, ss2986951854, ss3343493865, ss3655022043, ss3727121301, ss3746308891, ss3826215754, ss3849023537, ss3894051679, ss5144327598, ss5319265724, ss5505880771, ss5625696746, ss5832073420, ss5937535409 NC_000001.10:67624230:G:A NC_000001.11:67158547:G:A (self)
2511022, 13821831, 1055144, 3044886, 16315654, 7137362671, ss2163206738, ss3023634697, ss3686937477, ss3799315634, ss3944677143, ss4452709319, ss5242561404, ss5443595618, ss5514985087, ss5669207782, ss5800670071, ss5848942628, ss5908598480 NC_000001.11:67158547:G:A NC_000001.11:67158547:G:A (self)
ss18084627 NT_032977.6:29187299:G:A NC_000001.11:67158547:G:A (self)
ss102749440 NT_032977.9:37596148:G:A NC_000001.11:67158547:G:A (self)
7137362671 NC_000001.11:67158547:G:T NC_000001.11:67158547:G: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 rs12029362

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.post761+d5e8e07