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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.

rs35628909

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:69529059 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.205327 (54348/264690, TOPMED)
G=0.208584 (29228/140126, GnomAD)
G=0.17611 (6825/38754, ALFA) (+ 17 more)
G=0.02831 (800/28258, 14KJPN)
G=0.02751 (461/16760, 8.3KJPN)
G=0.1932 (1237/6404, 1000G_30x)
G=0.1857 (930/5008, 1000G)
G=0.1462 (655/4480, Estonian)
G=0.1175 (453/3854, ALSPAC)
G=0.1127 (418/3708, TWINSUK)
G=0.0216 (63/2922, KOREAN)
G=0.2101 (397/1890, HapMap)
G=0.1743 (197/1130, Daghestan)
G=0.116 (116/998, GoNL)
G=0.128 (77/600, NorthernSweden)
G=0.162 (35/216, Qatari)
G=0.042 (9/216, Vietnamese)
A=0.469 (60/128, SGDP_PRJ)
G=0.10 (4/40, GENOME_DK)
A=0.44 (7/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OCLN : 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 38754 A=0.82389 G=0.17611
European Sub 28620 A=0.87362 G=0.12638
African Sub 6942 A=0.6029 G=0.3971
African Others Sub 242 A=0.525 G=0.475
African American Sub 6700 A=0.6057 G=0.3943
Asian Sub 138 A=0.964 G=0.036
East Asian Sub 110 A=0.964 G=0.036
Other Asian Sub 28 A=0.96 G=0.04
Latin American 1 Sub 182 A=0.802 G=0.198
Latin American 2 Sub 752 A=0.891 G=0.109
South Asian Sub 114 A=0.895 G=0.105
Other Sub 2006 A=0.8425 G=0.1575


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=0.794673 G=0.205327
gnomAD - Genomes Global Study-wide 140126 A=0.791416 G=0.208584
gnomAD - Genomes European Sub 75924 A=0.87020 G=0.12980
gnomAD - Genomes African Sub 41948 A=0.60129 G=0.39871
gnomAD - Genomes American Sub 13652 A=0.88068 G=0.11932
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.8378 G=0.1622
gnomAD - Genomes East Asian Sub 3128 A=0.9722 G=0.0278
gnomAD - Genomes Other Sub 2150 A=0.8172 G=0.1828
Allele Frequency Aggregator Total Global 38754 A=0.82389 G=0.17611
Allele Frequency Aggregator European Sub 28620 A=0.87362 G=0.12638
Allele Frequency Aggregator African Sub 6942 A=0.6029 G=0.3971
Allele Frequency Aggregator Other Sub 2006 A=0.8425 G=0.1575
Allele Frequency Aggregator Latin American 2 Sub 752 A=0.891 G=0.109
Allele Frequency Aggregator Latin American 1 Sub 182 A=0.802 G=0.198
Allele Frequency Aggregator Asian Sub 138 A=0.964 G=0.036
Allele Frequency Aggregator South Asian Sub 114 A=0.895 G=0.105
14KJPN JAPANESE Study-wide 28258 A=0.97169 G=0.02831
8.3KJPN JAPANESE Study-wide 16760 A=0.97249 G=0.02751
1000Genomes_30x Global Study-wide 6404 A=0.8068 G=0.1932
1000Genomes_30x African Sub 1786 A=0.5588 G=0.4412
1000Genomes_30x Europe Sub 1266 A=0.8626 G=0.1374
1000Genomes_30x South Asian Sub 1202 A=0.9093 G=0.0907
1000Genomes_30x East Asian Sub 1170 A=0.9786 G=0.0214
1000Genomes_30x American Sub 980 A=0.856 G=0.144
1000Genomes Global Study-wide 5008 A=0.8143 G=0.1857
1000Genomes African Sub 1322 A=0.5575 G=0.4425
1000Genomes East Asian Sub 1008 A=0.9752 G=0.0248
1000Genomes Europe Sub 1006 A=0.8678 G=0.1322
1000Genomes South Asian Sub 978 A=0.916 G=0.084
1000Genomes American Sub 694 A=0.849 G=0.151
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8538 G=0.1462
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8825 G=0.1175
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8873 G=0.1127
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9784 G=0.0216
HapMap Global Study-wide 1890 A=0.7899 G=0.2101
HapMap American Sub 770 A=0.856 G=0.144
HapMap African Sub 690 A=0.629 G=0.371
HapMap Asian Sub 254 A=0.969 G=0.031
HapMap Europe Sub 176 A=0.875 G=0.125
Genome-wide autozygosity in Daghestan Global Study-wide 1130 A=0.8257 G=0.1743
Genome-wide autozygosity in Daghestan Daghestan Sub 622 A=0.780 G=0.220
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.854 G=0.146
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.885 G=0.115
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.861 G=0.139
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.92 G=0.08
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.94 G=0.06
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.884 G=0.116
Northern Sweden ACPOP Study-wide 600 A=0.872 G=0.128
Qatari Global Study-wide 216 A=0.838 G=0.162
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.958 G=0.042
SGDP_PRJ Global Study-wide 128 A=0.469 G=0.531
The Danish reference pan genome Danish Study-wide 40 A=0.90 G=0.10
Siberian Global Study-wide 16 A=0.44 G=0.56
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 5 NC_000005.10:g.69529059A>G
GRCh37.p13 chr 5 NC_000005.9:g.68824886A>G
OCLN RefSeqGene NG_028291.1:g.41768A>G
GRCh38.p14 chr 5 alt locus HSCHR5_2_CTG1_1 NW_003315917.2:g.311999A>G
GRCh38.p14 chr 5 fix patch HG2405_PATCH NW_025791777.1:g.195765A>G
Gene: OCLN, occludin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
OCLN transcript variant 2 NM_001205254.2:c.892-5635…

NM_001205254.2:c.892-5635A>G

N/A Intron Variant
OCLN transcript variant 3 NM_001205255.1:c.139-5635…

NM_001205255.1:c.139-5635A>G

N/A Intron Variant
OCLN transcript variant 1 NM_002538.4:c.892-5635A>G N/A Intron Variant
OCLN transcript variant X3 XM_017008913.3:c.730-5635…

XM_017008913.3:c.730-5635A>G

N/A Intron Variant
OCLN transcript variant X4 XM_017008914.3:c.730-5635…

XM_017008914.3:c.730-5635A>G

N/A Intron Variant
OCLN transcript variant X1 XM_047416593.1:c.892-5635…

XM_047416593.1:c.892-5635A>G

N/A Intron Variant
OCLN transcript variant X2 XM_047416594.1:c.892-5635…

XM_047416594.1:c.892-5635A>G

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
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.p14 chr 5 NC_000005.10:g.69529059= NC_000005.10:g.69529059A>G
GRCh37.p13 chr 5 NC_000005.9:g.68824886= NC_000005.9:g.68824886A>G
OCLN RefSeqGene NG_028291.1:g.41768= NG_028291.1:g.41768A>G
GRCh38.p14 chr 5 alt locus HSCHR5_2_CTG1_1 NW_003315917.2:g.311999= NW_003315917.2:g.311999A>G
GRCh38.p14 chr 5 fix patch HG2405_PATCH NW_025791777.1:g.195765= NW_025791777.1:g.195765A>G
OCLN transcript variant 2 NM_001205254.1:c.892-5635= NM_001205254.1:c.892-5635A>G
OCLN transcript variant 2 NM_001205254.2:c.892-5635= NM_001205254.2:c.892-5635A>G
OCLN transcript variant 3 NM_001205255.1:c.139-5635= NM_001205255.1:c.139-5635A>G
OCLN transcript variant 1 NM_002538.3:c.892-5635= NM_002538.3:c.892-5635A>G
OCLN transcript variant 1 NM_002538.4:c.892-5635= NM_002538.4:c.892-5635A>G
OCLN transcript variant X3 XM_017008913.3:c.730-5635= XM_017008913.3:c.730-5635A>G
OCLN transcript variant X4 XM_017008914.3:c.730-5635= XM_017008914.3:c.730-5635A>G
OCLN transcript variant X1 XM_047416593.1:c.892-5635= XM_047416593.1:c.892-5635A>G
OCLN transcript variant X2 XM_047416594.1:c.892-5635= XM_047416594.1:c.892-5635A>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#.

74 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 ABI ss42637826 Mar 15, 2006 (126)
2 ILLUMINA ss74972443 Dec 06, 2007 (129)
3 HUMANGENOME_JCVI ss98732290 Feb 05, 2009 (130)
4 1000GENOMES ss109114150 Feb 13, 2009 (130)
5 1000GENOMES ss111983565 Jan 25, 2009 (130)
6 KRIBB_YJKIM ss119917788 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss165180611 Jul 04, 2010 (132)
8 ILLUMINA ss173603028 Jul 04, 2010 (132)
9 BUSHMAN ss200366759 Jul 04, 2010 (132)
10 1000GENOMES ss221731804 Jul 14, 2010 (132)
11 1000GENOMES ss232984684 Jul 14, 2010 (132)
12 1000GENOMES ss240148210 Jul 15, 2010 (132)
13 ILLUMINA ss483102444 May 04, 2012 (137)
14 ILLUMINA ss485071218 May 04, 2012 (137)
15 ILLUMINA ss535292770 Sep 08, 2015 (146)
16 TISHKOFF ss558453813 Apr 25, 2013 (138)
17 SSMP ss652323806 Apr 25, 2013 (138)
18 ILLUMINA ss780151841 Sep 08, 2015 (146)
19 ILLUMINA ss781994551 Sep 08, 2015 (146)
20 ILLUMINA ss835635446 Sep 08, 2015 (146)
21 EVA-GONL ss981671249 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1072707601 Aug 21, 2014 (142)
23 1000GENOMES ss1315498458 Aug 21, 2014 (142)
24 HAMMER_LAB ss1397415749 Sep 08, 2015 (146)
25 DDI ss1430374521 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1581178278 Apr 01, 2015 (144)
27 EVA_DECODE ss1591190365 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1613101301 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1656095334 Apr 01, 2015 (144)
30 EVA_SVP ss1712771228 Apr 01, 2015 (144)
31 HAMMER_LAB ss1803648332 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1924926805 Feb 12, 2016 (147)
33 JJLAB ss2023068597 Sep 14, 2016 (149)
34 USC_VALOUEV ss2151224518 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2274536820 Dec 20, 2016 (150)
36 ILLUMINA ss2634290609 Nov 08, 2017 (151)
37 GNOMAD ss2825760131 Nov 08, 2017 (151)
38 SWEGEN ss2997095600 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3025318780 Nov 08, 2017 (151)
40 CSHL ss3346432443 Nov 08, 2017 (151)
41 ILLUMINA ss3629255207 Oct 12, 2018 (152)
42 ILLUMINA ss3632217237 Oct 12, 2018 (152)
43 ILLUMINA ss3638558763 Oct 12, 2018 (152)
44 ILLUMINA ss3642420095 Oct 12, 2018 (152)
45 ILLUMINA ss3643504299 Oct 12, 2018 (152)
46 URBANLAB ss3648082652 Oct 12, 2018 (152)
47 EGCUT_WGS ss3664979846 Jul 13, 2019 (153)
48 EVA_DECODE ss3714878350 Jul 13, 2019 (153)
49 ACPOP ss3732443053 Jul 13, 2019 (153)
50 EVA ss3763550969 Jul 13, 2019 (153)
51 PACBIO ss3785137471 Jul 13, 2019 (153)
52 PACBIO ss3790539604 Jul 13, 2019 (153)
53 PACBIO ss3795416291 Jul 13, 2019 (153)
54 KHV_HUMAN_GENOMES ss3806719200 Jul 13, 2019 (153)
55 EVA ss3829294216 Apr 26, 2020 (154)
56 EVA ss3838120274 Apr 26, 2020 (154)
57 EVA ss3843561233 Apr 26, 2020 (154)
58 SGDP_PRJ ss3862060279 Apr 26, 2020 (154)
59 KRGDB ss3908620439 Apr 26, 2020 (154)
60 EVA ss4017211509 Apr 26, 2021 (155)
61 TOPMED ss4663488379 Apr 26, 2021 (155)
62 TOMMO_GENOMICS ss5172193458 Apr 26, 2021 (155)
63 1000G_HIGH_COVERAGE ss5264325294 Oct 13, 2022 (156)
64 EVA ss5315058157 Oct 13, 2022 (156)
65 EVA ss5358211320 Oct 13, 2022 (156)
66 HUGCELL_USP ss5462469273 Oct 13, 2022 (156)
67 1000G_HIGH_COVERAGE ss5548158309 Oct 13, 2022 (156)
68 SANFORD_IMAGENETICS ss5638005101 Oct 13, 2022 (156)
69 TOMMO_GENOMICS ss5708718784 Oct 13, 2022 (156)
70 YY_MCH ss5806405208 Oct 13, 2022 (156)
71 EVA ss5835063009 Oct 13, 2022 (156)
72 EVA ss5854852763 Oct 13, 2022 (156)
73 EVA ss5894589160 Oct 13, 2022 (156)
74 EVA ss5966437843 Oct 13, 2022 (156)
75 1000Genomes NC_000005.9 - 68824886 Oct 12, 2018 (152)
76 1000Genomes_30x NC_000005.10 - 69529059 Oct 13, 2022 (156)
77 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 68824886 Oct 12, 2018 (152)
78 Genome-wide autozygosity in Daghestan NC_000005.8 - 68860642 Apr 26, 2020 (154)
79 Genetic variation in the Estonian population NC_000005.9 - 68824886 Oct 12, 2018 (152)
80 The Danish reference pan genome NC_000005.9 - 68824886 Apr 26, 2020 (154)
81 gnomAD - Genomes NC_000005.10 - 69529059 Apr 26, 2021 (155)
82 Genome of the Netherlands Release 5 NC_000005.9 - 68824886 Apr 26, 2020 (154)
83 HapMap NC_000005.10 - 69529059 Apr 26, 2020 (154)
84 KOREAN population from KRGDB NC_000005.9 - 68824886 Apr 26, 2020 (154)
85 Northern Sweden NC_000005.9 - 68824886 Jul 13, 2019 (153)
86 Qatari NC_000005.9 - 68824886 Apr 26, 2020 (154)
87 SGDP_PRJ NC_000005.9 - 68824886 Apr 26, 2020 (154)
88 Siberian NC_000005.9 - 68824886 Apr 26, 2020 (154)
89 8.3KJPN NC_000005.9 - 68824886 Apr 26, 2021 (155)
90 14KJPN NC_000005.10 - 69529059 Oct 13, 2022 (156)
91 TopMed NC_000005.10 - 69529059 Apr 26, 2021 (155)
92 UK 10K study - Twins NC_000005.9 - 68824886 Oct 12, 2018 (152)
93 A Vietnamese Genetic Variation Database NC_000005.9 - 68824886 Jul 13, 2019 (153)
94 ALFA NC_000005.10 - 69529059 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
390757, ss109114150, ss111983565, ss165180611, ss200366759, ss485071218, ss1397415749, ss1591190365, ss1712771228, ss3643504299 NC_000005.8:68860641:A:G NC_000005.10:69529058:A:G (self)
27112980, 15074257, 10718094, 7343217, 6701771, 15797833, 5727918, 6968735, 14077259, 3740872, 30162765, 15074257, 3346506, ss221731804, ss232984684, ss240148210, ss483102444, ss535292770, ss558453813, ss652323806, ss780151841, ss781994551, ss835635446, ss981671249, ss1072707601, ss1315498458, ss1430374521, ss1581178278, ss1613101301, ss1656095334, ss1803648332, ss1924926805, ss2023068597, ss2151224518, ss2634290609, ss2825760131, ss2997095600, ss3346432443, ss3629255207, ss3632217237, ss3638558763, ss3642420095, ss3664979846, ss3732443053, ss3763550969, ss3785137471, ss3790539604, ss3795416291, ss3829294216, ss3838120274, ss3862060279, ss3908620439, ss4017211509, ss5172193458, ss5315058157, ss5358211320, ss5638005101, ss5835063009, ss5966437843 NC_000005.9:68824885:A:G NC_000005.10:69529058:A:G (self)
35684244, 191615257, 2886335, 42555888, 500865936, 10297772515, ss2274536820, ss3025318780, ss3648082652, ss3714878350, ss3806719200, ss3843561233, ss4663488379, ss5264325294, ss5462469273, ss5548158309, ss5708718784, ss5806405208, ss5854852763, ss5894589160 NC_000005.10:69529058:A:G NC_000005.10:69529058:A:G (self)
ss42637826, ss74972443, ss98732290, ss119917788, ss173603028 NT_006713.15:19419244:A:G NC_000005.10:69529058: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.

No publications for rs35628909

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