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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.

rs12529107

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:32390234 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.142665 (37762/264690, TOPMED)
A=0.154858 (21659/139864, GnomAD)
A=0.07333 (3302/45028, ALFA) (+ 16 more)
A=0.28488 (8050/28258, 14KJPN)
A=0.28496 (4776/16760, 8.3KJPN)
A=0.1651 (1057/6404, 1000G_30x)
A=0.1683 (843/5008, 1000G)
A=0.1679 (752/4480, Estonian)
A=0.1430 (551/3854, ALSPAC)
A=0.1321 (490/3708, TWINSUK)
A=0.2303 (673/2922, KOREAN)
A=0.083 (83/998, GoNL)
A=0.145 (87/600, NorthernSweden)
A=0.106 (23/216, Qatari)
G=0.468 (73/156, SGDP_PRJ)
A=0.017 (2/118, HapMap)
A=0.10 (4/40, GENOME_DK)
G=0.50 (9/18, Siberian)
A=0.50 (9/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TSBP1-AS1 : Intron Variant
HCG23 : 2KB Upstream 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 45028 G=0.92667 A=0.07333
European Sub 34482 G=0.93533 A=0.06467
African Sub 3244 G=0.8567 A=0.1433
African Others Sub 114 G=0.825 A=0.175
African American Sub 3130 G=0.8578 A=0.1422
Asian Sub 134 G=0.910 A=0.090
East Asian Sub 104 G=0.894 A=0.106
Other Asian Sub 30 G=0.97 A=0.03
Latin American 1 Sub 162 G=0.870 A=0.130
Latin American 2 Sub 644 G=0.837 A=0.163
South Asian Sub 114 G=0.868 A=0.132
Other Sub 6248 G=0.9273 A=0.0727


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=0.857335 A=0.142665
gnomAD - Genomes Global Study-wide 139864 G=0.845142 A=0.154858
gnomAD - Genomes European Sub 75768 G=0.83459 A=0.16541
gnomAD - Genomes African Sub 41870 G=0.85125 A=0.14875
gnomAD - Genomes American Sub 13642 G=0.85896 A=0.14104
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.9205 A=0.0795
gnomAD - Genomes East Asian Sub 3116 G=0.8806 A=0.1194
gnomAD - Genomes Other Sub 2148 G=0.8426 A=0.1574
Allele Frequency Aggregator Total Global 45028 G=0.92667 A=0.07333
Allele Frequency Aggregator European Sub 34482 G=0.93533 A=0.06467
Allele Frequency Aggregator Other Sub 6248 G=0.9273 A=0.0727
Allele Frequency Aggregator African Sub 3244 G=0.8567 A=0.1433
Allele Frequency Aggregator Latin American 2 Sub 644 G=0.837 A=0.163
Allele Frequency Aggregator Latin American 1 Sub 162 G=0.870 A=0.130
Allele Frequency Aggregator Asian Sub 134 G=0.910 A=0.090
Allele Frequency Aggregator South Asian Sub 114 G=0.868 A=0.132
14KJPN JAPANESE Study-wide 28258 G=0.71512 A=0.28488
8.3KJPN JAPANESE Study-wide 16760 G=0.71504 A=0.28496
1000Genomes_30x Global Study-wide 6404 G=0.8349 A=0.1651
1000Genomes_30x African Sub 1786 G=0.8460 A=0.1540
1000Genomes_30x Europe Sub 1266 G=0.8365 A=0.1635
1000Genomes_30x South Asian Sub 1202 G=0.7987 A=0.2013
1000Genomes_30x East Asian Sub 1170 G=0.8547 A=0.1453
1000Genomes_30x American Sub 980 G=0.834 A=0.166
1000Genomes Global Study-wide 5008 G=0.8317 A=0.1683
1000Genomes African Sub 1322 G=0.8427 A=0.1573
1000Genomes East Asian Sub 1008 G=0.8423 A=0.1577
1000Genomes Europe Sub 1006 G=0.8370 A=0.1630
1000Genomes South Asian Sub 978 G=0.799 A=0.201
1000Genomes American Sub 694 G=0.834 A=0.166
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8321 A=0.1679
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8570 A=0.1430
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8679 A=0.1321
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.7697 A=0.2303
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.917 A=0.083
Northern Sweden ACPOP Study-wide 600 G=0.855 A=0.145
Qatari Global Study-wide 216 G=0.894 A=0.106
SGDP_PRJ Global Study-wide 156 G=0.468 A=0.532
HapMap Global Study-wide 118 G=0.983 A=0.017
HapMap African Sub 118 G=0.983 A=0.017
The Danish reference pan genome Danish Study-wide 40 G=0.90 A=0.10
Siberian Global Study-wide 18 G=0.50 A=0.50
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 6 NC_000006.12:g.32390234G>A
GRCh37.p13 chr 6 NC_000006.11:g.32358011G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.3828334G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.3828440G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.3613274G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.3618870G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.3631325G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.3636910G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.3706155G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.3705453G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.3695226G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.3700846G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.3731983G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.3737568G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.3722465G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.3672381G>A
GRCh38.p14 chr 6 alt locus HSCHR6_8_CTG1 NT_187692.1:g.63732T>C
Gene: TSBP1-AS1, TSBP1 and BTNL2 antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TSBP1-AS1 transcript variant 2 NR_136245.1:n. N/A Intron Variant
TSBP1-AS1 transcript variant 1 NR_136244.1:n. N/A Genic Downstream Transcript Variant
TSBP1-AS1 transcript variant 3 NR_136246.1:n. N/A Genic Downstream Transcript Variant
Gene: HCG23, HLA complex group 23 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
HCG23 transcript NR_044996.1:n. N/A 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
GRCh38.p14 chr 6 NC_000006.12:g.32390234= NC_000006.12:g.32390234G>A
GRCh37.p13 chr 6 NC_000006.11:g.32358011= NC_000006.11:g.32358011G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.3828334= NT_113891.3:g.3828334G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.3828440= NT_113891.2:g.3828440G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.3613274= NT_167248.2:g.3613274G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.3618870= NT_167248.1:g.3618870G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.3631325= NT_167245.2:g.3631325G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.3636910= NT_167245.1:g.3636910G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.3706155= NT_167249.2:g.3706155G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.3705453= NT_167249.1:g.3705453G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.3695226= NT_167246.2:g.3695226G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.3700846= NT_167246.1:g.3700846G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.3731983= NT_167247.2:g.3731983G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.3737568= NT_167247.1:g.3737568G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.3722465= NT_167244.2:g.3722465G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.3672381= NT_167244.1:g.3672381G>A
GRCh38.p14 chr 6 alt locus HSCHR6_8_CTG1 NT_187692.1:g.63732T>C NT_187692.1:g.63732=
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#.

67 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19686872 Feb 28, 2004 (120)
2 FHCRC ss23138245 Sep 20, 2004 (126)
3 HGSV ss82692077 Dec 15, 2007 (130)
4 HGSV ss83004094 Dec 15, 2007 (130)
5 HGSV ss83334593 Dec 15, 2007 (130)
6 BCMHGSC_JDW ss93437699 Mar 24, 2008 (129)
7 1000GENOMES ss109905926 Feb 13, 2009 (137)
8 ILLUMINA ss160279588 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss163354133 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss166439539 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss207718510 Jul 04, 2010 (132)
12 1000GENOMES ss211813451 Jul 14, 2010 (137)
13 1000GENOMES ss222306769 Jul 14, 2010 (137)
14 1000GENOMES ss233401632 Jul 14, 2010 (137)
15 1000GENOMES ss240472185 Jul 15, 2010 (137)
16 GMI ss278730085 May 04, 2012 (137)
17 ILLUMINA ss480335033 Sep 08, 2015 (146)
18 ILLUMINA ss532889833 Sep 08, 2015 (146)
19 TISHKOFF ss559117616 Apr 25, 2013 (138)
20 SSMP ss653040141 Apr 25, 2013 (138)
21 ILLUMINA ss834150742 Sep 08, 2015 (146)
22 EVA-GONL ss982773051 Aug 21, 2014 (142)
23 1000GENOMES ss1319578030 Aug 21, 2014 (142)
24 EVA_GENOME_DK ss1581609720 Apr 01, 2015 (144)
25 EVA_DECODE ss1592316709 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1615288439 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1658282472 Apr 01, 2015 (144)
28 HAMMER_LAB ss1804360739 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1926025045 Feb 12, 2016 (147)
30 JJLAB ss2023646372 Sep 14, 2016 (149)
31 USC_VALOUEV ss2151813572 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2282982046 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2626310886 Nov 08, 2017 (151)
34 ILLUMINA ss2634432245 Nov 08, 2017 (151)
35 GRF ss2707407523 Nov 08, 2017 (151)
36 SWEGEN ss2998807125 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3025610295 Nov 08, 2017 (151)
38 ILLUMINA ss3629508346 Oct 12, 2018 (152)
39 ILLUMINA ss3632350472 Oct 12, 2018 (152)
40 ILLUMINA ss3636780152 Oct 12, 2018 (152)
41 EGCUT_WGS ss3666720501 Jul 13, 2019 (153)
42 EVA_DECODE ss3716920905 Jul 13, 2019 (153)
43 ACPOP ss3733368030 Jul 13, 2019 (153)
44 ILLUMINA ss3744551068 Jul 13, 2019 (153)
45 EVA ss3764830452 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3807985119 Jul 13, 2019 (153)
47 EVA ss3829836484 Apr 26, 2020 (154)
48 EVA ss3838396768 Apr 26, 2020 (154)
49 EVA ss3843838966 Apr 26, 2020 (154)
50 SGDP_PRJ ss3864267088 Apr 26, 2020 (154)
51 KRGDB ss3911044475 Apr 26, 2020 (154)
52 VINODS ss4025210666 Apr 26, 2021 (155)
53 VINODS ss4025268186 Apr 26, 2021 (155)
54 VINODS ss4025289020 Apr 26, 2021 (155)
55 TOPMED ss4698551129 Apr 26, 2021 (155)
56 TOMMO_GENOMICS ss5176862727 Apr 26, 2021 (155)
57 1000G_HIGH_COVERAGE ss5267955270 Oct 13, 2022 (156)
58 EVA ss5364754551 Oct 13, 2022 (156)
59 HUGCELL_USP ss5465686750 Oct 13, 2022 (156)
60 EVA ss5508432469 Oct 13, 2022 (156)
61 1000G_HIGH_COVERAGE ss5553618694 Oct 13, 2022 (156)
62 SANFORD_IMAGENETICS ss5640100690 Oct 13, 2022 (156)
63 TOMMO_GENOMICS ss5714726305 Oct 13, 2022 (156)
64 YY_MCH ss5807314390 Oct 13, 2022 (156)
65 EVA ss5842036336 Oct 13, 2022 (156)
66 EVA ss5883263063 Oct 13, 2022 (156)
67 EVA ss5968602509 Oct 13, 2022 (156)
68 1000Genomes NC_000006.11 - 32358011 Oct 12, 2018 (152)
69 1000Genomes_30x NC_000006.12 - 32390234 Oct 13, 2022 (156)
70 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 32358011 Oct 12, 2018 (152)
71 Genetic variation in the Estonian population NC_000006.11 - 32358011 Oct 12, 2018 (152)
72 The Danish reference pan genome NC_000006.11 - 32358011 Apr 26, 2020 (154)
73 gnomAD - Genomes NC_000006.12 - 32390234 Apr 26, 2021 (155)
74 Genome of the Netherlands Release 5 NC_000006.11 - 32358011 Apr 26, 2020 (154)
75 HapMap NC_000006.12 - 32390234 Apr 26, 2020 (154)
76 KOREAN population from KRGDB NC_000006.11 - 32358011 Apr 26, 2020 (154)
77 Northern Sweden NC_000006.11 - 32358011 Jul 13, 2019 (153)
78 Qatari NC_000006.11 - 32358011 Apr 26, 2020 (154)
79 SGDP_PRJ NC_000006.11 - 32358011 Apr 26, 2020 (154)
80 Siberian NC_000006.11 - 32358011 Apr 26, 2020 (154)
81 8.3KJPN NC_000006.11 - 32358011 Apr 26, 2021 (155)
82 14KJPN NC_000006.12 - 32390234 Oct 13, 2022 (156)
83 TopMed NC_000006.12 - 32390234 Apr 26, 2021 (155)
84 UK 10K study - Twins NC_000006.11 - 32358011 Oct 12, 2018 (152)
85 ALFA NC_000006.12 - 32390234 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)
rs17208643 Mar 10, 2006 (126)
rs59230063 May 25, 2008 (130)
rs114098974 May 04, 2012 (137)
rs118147714 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82692077, ss83004094, ss83334593 NC_000006.9:32465988:G:A NC_000006.12:32390233:G:A (self)
ss93437699, ss109905926, ss163354133, ss166439539, ss207718510, ss211813451, ss278730085, ss1592316709 NC_000006.10:32465988:G:A NC_000006.12:32390233:G:A (self)
31346334, 17479316, 12458749, 7774659, 7771386, 18221869, 6652895, 8066975, 16284068, 4329926, 34832034, 17479316, ss222306769, ss233401632, ss240472185, ss480335033, ss532889833, ss559117616, ss653040141, ss834150742, ss982773051, ss1319578030, ss1581609720, ss1615288439, ss1658282472, ss1804360739, ss1926025045, ss2023646372, ss2151813572, ss2626310886, ss2634432245, ss2707407523, ss2998807125, ss3629508346, ss3632350472, ss3636780152, ss3666720501, ss3733368030, ss3744551068, ss3764830452, ss3829836484, ss3838396768, ss3864267088, ss3911044475, ss5176862727, ss5364754551, ss5508432469, ss5640100690, ss5842036336, ss5968602509 NC_000006.11:32358010:G:A NC_000006.12:32390233:G:A (self)
41144629, 221362386, 3101847, 48563409, 535928687, 3412117435, ss2282982046, ss3025610295, ss3716920905, ss3807985119, ss3843838966, ss4698551129, ss5267955270, ss5465686750, ss5553618694, ss5714726305, ss5807314390, ss5883263063 NC_000006.12:32390233:G:A NC_000006.12:32390233:G:A (self)
ss19686872 NT_007592.13:23179480:G:A NC_000006.12:32390233:G:A (self)
ss23138245, ss160279588 NT_007592.15:32298010:G:A NC_000006.12:32390233:G:A (self)
ss4025210666 NT_167245.2:3631324:G:A NC_000006.12:32390233:G:A (self)
ss4025268186 NT_167248.2:3613273:G:A NC_000006.12:32390233:G:A (self)
ss4025289020 NT_167249.2:3706154:G:A NC_000006.12:32390233:G:A (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 rs12529107

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