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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.

rs66650371

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr6:135097495-135097499 (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
delCTA / dupCTA
Variation Type
Indel Insertion and Deletion
Frequency
delCTA=0.178174 (47161/264690, TOPMED)
delCTA=0.195637 (27399/140050, GnomAD)
delCTA=0.21028 (16548/78694, PAGE_STUDY) (+ 11 more)
delCTA=0.22905 (4242/18520, ALFA)
delCTA=0.33968 (5693/16760, 8.3KJPN)
delCTA=0.1536 (769/5008, 1000G)
delCTA=0.3047 (1365/4480, Estonian)
delCTA=0.2634 (1015/3854, ALSPAC)
delCTA=0.2627 (974/3708, TWINSUK)
delCTA=0.3199 (586/1832, Korea1K)
delCTA=0.262 (261/998, GoNL)
delCTA=0.337 (202/600, NorthernSweden)
delCTA=0.238 (51/214, Vietnamese)
delCTA=0.33 (13/40, GENOME_DK)
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 18520 TACTA=0.77095 TA=0.22905
European Sub 14152 TACTA=0.72972 TA=0.27028
African Sub 2898 TACTA=0.9369 TA=0.0631
African Others Sub 114 TACTA=0.965 TA=0.035
African American Sub 2784 TACTA=0.9357 TA=0.0643
Asian Sub 112 TACTA=0.750 TA=0.250
East Asian Sub 86 TACTA=0.77 TA=0.23
Other Asian Sub 26 TACTA=0.69 TA=0.31
Latin American 1 Sub 146 TACTA=0.890 TA=0.110
Latin American 2 Sub 610 TACTA=0.851 TA=0.149
South Asian Sub 98 TACTA=0.86 TA=0.14
Other Sub 504 TACTA=0.831 TA=0.169


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 TACTA=0.821826 delCTA=0.178174
gnomAD - Genomes Global Study-wide 140050 TACTA=0.804363 delCTA=0.195637
gnomAD - Genomes European Sub 75798 TACTA=0.73039 delCTA=0.26961
gnomAD - Genomes African Sub 42006 TACTA=0.93263 delCTA=0.06737
gnomAD - Genomes American Sub 13642 TACTA=0.83617 delCTA=0.16383
gnomAD - Genomes Ashkenazi Jewish Sub 3324 TACTA=0.7684 delCTA=0.2316
gnomAD - Genomes East Asian Sub 3130 TACTA=0.7620 delCTA=0.2380
gnomAD - Genomes Other Sub 2150 TACTA=0.8219 delCTA=0.1781
The PAGE Study Global Study-wide 78694 TACTA=0.78972 delCTA=0.21028
The PAGE Study AfricanAmerican Sub 32510 TACTA=0.78582 delCTA=0.21418
The PAGE Study Mexican Sub 10810 TACTA=0.84958 delCTA=0.15042
The PAGE Study Asian Sub 8316 TACTA=0.6619 delCTA=0.3381
The PAGE Study PuertoRican Sub 7918 TACTA=0.7929 delCTA=0.2071
The PAGE Study NativeHawaiian Sub 4534 TACTA=0.8311 delCTA=0.1689
The PAGE Study Cuban Sub 4230 TACTA=0.8069 delCTA=0.1931
The PAGE Study Dominican Sub 3828 TACTA=0.7941 delCTA=0.2059
The PAGE Study CentralAmerican Sub 2450 TACTA=0.8347 delCTA=0.1653
The PAGE Study SouthAmerican Sub 1982 TACTA=0.8224 delCTA=0.1776
The PAGE Study NativeAmerican Sub 1260 TACTA=0.7746 delCTA=0.2254
The PAGE Study SouthAsian Sub 856 TACTA=0.889 delCTA=0.111
8.3KJPN JAPANESE Study-wide 16760 TACTA=0.66032 delCTA=0.33968
1000Genomes Global Study-wide 5008 TACTA=0.8464 delCTA=0.1536
1000Genomes African Sub 1322 TACTA=0.9592 delCTA=0.0408
1000Genomes East Asian Sub 1008 TACTA=0.7550 delCTA=0.2450
1000Genomes Europe Sub 1006 TACTA=0.7396 delCTA=0.2604
1000Genomes South Asian Sub 978 TACTA=0.895 delCTA=0.105
1000Genomes American Sub 694 TACTA=0.852 delCTA=0.148
Genetic variation in the Estonian population Estonian Study-wide 4480 TACTA=0.6953 delCTA=0.3047
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 TACTA=0.7366 delCTA=0.2634
UK 10K study - Twins TWIN COHORT Study-wide 3708 TACTA=0.7373 delCTA=0.2627
Korean Genome Project KOREAN Study-wide 1832 TACTA=0.6801 delCTA=0.3199
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 TACTA=0.738 delCTA=0.262
Northern Sweden ACPOP Study-wide 600 TACTA=0.663 delCTA=0.337
A Vietnamese Genetic Variation Database Global Study-wide 214 TACTA=0.762 delCTA=0.238
The Danish reference pan genome Danish Study-wide 40 TACTA=0.68 delCTA=0.33
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.135097497_135097499del
GRCh38.p13 chr 6 NC_000006.12:g.135097497_135097499dup
GRCh37.p13 chr 6 NC_000006.11:g.135418635_135418637del
GRCh37.p13 chr 6 NC_000006.11:g.135418635_135418637dup
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 TACTA= delCTA dupCTA
GRCh38.p13 chr 6 NC_000006.12:g.135097495_135097499= NC_000006.12:g.135097497_135097499del NC_000006.12:g.135097497_135097499dup
GRCh37.p13 chr 6 NC_000006.11:g.135418633_135418637= NC_000006.11:g.135418635_135418637del NC_000006.11:g.135418635_135418637dup
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#.

50 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss81040585 Apr 25, 2013 (138)
2 HGSV ss81044017 Apr 25, 2013 (138)
3 HGSV ss82041206 Apr 25, 2013 (138)
4 HGSV ss82065626 Apr 25, 2013 (138)
5 HUMANGENOME_JCVI ss95443325 Mar 15, 2016 (147)
6 BCMHGSC_JDW ss103739646 Mar 15, 2016 (147)
7 GMI ss155094922 Dec 01, 2009 (131)
8 GMI ss287802733 May 09, 2011 (134)
9 GMI ss288803145 May 04, 2012 (137)
10 PJP ss295309046 May 09, 2011 (135)
11 PJP ss295309047 Aug 21, 2014 (142)
12 1000GENOMES ss326866017 May 09, 2011 (135)
13 1000GENOMES ss326916606 May 09, 2011 (135)
14 1000GENOMES ss499665243 May 04, 2012 (137)
15 LUNTER ss551669869 Apr 25, 2013 (138)
16 LUNTER ss553271312 Apr 25, 2013 (138)
17 SSMP ss663655443 Apr 01, 2015 (144)
18 BILGI_BIOE ss666375787 Apr 25, 2013 (138)
19 EVA-GONL ss983542781 Aug 21, 2014 (142)
20 1000GENOMES ss1376234781 Aug 21, 2014 (142)
21 DDI ss1536524185 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1576865073 Apr 01, 2015 (144)
23 EVA_DECODE ss1593112811 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1705381731 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1705381765 Apr 01, 2015 (144)
26 HAMMER_LAB ss1804689735 Sep 08, 2015 (146)
27 ILLUMINA ss1958953407 Feb 12, 2016 (147)
28 JJLAB ss2030798861 Sep 14, 2016 (149)
29 TOPMED ss2457399518 Dec 20, 2016 (150)
30 SYSTEMSBIOZJU ss2626519350 Nov 08, 2017 (151)
31 SWEGEN ss3000015269 Nov 08, 2017 (151)
32 ILLUMINA ss3022669916 Nov 08, 2017 (151)
33 TOPMED ss3512939374 Nov 08, 2017 (151)
34 BEROUKHIMLAB ss3644224132 Oct 12, 2018 (152)
35 BIOINF_KMB_FNS_UNIBA ss3645989135 Oct 12, 2018 (152)
36 URBANLAB ss3648479726 Oct 12, 2018 (152)
37 ILLUMINA ss3653192670 Oct 12, 2018 (152)
38 EGCUT_WGS ss3667935682 Jul 13, 2019 (153)
39 EVA_DECODE ss3718356822 Jul 13, 2019 (153)
40 ILLUMINA ss3726387478 Jul 13, 2019 (153)
41 ACPOP ss3734018576 Jul 13, 2019 (153)
42 PAGE_CC ss3771325481 Jul 13, 2019 (153)
43 KHV_HUMAN_GENOMES ss3808876100 Jul 13, 2019 (153)
44 EVA ss3830212687 Apr 26, 2020 (154)
45 EVA ss3838593780 Apr 26, 2020 (154)
46 EVA ss3844043942 Apr 26, 2020 (154)
47 KOGIC ss3960145349 Apr 26, 2020 (154)
48 GNOMAD ss4152112760 Apr 26, 2021 (155)
49 TOPMED ss4723247597 Apr 26, 2021 (155)
50 TOMMO_GENOMICS ss5180110233 Apr 26, 2021 (155)
51 1000Genomes NC_000006.11 - 135418633 Oct 12, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 135418633 Oct 12, 2018 (152)
53 Genetic variation in the Estonian population NC_000006.11 - 135418633 Oct 12, 2018 (152)
54 The Danish reference pan genome NC_000006.11 - 135418633 Apr 26, 2020 (154)
55 gnomAD - Genomes NC_000006.12 - 135097495 Apr 26, 2021 (155)
56 Genome of the Netherlands Release 5 NC_000006.11 - 135418633 Apr 26, 2020 (154)
57 Korean Genome Project NC_000006.12 - 135097495 Apr 26, 2020 (154)
58 Northern Sweden NC_000006.11 - 135418633 Jul 13, 2019 (153)
59 The PAGE Study NC_000006.12 - 135097495 Jul 13, 2019 (153)
60 8.3KJPN NC_000006.11 - 135418633 Apr 26, 2021 (155)
61 TopMed NC_000006.12 - 135097495 Apr 26, 2021 (155)
62 UK 10K study - Twins NC_000006.11 - 135418633 Oct 12, 2018 (152)
63 A Vietnamese Genetic Variation Database NC_000006.11 - 135418633 Jul 13, 2019 (153)
64 ALFA NC_000006.12 - 135097495 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)
rs66650372 Feb 26, 2009 (130)
rs140089842 Sep 17, 2011 (135)
rs141305824 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81040585, ss81044017, ss82041206, ss82065626 NC_000006.9:135460327:CTA: NC_000006.12:135097494:TACTA:TA (self)
ss288803145, ss295309046, ss326866017, ss326916606, ss551669869, ss553271312, ss1593112811 NC_000006.10:135460325:TAC: NC_000006.12:135097494:TACTA:TA (self)
ss295309047 NC_000006.10:135460327:CTA: NC_000006.12:135097494:TACTA:TA (self)
34306981, 19121713, 13673930, 1111025, 8516662, 7303441, 38079540, 19121713, 4256768, ss499665243, ss663655443, ss666375787, ss983542781, ss1376234781, ss1576865073, ss1705381731, ss1705381765, ss1804689735, ss1958953407, ss2030798861, ss2457399518, ss2626519350, ss3000015269, ss3022669916, ss3644224132, ss3653192670, ss3667935682, ss3734018576, ss3830212687, ss3838593780, ss5180110233 NC_000006.11:135418632:TAC: NC_000006.12:135097494:TACTA:TA (self)
242278808, 16523350, 546950, 350670724, 560625155, ss3512939374, ss3645989135, ss3648479726, ss3718356822, ss3726387478, ss3771325481, ss3808876100, ss3844043942, ss3960145349, ss4152112760, ss4723247597 NC_000006.12:135097494:TAC: NC_000006.12:135097494:TACTA:TA (self)
7113224573 NC_000006.12:135097494:TACTA:TA NC_000006.12:135097494:TACTA:TA (self)
ss155094922, ss287802733 NT_025741.15:39588089:TAC: NC_000006.12:135097494:TACTA:TA (self)
ss95443325, ss103739646 NT_025741.15:39588091:CTA: NC_000006.12:135097494:TACTA:TA (self)
ss1536524185 NC_000006.11:135418632::TAC NC_000006.12:135097494:TACTA:TACTA…

NC_000006.12:135097494:TACTA:TACTACTA

(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 rs66650371
PMID Title Author Year Journal
24614105 HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers. Stadhouders R et al. 2014 The Journal of clinical investigation
27354268 Dissection of the Major Hematopoietic Quantitative Trait Locus in Chromosome 6q23.3 Identifies miR-3662 as a Player in Hematopoiesis and Acute Myeloid Leukemia. Maharry SE et al. 2016 Cancer discovery
29227829 A long noncoding RNA from the HBS1L-MYB intergenic region on chr6q23 regulates human fetal hemoglobin expression. Morrison TA et al. 2018 Blood cells, molecules & diseases
29437638 <i>g(HbF)</i>: a genetic model of fetal hemoglobin in sickle cell disease. Gardner K et al. 2018 Blood advances
29879141 A survey of genetic fetal-haemoglobin modifiers in Nigerian patients with sickle cell anaemia. Adeyemo TA et al. 2018 PloS one
30478714 Genetic Modifiers of Fetal Haemoglobin in Sickle Cell Disease. Menzel S et al. 2019 Molecular diagnosis & therapy
32319326 Multi-Locus Models to Address Hb F Variability in Portuguese β-Thalassemia Carriers. Manco L et al. 2020 Hemoglobin
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.post629+eb05767