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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.

rs9389268

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr6:135098493 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.224644 (59461/264690, TOPMED)
G=0.238077 (33257/139690, GnomAD)
G=0.25079 (4737/18888, ALFA) (+ 14 more)
G=0.34004 (5699/16760, 8.3KJPN)
G=0.2041 (1022/5008, 1000G)
G=0.3017 (1351/4478, Estonian)
G=0.2613 (1007/3854, ALSPAC)
G=0.2597 (963/3708, TWINSUK)
G=0.3157 (925/2930, KOREAN)
G=0.3199 (586/1832, Korea1K)
G=0.262 (261/998, GoNL)
G=0.338 (203/600, NorthernSweden)
G=0.259 (84/324, HapMap)
G=0.171 (37/216, Qatari)
A=0.440 (88/200, SGDP_PRJ)
G=0.33 (13/40, GENOME_DK)
A=0.31 (10/32, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
7 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18888 A=0.74921 G=0.25079
European Sub 14284 A=0.73012 G=0.26988
African Sub 2946 A=0.8045 G=0.1955
African Others Sub 114 A=0.798 G=0.202
African American Sub 2832 A=0.8047 G=0.1953
Asian Sub 112 A=0.750 G=0.250
East Asian Sub 86 A=0.77 G=0.23
Other Asian Sub 26 A=0.69 G=0.31
Latin American 1 Sub 146 A=0.870 G=0.130
Latin American 2 Sub 610 A=0.849 G=0.151
South Asian Sub 98 A=0.86 G=0.14
Other Sub 692 A=0.779 G=0.221


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 A=0.775356 G=0.224644
gnomAD - Genomes Global Study-wide 139690 A=0.761923 G=0.238077
gnomAD - Genomes European Sub 75662 A=0.72984 G=0.27016
gnomAD - Genomes African Sub 41852 A=0.79927 G=0.20073
gnomAD - Genomes American Sub 13612 A=0.81972 G=0.18028
gnomAD - Genomes Ashkenazi Jewish Sub 3310 A=0.7686 G=0.2314
gnomAD - Genomes East Asian Sub 3108 A=0.7619 G=0.2381
gnomAD - Genomes Other Sub 2146 A=0.7880 G=0.2120
8.3KJPN JAPANESE Study-wide 16760 A=0.65996 G=0.34004
1000Genomes Global Study-wide 5008 A=0.7959 G=0.2041
1000Genomes African Sub 1322 A=0.7776 G=0.2224
1000Genomes East Asian Sub 1008 A=0.7560 G=0.2440
1000Genomes Europe Sub 1006 A=0.7356 G=0.2644
1000Genomes South Asian Sub 978 A=0.894 G=0.106
1000Genomes American Sub 694 A=0.839 G=0.161
Genetic variation in the Estonian population Estonian Study-wide 4478 A=0.6983 G=0.3017
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7387 G=0.2613
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.7403 G=0.2597
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6843 G=0.3157
Korean Genome Project KOREAN Study-wide 1832 A=0.6801 G=0.3199
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.738 G=0.262
Northern Sweden ACPOP Study-wide 600 A=0.662 G=0.338
HapMap Global Study-wide 324 A=0.741 G=0.259
HapMap American Sub 120 A=0.775 G=0.225
HapMap African Sub 116 A=0.776 G=0.224
HapMap Asian Sub 88 A=0.65 G=0.35
Qatari Global Study-wide 216 A=0.829 G=0.171
SGDP_PRJ Global Study-wide 200 A=0.440 G=0.560
The Danish reference pan genome Danish Study-wide 40 A=0.68 G=0.33
Siberian Global Study-wide 32 A=0.31 G=0.69
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 6 NC_000006.12:g.135098493A>G
GRCh37.p13 chr 6 NC_000006.11:g.135419631A>G
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 A= G
GRCh38.p13 chr 6 NC_000006.12:g.135098493= NC_000006.12:g.135098493A>G
GRCh37.p13 chr 6 NC_000006.11:g.135419631= NC_000006.11:g.135419631A>G
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#.

63 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12884702 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss17137562 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss20288229 Feb 27, 2004 (120)
4 SSAHASNP ss22447111 Apr 05, 2004 (121)
5 ABI ss42798910 Mar 13, 2006 (126)
6 CGM_KYOTO ss76875217 Dec 07, 2007 (129)
7 BCMHGSC_JDW ss93565710 Mar 24, 2008 (129)
8 HUMANGENOME_JCVI ss98544190 Feb 04, 2009 (130)
9 1000GENOMES ss110968451 Jan 25, 2009 (130)
10 ILLUMINA-UK ss116729522 Dec 01, 2009 (131)
11 ENSEMBL ss142754629 Dec 01, 2009 (131)
12 ENSEMBL ss144322606 Dec 01, 2009 (131)
13 GMI ss157627649 Dec 01, 2009 (131)
14 ILLUMINA ss160983655 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss162839456 Jul 04, 2010 (132)
16 BUSHMAN ss202456153 Jul 04, 2010 (132)
17 1000GENOMES ss211930991 Jul 14, 2010 (132)
18 1000GENOMES ss222696899 Jul 14, 2010 (132)
19 1000GENOMES ss233699178 Jul 15, 2010 (132)
20 1000GENOMES ss240709785 Jul 15, 2010 (132)
21 GMI ss279036587 May 04, 2012 (137)
22 GMI ss285511030 Apr 25, 2013 (138)
23 ILLUMINA ss482879480 Sep 08, 2015 (146)
24 TISHKOFF ss559550189 Apr 25, 2013 (138)
25 SSMP ss653824627 Apr 25, 2013 (138)
26 EVA-GONL ss983542789 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1074065854 Aug 21, 2014 (142)
28 1000GENOMES ss1322431920 Aug 21, 2014 (142)
29 DDI ss1430907146 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1581913514 Apr 01, 2015 (144)
31 EVA_DECODE ss1593112819 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1616781726 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1659775759 Apr 01, 2015 (144)
34 HAMMER_LAB ss1804689743 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1926787522 Feb 12, 2016 (147)
36 ILLUMINA ss1958953415 Feb 12, 2016 (147)
37 JJLAB ss2024051832 Sep 14, 2016 (149)
38 USC_VALOUEV ss2152244570 Dec 20, 2016 (150)
39 TOPMED ss2457399577 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2626519356 Nov 08, 2017 (151)
41 GRF ss2707876580 Nov 08, 2017 (151)
42 GNOMAD ss2845578518 Nov 08, 2017 (151)
43 SWEGEN ss3000015284 Nov 08, 2017 (151)
44 ILLUMINA ss3022669924 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3025818590 Nov 08, 2017 (151)
46 CSHL ss3347247159 Nov 08, 2017 (151)
47 TOPMED ss3512939566 Nov 08, 2017 (151)
48 ILLUMINA ss3636815746 Oct 12, 2018 (152)
49 URBANLAB ss3648479734 Oct 12, 2018 (152)
50 ILLUMINA ss3653192680 Oct 12, 2018 (152)
51 EGCUT_WGS ss3667935699 Jul 13, 2019 (153)
52 EVA_DECODE ss3718356843 Jul 13, 2019 (153)
53 ACPOP ss3734018588 Jul 13, 2019 (153)
54 EVA ss3765718177 Jul 13, 2019 (153)
55 KHV_HUMAN_GENOMES ss3808876116 Jul 13, 2019 (153)
56 EVA ss3830212701 Apr 26, 2020 (154)
57 EVA ss3838593784 Apr 26, 2020 (154)
58 EVA ss3844043950 Apr 26, 2020 (154)
59 SGDP_PRJ ss3865793349 Apr 26, 2020 (154)
60 KRGDB ss3912753994 Apr 26, 2020 (154)
61 KOGIC ss3960145368 Apr 26, 2020 (154)
62 TOPMED ss4723247806 Apr 26, 2021 (155)
63 TOMMO_GENOMICS ss5180110271 Apr 26, 2021 (155)
64 1000Genomes NC_000006.11 - 135419631 Oct 12, 2018 (152)
65 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 135419631 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000006.11 - 135419631 Oct 12, 2018 (152)
67 The Danish reference pan genome NC_000006.11 - 135419631 Apr 26, 2020 (154)
68 gnomAD - Genomes NC_000006.12 - 135098493 Apr 26, 2021 (155)
69 Genome of the Netherlands Release 5 NC_000006.11 - 135419631 Apr 26, 2020 (154)
70 HapMap NC_000006.12 - 135098493 Apr 26, 2020 (154)
71 KOREAN population from KRGDB NC_000006.11 - 135419631 Apr 26, 2020 (154)
72 Korean Genome Project NC_000006.12 - 135098493 Apr 26, 2020 (154)
73 Northern Sweden NC_000006.11 - 135419631 Jul 13, 2019 (153)
74 Qatari NC_000006.11 - 135419631 Apr 26, 2020 (154)
75 SGDP_PRJ NC_000006.11 - 135419631 Apr 26, 2020 (154)
76 Siberian NC_000006.11 - 135419631 Apr 26, 2020 (154)
77 8.3KJPN NC_000006.11 - 135419631 Apr 26, 2021 (155)
78 TopMed NC_000006.12 - 135098493 Apr 26, 2021 (155)
79 UK 10K study - Twins NC_000006.11 - 135419631 Oct 12, 2018 (152)
80 ALFA NC_000006.12 - 135098493 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss93565710, ss110968451, ss116729522, ss162839456, ss202456153, ss211930991, ss279036587, ss285511030, ss1593112819 NC_000006.10:135461323:A:G NC_000006.12:135098492:A:G (self)
34307015, 19121734, 13673947, 8078453, 8516670, 19931388, 7303453, 8829452, 17810329, 4760924, 38079578, 19121734, ss222696899, ss233699178, ss240709785, ss482879480, ss559550189, ss653824627, ss983542789, ss1074065854, ss1322431920, ss1430907146, ss1581913514, ss1616781726, ss1659775759, ss1804689743, ss1926787522, ss1958953415, ss2024051832, ss2152244570, ss2457399577, ss2626519356, ss2707876580, ss2845578518, ss3000015284, ss3022669924, ss3347247159, ss3636815746, ss3653192680, ss3667935699, ss3734018588, ss3765718177, ss3830212701, ss3838593784, ss3865793349, ss3912753994, ss5180110271 NC_000006.11:135419630:A:G NC_000006.12:135098492:A:G (self)
242278995, 3258019, 16523369, 350670863, 560625364, 2543991984, ss3025818590, ss3512939566, ss3648479734, ss3718356843, ss3808876116, ss3844043950, ss3960145368, ss4723247806 NC_000006.12:135098492:A:G NC_000006.12:135098492:A:G (self)
ss12884702 NT_025741.12:39524059:A:G NC_000006.12:135098492:A:G (self)
ss17137562, ss20288229, ss22447111 NT_025741.13:39524059:A:G NC_000006.12:135098492:A:G (self)
ss42798910, ss76875217, ss98544190, ss142754629, ss144322606, ss157627649, ss160983655 NT_025741.15:39589087:A:G NC_000006.12:135098492:A:G (self)
Help

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

7 citations for rs9389268
PMID Title Author Year Journal
18667698 DNA polymorphisms at the BCL11A, HBS1L-MYB, and beta-globin loci associate with fetal hemoglobin levels and pain crises in sickle cell disease. Lettre G et al. 2008 Proceedings of the National Academy of Sciences of the United States of America
19696200 Amelioration of Sardinian beta0 thalassemia by genetic modifiers. Galanello R et al. 2009 Blood
20401335 Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype. Driss A et al. 2009 Genomics insights
21772954 Recent advances in β-thalassemias. Cao A et al. 2011 Pediatric reports
22058279 Beta-thalassemia: from genotype to phenotype. Danjou F et al. 2011 Haematologica
28361591 Genetic Variants at BCL11A and HBS1L-MYB loci Influence Hb F Levels in Chinese Zhuang β-Thalassemia Intermedia Patients. Lai Y et al. 2016 Hemoglobin
32772141 Association between BCL11A, HSB1L-MYB, and XmnI γG-158 (C/T) gene polymorphism and hemoglobin F level in Egyptian sickle cell disease patients. El-Ghamrawy M et al. 2020 Annals of hematology
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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.post629+eb05767