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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.

rs133

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:24913359 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.259145 (68593/264690, TOPMED)
T=0.259430 (36286/139868, GnomAD)
T=0.26343 (7658/29070, ALFA) (+ 18 more)
T=0.31782 (5326/16758, 8.3KJPN)
T=0.2885 (1445/5008, 1000G)
T=0.2777 (1244/4480, Estonian)
T=0.2839 (1094/3854, ALSPAC)
T=0.2867 (1063/3708, TWINSUK)
T=0.2863 (839/2930, KOREAN)
T=0.2659 (503/1892, HapMap)
T=0.2997 (549/1832, Korea1K)
T=0.2782 (316/1136, Daghestan)
T=0.281 (280/998, GoNL)
T=0.315 (197/626, Chileans)
T=0.290 (174/600, NorthernSweden)
G=0.413 (124/300, SGDP_PRJ)
T=0.222 (48/216, Qatari)
T=0.347 (75/216, Vietnamese)
T=0.13 (10/76, Ancient Sardinia)
T=0.30 (12/40, GENOME_DK)
G=0.38 (10/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OSBPL3 : Intron Variant
Publications
1 citation
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 7 NC_000007.14:g.24913359G>T
GRCh37.p13 chr 7 NC_000007.13:g.24952978G>T
Gene: OSBPL3, oxysterol binding protein like 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
OSBPL3 transcript variant 1 NM_015550.4:c.-149-20738C…

NM_015550.4:c.-149-20738C>A

N/A Intron Variant
OSBPL3 transcript variant 2 NM_145320.2:c. N/A Genic Upstream Transcript Variant
OSBPL3 transcript variant 3 NM_145321.2:c. N/A Genic Upstream Transcript Variant
OSBPL3 transcript variant 4 NM_145322.2:c. N/A Genic Upstream Transcript Variant
OSBPL3 transcript variant 5 NR_104111.1:n. N/A Genic Upstream Transcript Variant
OSBPL3 transcript variant 6 NR_104112.1:n. N/A Genic Upstream Transcript Variant
OSBPL3 transcript variant X2 XM_005249698.3:c.-150+468…

XM_005249698.3:c.-150+4688C>A

N/A Intron Variant
OSBPL3 transcript variant X3 XM_006715681.3:c.-149-207…

XM_006715681.3:c.-149-20738C>A

N/A Intron Variant
OSBPL3 transcript variant X4 XM_006715682.3:c.-149-207…

XM_006715682.3:c.-149-20738C>A

N/A Intron Variant
OSBPL3 transcript variant X7 XM_006715683.3:c.-149-207…

XM_006715683.3:c.-149-20738C>A

N/A Intron Variant
OSBPL3 transcript variant X15 XM_006715684.4:c.-1192-20…

XM_006715684.4:c.-1192-20738C>A

N/A Intron Variant
OSBPL3 transcript variant X1 XM_011515258.2:c.-150+459…

XM_011515258.2:c.-150+4598C>A

N/A Intron Variant
OSBPL3 transcript variant X5 XM_011515259.2:c.-628-207…

XM_011515259.2:c.-628-20738C>A

N/A Intron Variant
OSBPL3 transcript variant X6 XM_017011948.1:c.-491-207…

XM_017011948.1:c.-491-20738C>A

N/A Intron Variant
OSBPL3 transcript variant X8 XM_017011949.1:c.-628-207…

XM_017011949.1:c.-628-20738C>A

N/A Intron Variant
OSBPL3 transcript variant X13 XR_001744620.1:n. N/A Intron Variant
OSBPL3 transcript variant X9 XR_428073.3:n. N/A Intron Variant
OSBPL3 transcript variant X11 XR_428074.3:n. N/A Intron Variant
OSBPL3 transcript variant X12 XR_428075.3:n. N/A Intron Variant
OSBPL3 transcript variant X10 XR_926927.2:n. N/A Intron Variant
OSBPL3 transcript variant X14 XR_926929.1: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 29070 G=0.73657 T=0.26343
European Sub 17482 G=0.72183 T=0.27817
African Sub 6688 G=0.8086 T=0.1914
African Others Sub 210 G=0.786 T=0.214
African American Sub 6478 G=0.8094 T=0.1906
Asian Sub 162 G=0.611 T=0.389
East Asian Sub 104 G=0.625 T=0.375
Other Asian Sub 58 G=0.59 T=0.41
Latin American 1 Sub 292 G=0.771 T=0.229
Latin American 2 Sub 2770 G=0.6852 T=0.3148
South Asian Sub 112 G=0.598 T=0.402
Other Sub 1564 G=0.7008 T=0.2992


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=0.740855 T=0.259145
gnomAD - Genomes Global Study-wide 139868 G=0.740570 T=0.259430
gnomAD - Genomes European Sub 75772 G=0.72432 T=0.27568
gnomAD - Genomes African Sub 41880 G=0.80246 T=0.19754
gnomAD - Genomes American Sub 13626 G=0.68795 T=0.31205
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.6368 T=0.3632
gnomAD - Genomes East Asian Sub 3122 G=0.6438 T=0.3562
gnomAD - Genomes Other Sub 2150 G=0.7419 T=0.2581
8.3KJPN JAPANESE Study-wide 16758 G=0.68218 T=0.31782
1000Genomes Global Study-wide 5008 G=0.7115 T=0.2885
1000Genomes African Sub 1322 G=0.8336 T=0.1664
1000Genomes East Asian Sub 1008 G=0.6181 T=0.3819
1000Genomes Europe Sub 1006 G=0.7117 T=0.2883
1000Genomes South Asian Sub 978 G=0.662 T=0.338
1000Genomes American Sub 694 G=0.684 T=0.316
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7223 T=0.2777
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7161 T=0.2839
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7133 T=0.2867
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7137 T=0.2863
HapMap Global Study-wide 1892 G=0.7341 T=0.2659
HapMap American Sub 770 G=0.696 T=0.304
HapMap African Sub 692 G=0.806 T=0.194
HapMap Asian Sub 254 G=0.630 T=0.370
HapMap Europe Sub 176 G=0.767 T=0.233
Korean Genome Project KOREAN Study-wide 1832 G=0.7003 T=0.2997
Genome-wide autozygosity in Daghestan Global Study-wide 1136 G=0.7218 T=0.2782
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=0.740 T=0.260
Genome-wide autozygosity in Daghestan Near_East Sub 144 G=0.722 T=0.278
Genome-wide autozygosity in Daghestan Central Asia Sub 122 G=0.672 T=0.328
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.750 T=0.250
Genome-wide autozygosity in Daghestan South Asian Sub 98 G=0.63 T=0.37
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.72 T=0.28
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.719 T=0.281
Chileans Chilean Study-wide 626 G=0.685 T=0.315
Northern Sweden ACPOP Study-wide 600 G=0.710 T=0.290
SGDP_PRJ Global Study-wide 300 G=0.413 T=0.587
Qatari Global Study-wide 216 G=0.778 T=0.222
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.653 T=0.347
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 76 G=0.87 T=0.13
The Danish reference pan genome Danish Study-wide 40 G=0.70 T=0.30
Siberian Global Study-wide 26 G=0.38 T=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 G= T
GRCh38.p13 chr 7 NC_000007.14:g.24913359= NC_000007.14:g.24913359G>T
GRCh37.p13 chr 7 NC_000007.13:g.24952978= NC_000007.13:g.24952978G>T
OSBPL3 transcript variant 1 NM_015550.2:c.-149-20738= NM_015550.2:c.-149-20738C>A
OSBPL3 transcript variant 1 NM_015550.4:c.-149-20738= NM_015550.4:c.-149-20738C>A
OSBPL3 transcript variant 2 NM_145320.1:c.-149-20738= NM_145320.1:c.-149-20738C>A
OSBPL3 transcript variant 3 NM_145321.1:c.-149-20738= NM_145321.1:c.-149-20738C>A
OSBPL3 transcript variant 4 NM_145322.1:c.-149-20738= NM_145322.1:c.-149-20738C>A
OSBPL3 transcript variant X1 XM_005249698.1:c.-150+4688= XM_005249698.1:c.-150+4688C>A
OSBPL3 transcript variant X2 XM_005249698.3:c.-150+4688= XM_005249698.3:c.-150+4688C>A
OSBPL3 transcript variant X3 XM_006715681.3:c.-149-20738= XM_006715681.3:c.-149-20738C>A
OSBPL3 transcript variant X4 XM_006715682.3:c.-149-20738= XM_006715682.3:c.-149-20738C>A
OSBPL3 transcript variant X7 XM_006715683.3:c.-149-20738= XM_006715683.3:c.-149-20738C>A
OSBPL3 transcript variant X15 XM_006715684.4:c.-1192-20738= XM_006715684.4:c.-1192-20738C>A
OSBPL3 transcript variant X1 XM_011515258.2:c.-150+4598= XM_011515258.2:c.-150+4598C>A
OSBPL3 transcript variant X5 XM_011515259.2:c.-628-20738= XM_011515259.2:c.-628-20738C>A
OSBPL3 transcript variant X6 XM_017011948.1:c.-491-20738= XM_017011948.1:c.-491-20738C>A
OSBPL3 transcript variant X8 XM_017011949.1:c.-628-20738= XM_017011949.1:c.-628-20738C>A
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#.

62 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss133 Sep 19, 2000 (36)
2 WI_SSAHASNP ss11887326 Jul 11, 2003 (116)
3 PERLEGEN ss23983791 Sep 20, 2004 (123)
4 AFFY ss66328520 Dec 01, 2006 (127)
5 PERLEGEN ss69009667 May 17, 2007 (127)
6 AFFY ss76023351 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss81403822 Dec 15, 2007 (130)
8 ILLUMINA-UK ss115987577 Feb 14, 2009 (130)
9 GMI ss154528855 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss166294766 Jul 04, 2010 (132)
11 AFFY ss170539928 Jul 04, 2010 (132)
12 BUSHMAN ss203089267 Jul 04, 2010 (132)
13 1000GENOMES ss212009556 Jul 14, 2010 (132)
14 1000GENOMES ss222968571 Jul 14, 2010 (132)
15 1000GENOMES ss233894381 Jul 15, 2010 (132)
16 1000GENOMES ss240865926 Jul 15, 2010 (132)
17 BL ss254128018 May 09, 2011 (134)
18 GMI ss279229045 May 04, 2012 (137)
19 TISHKOFF ss559875631 Apr 25, 2013 (138)
20 SSMP ss654228949 Apr 25, 2013 (138)
21 EVA-GONL ss984064004 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1074451312 Aug 21, 2014 (142)
23 1000GENOMES ss1324345859 Aug 21, 2014 (142)
24 HAMMER_LAB ss1397488211 Sep 08, 2015 (146)
25 DDI ss1431061175 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1582116609 Apr 01, 2015 (144)
27 EVA_DECODE ss1593632855 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1617794064 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1660788097 Apr 01, 2015 (144)
30 EVA_SVP ss1712939930 Apr 01, 2015 (144)
31 HAMMER_LAB ss1804916754 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1927309051 Feb 12, 2016 (147)
33 GENOMED ss1970651554 Jul 19, 2016 (147)
34 JJLAB ss2024331592 Sep 14, 2016 (149)
35 USC_VALOUEV ss2152527736 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2292525596 Dec 20, 2016 (150)
37 TOPMED ss2461386373 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2626654739 Nov 08, 2017 (151)
39 GRF ss2708184565 Nov 08, 2017 (151)
40 GNOMAD ss2850928621 Nov 08, 2017 (151)
41 SWEGEN ss3000794032 Nov 08, 2017 (151)
42 ILLUMINA ss3022718077 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3025960089 Nov 08, 2017 (151)
44 CSHL ss3347488233 Nov 08, 2017 (151)
45 TOPMED ss3525172499 Nov 08, 2017 (151)
46 ILLUMINA ss3653246300 Oct 12, 2018 (152)
47 EGCUT_WGS ss3668722807 Jul 13, 2019 (153)
48 EVA_DECODE ss3719304270 Jul 13, 2019 (153)
49 ILLUMINA ss3726429331 Jul 13, 2019 (153)
50 ACPOP ss3734451762 Jul 13, 2019 (153)
51 EVA ss3766316690 Jul 13, 2019 (153)
52 KHV_HUMAN_GENOMES ss3809484113 Jul 13, 2019 (153)
53 EVA ss3830470507 Apr 26, 2020 (154)
54 EVA ss3838722507 Apr 26, 2020 (154)
55 EVA ss3844173764 Apr 26, 2020 (154)
56 SGDP_PRJ ss3866853065 Apr 26, 2020 (154)
57 KRGDB ss3913891363 Apr 26, 2020 (154)
58 KOGIC ss3961077486 Apr 26, 2020 (154)
59 EVA ss3985283833 Apr 26, 2021 (155)
60 TOPMED ss4739177459 Apr 26, 2021 (155)
61 TOMMO_GENOMICS ss5182269208 Apr 26, 2021 (155)
62 EVA ss5237417419 Apr 26, 2021 (155)
63 1000Genomes NC_000007.13 - 24952978 Oct 12, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 24952978 Oct 12, 2018 (152)
65 Chileans NC_000007.13 - 24952978 Apr 26, 2020 (154)
66 Genome-wide autozygosity in Daghestan NC_000007.12 - 24919503 Apr 26, 2020 (154)
67 Genetic variation in the Estonian population NC_000007.13 - 24952978 Oct 12, 2018 (152)
68 The Danish reference pan genome NC_000007.13 - 24952978 Apr 26, 2020 (154)
69 gnomAD - Genomes NC_000007.14 - 24913359 Apr 26, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000007.13 - 24952978 Apr 26, 2020 (154)
71 HapMap NC_000007.14 - 24913359 Apr 26, 2020 (154)
72 KOREAN population from KRGDB NC_000007.13 - 24952978 Apr 26, 2020 (154)
73 Korean Genome Project NC_000007.14 - 24913359 Apr 26, 2020 (154)
74 Northern Sweden NC_000007.13 - 24952978 Jul 13, 2019 (153)
75 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000007.13 - 24952978 Apr 26, 2021 (155)
76 Qatari NC_000007.13 - 24952978 Apr 26, 2020 (154)
77 SGDP_PRJ NC_000007.13 - 24952978 Apr 26, 2020 (154)
78 Siberian NC_000007.13 - 24952978 Apr 26, 2020 (154)
79 8.3KJPN NC_000007.13 - 24952978 Apr 26, 2021 (155)
80 TopMed NC_000007.14 - 24913359 Apr 26, 2021 (155)
81 UK 10K study - Twins NC_000007.13 - 24952978 Oct 12, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000007.13 - 24952978 Jul 13, 2019 (153)
83 ALFA NC_000007.14 - 24913359 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)
rs58854507 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
462465, ss115987577, ss166294766, ss203089267, ss212009556, ss254128018, ss279229045, ss1397488211, ss1593632855, ss1712939930 NC_000007.12:24919502:G:T NC_000007.14:24913358:G:T (self)
36287814, 20229965, 404141, 14461055, 8281548, 9019651, 21068757, 7736627, 509760, 9350981, 18870045, 5044090, 40238515, 20229965, 4507530, ss222968571, ss233894381, ss240865926, ss559875631, ss654228949, ss984064004, ss1074451312, ss1324345859, ss1431061175, ss1582116609, ss1617794064, ss1660788097, ss1804916754, ss1927309051, ss1970651554, ss2024331592, ss2152527736, ss2461386373, ss2626654739, ss2708184565, ss2850928621, ss3000794032, ss3022718077, ss3347488233, ss3653246300, ss3668722807, ss3734451762, ss3766316690, ss3830470507, ss3838722507, ss3866853065, ss3913891363, ss3985283833, ss5182269208, ss5237417419 NC_000007.13:24952977:G:T NC_000007.14:24913358:G:T (self)
255870375, 3358820, 17455487, 360669350, 576555018, 3164577590, ss2292525596, ss3025960089, ss3525172499, ss3719304270, ss3726429331, ss3809484113, ss3844173764, ss3961077486, ss4739177459 NC_000007.14:24913358:G:T NC_000007.14:24913358:G:T (self)
ss11887326 NT_007819.13:24246585:G:T NC_000007.14:24913358:G:T (self)
ss133, ss23983791, ss66328520, ss69009667, ss76023351, ss81403822, ss154528855, ss170539928 NT_007819.17:24942977:G:T NC_000007.14:24913358:G:T (self)
Help

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

1 citation for rs133
PMID Title Author Year Journal
32821685 Assessment of single nucleotide polymorphisms associated with steroid-induced ocular hypertension. Badrinarayanan L et al. 2020 International journal of ophthalmology
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