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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.

rs7469569

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr9:137031950 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.331985 (87873/264690, TOPMED)
T=0.332090 (82826/249408, GnomAD_exome)
T=0.341386 (47596/139420, GnomAD) (+ 17 more)
T=0.328286 (39328/119798, ExAC)
T=0.35085 (19696/56138, ALFA)
T=0.25248 (4225/16734, 8.3KJPN)
T=0.33331 (4329/12988, GO-ESP)
T=0.3005 (1505/5008, 1000G)
T=0.3719 (1660/4464, Estonian)
T=0.3521 (1357/3854, ALSPAC)
T=0.3522 (1306/3708, TWINSUK)
T=0.2375 (694/2922, KOREAN)
T=0.2796 (529/1892, HapMap)
T=0.342 (205/600, NorthernSweden)
C=0.125 (67/534, MGP)
T=0.254 (129/508, SGDP_PRJ)
T=0.390 (117/300, FINRISK)
T=0.389 (84/216, Qatari)
T=0.26 (14/54, Siberian)
T=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FUT7 : Intron Variant
LINC02908 : 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 9 NC_000009.12:g.137031950T>A
GRCh38.p13 chr 9 NC_000009.12:g.137031950T>C
GRCh37.p13 chr 9 NC_000009.11:g.139926402T>A
GRCh37.p13 chr 9 NC_000009.11:g.139926402T>C
ABCA2 RefSeqGene NG_011789.1:g.1973A>T
ABCA2 RefSeqGene NG_011789.1:g.1973A>G
FUT7 RefSeqGene NG_007527.1:g.5891A>T
FUT7 RefSeqGene NG_007527.1:g.5891A>G
Gene: FUT7, fucosyltransferase 7 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FUT7 transcript NM_004479.4:c.13+29A>T N/A Intron Variant
Gene: LINC02908, long intergenic non-protein coding RNA 2908 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC02908 transcript NR_171031.1:n. N/A Intron 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 56138 T=0.35085 C=0.64915
European Sub 37942 T=0.36052 C=0.63948
African Sub 5934 T=0.3043 C=0.6957
African Others Sub 184 T=0.348 C=0.652
African American Sub 5750 T=0.3030 C=0.6970
Asian Sub 498 T=0.285 C=0.715
East Asian Sub 400 T=0.278 C=0.723
Other Asian Sub 98 T=0.32 C=0.68
Latin American 1 Sub 356 T=0.368 C=0.632
Latin American 2 Sub 5466 T=0.3421 C=0.6579
South Asian Sub 154 T=0.357 C=0.643
Other Sub 5788 T=0.3478 C=0.6522


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 T=0.331985 C=0.668015
gnomAD - Exomes Global Study-wide 249408 T=0.332090 C=0.667910
gnomAD - Exomes European Sub 133818 T=0.354661 C=0.645339
gnomAD - Exomes Asian Sub 48964 T=0.26560 C=0.73440
gnomAD - Exomes American Sub 34514 T=0.33908 C=0.66092
gnomAD - Exomes African Sub 16042 T=0.29491 C=0.70509
gnomAD - Exomes Ashkenazi Jewish Sub 9974 T=0.3847 C=0.6153
gnomAD - Exomes Other Sub 6096 T=0.3428 C=0.6572
gnomAD - Genomes Global Study-wide 139420 T=0.341386 C=0.658614
gnomAD - Genomes European Sub 75582 T=0.36060 C=0.63940
gnomAD - Genomes African Sub 41672 T=0.30781 C=0.69219
gnomAD - Genomes American Sub 13602 T=0.34429 C=0.65571
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.3894 C=0.6106
gnomAD - Genomes East Asian Sub 3106 T=0.2624 C=0.7376
gnomAD - Genomes Other Sub 2140 T=0.3383 C=0.6617
ExAC Global Study-wide 119798 T=0.328286 C=0.671714
ExAC Europe Sub 72042 T=0.35365 C=0.64635
ExAC Asian Sub 25120 T=0.26250 C=0.73750
ExAC American Sub 11506 T=0.33704 C=0.66296
ExAC African Sub 10242 T=0.30121 C=0.69879
ExAC Other Sub 888 T=0.330 C=0.670
8.3KJPN JAPANESE Study-wide 16734 T=0.25248 C=0.74752
GO Exome Sequencing Project Global Study-wide 12988 T=0.33331 C=0.66669
GO Exome Sequencing Project European American Sub 8588 T=0.3505 C=0.6495
GO Exome Sequencing Project African American Sub 4400 T=0.2998 C=0.7002
1000Genomes Global Study-wide 5008 T=0.3005 C=0.6995
1000Genomes African Sub 1322 T=0.2852 C=0.7148
1000Genomes East Asian Sub 1008 T=0.2321 C=0.7679
1000Genomes Europe Sub 1006 T=0.3708 C=0.6292
1000Genomes South Asian Sub 978 T=0.252 C=0.748
1000Genomes American Sub 694 T=0.396 C=0.604
Genetic variation in the Estonian population Estonian Study-wide 4464 T=0.3719 C=0.6281
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.3521 C=0.6479
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.3522 C=0.6478
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.2375 A=0.0000, C=0.7625
HapMap Global Study-wide 1892 T=0.2796 C=0.7204
HapMap American Sub 770 T=0.295 C=0.705
HapMap African Sub 692 T=0.275 C=0.725
HapMap Asian Sub 254 T=0.220 C=0.780
HapMap Europe Sub 176 T=0.318 C=0.682
Northern Sweden ACPOP Study-wide 600 T=0.342 C=0.658
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.875 C=0.125
SGDP_PRJ Global Study-wide 508 T=0.254 C=0.746
FINRISK Finnish from FINRISK project Study-wide 300 T=0.390 C=0.610
Qatari Global Study-wide 216 T=0.389 C=0.611
Siberian Global Study-wide 54 T=0.26 C=0.74
The Danish reference pan genome Danish Study-wide 40 T=0.38 C=0.62
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 T= A C
GRCh38.p13 chr 9 NC_000009.12:g.137031950= NC_000009.12:g.137031950T>A NC_000009.12:g.137031950T>C
GRCh37.p13 chr 9 NC_000009.11:g.139926402= NC_000009.11:g.139926402T>A NC_000009.11:g.139926402T>C
ABCA2 RefSeqGene NG_011789.1:g.1973= NG_011789.1:g.1973A>T NG_011789.1:g.1973A>G
FUT7 RefSeqGene NG_007527.1:g.5891= NG_007527.1:g.5891A>T NG_007527.1:g.5891A>G
FUT7 transcript NM_004479.3:c.13+29= NM_004479.3:c.13+29A>T NM_004479.3:c.13+29A>G
FUT7 transcript NM_004479.4:c.13+29= NM_004479.4:c.13+29A>T NM_004479.4:c.13+29A>G
C9orf139 transcript NM_207511.1:c.-1066-48= NM_207511.1:c.-1066-48T>A NM_207511.1:c.-1066-48T>C
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#.

91 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss11279706 Jul 11, 2003 (116)
2 WI_SSAHASNP ss14360162 Dec 05, 2003 (119)
3 SC_SNP ss15717425 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss17259672 Feb 27, 2004 (120)
5 SSAHASNP ss22828301 Apr 05, 2004 (121)
6 ILLUMINA ss74967027 Dec 06, 2007 (129)
7 BCMHGSC_JDW ss94201479 Mar 25, 2008 (129)
8 HUMANGENOME_JCVI ss97837809 Feb 04, 2009 (130)
9 BGI ss105708768 Feb 04, 2009 (130)
10 1000GENOMES ss109141697 Jan 23, 2009 (130)
11 ILLUMINA-UK ss115817480 Feb 14, 2009 (130)
12 KRIBB_YJKIM ss119554659 Dec 01, 2009 (131)
13 ENSEMBL ss133566070 Dec 01, 2009 (131)
14 ENSEMBL ss144409585 Dec 01, 2009 (131)
15 ILLUMINA ss152536285 Dec 01, 2009 (131)
16 GMI ss158068454 Dec 01, 2009 (131)
17 ILLUMINA ss159102614 Dec 01, 2009 (131)
18 ILLUMINA ss159845994 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss165076400 Jul 04, 2010 (132)
20 ILLUMINA ss168870635 Jul 04, 2010 (132)
21 ILLUMINA ss174379213 Jul 04, 2010 (132)
22 BUSHMAN ss201013036 Jul 04, 2010 (132)
23 1000GENOMES ss210874831 Jul 14, 2010 (132)
24 1000GENOMES ss224508560 Jul 14, 2010 (132)
25 1000GENOMES ss235009601 Jul 15, 2010 (132)
26 1000GENOMES ss241751218 Jul 15, 2010 (132)
27 GMI ss280436979 May 04, 2012 (137)
28 GMI ss286109528 Apr 25, 2013 (138)
29 PJP ss294392025 May 09, 2011 (134)
30 ILLUMINA ss479154411 Sep 08, 2015 (146)
31 1000GENOMES ss490990386 May 04, 2012 (137)
32 CLINSEQ_SNP ss491947155 May 04, 2012 (137)
33 ILLUMINA ss536521767 Sep 08, 2015 (146)
34 SSMP ss656200488 Apr 25, 2013 (138)
35 NHLBI-ESP ss712929480 Apr 25, 2013 (138)
36 ILLUMINA ss832615410 Jul 13, 2019 (153)
37 JMKIDD_LAB ss974473411 Aug 21, 2014 (142)
38 EVA-GONL ss987087440 Aug 21, 2014 (142)
39 JMKIDD_LAB ss1067509813 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1076682624 Aug 21, 2014 (142)
41 1000GENOMES ss1335872389 Aug 21, 2014 (142)
42 DDI ss1431991001 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1583298371 Apr 01, 2015 (144)
44 EVA_FINRISK ss1584066125 Apr 01, 2015 (144)
45 EVA_DECODE ss1596735231 Apr 01, 2015 (144)
46 EVA_UK10K_ALSPAC ss1623780241 Apr 01, 2015 (144)
47 EVA_UK10K_TWINSUK ss1666774274 Apr 01, 2015 (144)
48 EVA_EXAC ss1689767648 Apr 01, 2015 (144)
49 EVA_MGP ss1711244076 Apr 01, 2015 (144)
50 EVA_SVP ss1713148569 Apr 01, 2015 (144)
51 WEILL_CORNELL_DGM ss1930404196 Feb 12, 2016 (147)
52 JJLAB ss2025925110 Sep 14, 2016 (149)
53 USC_VALOUEV ss2154163540 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2315296230 Dec 20, 2016 (150)
55 TOPMED ss2485829085 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2627430662 Nov 08, 2017 (151)
57 GRF ss2710049006 Nov 08, 2017 (151)
58 GNOMAD ss2738038554 Nov 08, 2017 (151)
59 GNOMAD ss2748322038 Nov 08, 2017 (151)
60 GNOMAD ss2884388521 Nov 08, 2017 (151)
61 SWEGEN ss3005763715 Nov 08, 2017 (151)
62 ILLUMINA ss3022979336 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3026745166 Nov 08, 2017 (151)
64 CSHL ss3348906236 Nov 08, 2017 (151)
65 TOPMED ss3603270987 Nov 08, 2017 (151)
66 ILLUMINA ss3630383018 Oct 12, 2018 (152)
67 ILLUMINA ss3636987756 Oct 12, 2018 (152)
68 ILLUMINA ss3638842986 Oct 12, 2018 (152)
69 ILLUMINA ss3638842987 Oct 12, 2018 (152)
70 ILLUMINA ss3643767296 Oct 12, 2018 (152)
71 OMUKHERJEE_ADBS ss3646400826 Oct 12, 2018 (152)
72 URBANLAB ss3649262444 Oct 12, 2018 (152)
73 ILLUMINA ss3653536551 Oct 12, 2018 (152)
74 EGCUT_WGS ss3673300549 Jul 13, 2019 (153)
75 EVA_DECODE ss3724969333 Jul 13, 2019 (153)
76 ILLUMINA ss3726654795 Jul 13, 2019 (153)
77 ACPOP ss3736966416 Jul 13, 2019 (153)
78 EVA ss3769822420 Jul 13, 2019 (153)
79 KHV_HUMAN_GENOMES ss3812981905 Jul 13, 2019 (153)
80 EVA ss3824490212 Apr 26, 2020 (154)
81 EVA ss3825768709 Apr 26, 2020 (154)
82 EVA ss3831912832 Apr 26, 2020 (154)
83 EVA ss3839485289 Apr 26, 2020 (154)
84 EVA ss3844951152 Apr 26, 2020 (154)
85 SGDP_PRJ ss3873299435 Apr 26, 2020 (154)
86 KRGDB ss3921215319 Apr 26, 2020 (154)
87 FSA-LAB ss3984436462 Apr 26, 2021 (155)
88 FSA-LAB ss3984436463 Apr 26, 2021 (155)
89 EVA ss3986471457 Apr 26, 2021 (155)
90 TOPMED ss4839185541 Apr 26, 2021 (155)
91 TOMMO_GENOMICS ss5195791488 Apr 26, 2021 (155)
92 1000Genomes NC_000009.11 - 139926402 Oct 12, 2018 (152)
93 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 139926402 Oct 12, 2018 (152)
94 Genetic variation in the Estonian population NC_000009.11 - 139926402 Oct 12, 2018 (152)
95 ExAC NC_000009.11 - 139926402 Oct 12, 2018 (152)
96 FINRISK NC_000009.11 - 139926402 Apr 26, 2020 (154)
97 The Danish reference pan genome NC_000009.11 - 139926402 Apr 26, 2020 (154)
98 gnomAD - Genomes NC_000009.12 - 137031950 Apr 26, 2021 (155)
99 gnomAD - Exomes NC_000009.11 - 139926402 Jul 13, 2019 (153)
100 GO Exome Sequencing Project NC_000009.11 - 139926402 Oct 12, 2018 (152)
101 HapMap NC_000009.12 - 137031950 Apr 26, 2020 (154)
102 KOREAN population from KRGDB NC_000009.11 - 139926402 Apr 26, 2020 (154)
103 Medical Genome Project healthy controls from Spanish population NC_000009.11 - 139926402 Apr 26, 2020 (154)
104 Northern Sweden NC_000009.11 - 139926402 Jul 13, 2019 (153)
105 Qatari NC_000009.11 - 139926402 Apr 26, 2020 (154)
106 SGDP_PRJ NC_000009.11 - 139926402 Apr 26, 2020 (154)
107 Siberian NC_000009.11 - 139926402 Apr 26, 2020 (154)
108 8.3KJPN NC_000009.11 - 139926402 Apr 26, 2021 (155)
109 TopMed NC_000009.12 - 137031950 Apr 26, 2021 (155)
110 UK 10K study - Twins NC_000009.11 - 139926402 Oct 12, 2018 (152)
111 ALFA NC_000009.12 - 137031950 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
28392713, ss3921215319 NC_000009.11:139926401:T:A NC_000009.12:137031949:T:A (self)
ss94201479, ss109141697, ss115817480, ss165076400, ss201013036, ss210874831, ss280436979, ss286109528, ss294392025, ss491947155, ss1596735231, ss1713148569, ss3643767296 NC_000009.10:139046222:T:C NC_000009.12:137031949:T:C (self)
48204859, 26787470, 19038797, 9911309, 62586, 9463308, 7230214, 947946, 28392713, 359836, 10251281, 12446126, 25316415, 6679894, 53760795, 26787470, ss224508560, ss235009601, ss241751218, ss479154411, ss490990386, ss536521767, ss656200488, ss712929480, ss832615410, ss974473411, ss987087440, ss1067509813, ss1076682624, ss1335872389, ss1431991001, ss1583298371, ss1584066125, ss1623780241, ss1666774274, ss1689767648, ss1711244076, ss1930404196, ss2025925110, ss2154163540, ss2485829085, ss2627430662, ss2710049006, ss2738038554, ss2748322038, ss2884388521, ss3005763715, ss3022979336, ss3348906236, ss3630383018, ss3636987756, ss3638842986, ss3638842987, ss3646400826, ss3653536551, ss3673300549, ss3736966416, ss3769822420, ss3824490212, ss3825768709, ss3831912832, ss3839485289, ss3873299435, ss3921215319, ss3984436462, ss3984436463, ss3986471457, ss5195791488 NC_000009.11:139926401:T:C NC_000009.12:137031949:T:C (self)
340629476, 3937887, 422405701, 676563102, 4103592971, ss2315296230, ss3026745166, ss3603270987, ss3649262444, ss3724969333, ss3726654795, ss3812981905, ss3844951152, ss4839185541 NC_000009.12:137031949:T:C NC_000009.12:137031949:T:C (self)
ss11279706, ss14360162, ss15717425, ss17259672, ss22828301 NT_024000.15:677480:T:C NC_000009.12:137031949:T:C (self)
ss74967027, ss97837809, ss105708768, ss119554659, ss133566070, ss144409585, ss152536285, ss158068454, ss159102614, ss159845994, ss168870635, ss174379213 NT_024000.16:709404:T:C NC_000009.12:137031949:T:C (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 rs7469569

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