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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.

rs134

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:24911763 (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>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.241828 (33869/140054, GnomAD)
A=0.34473 (5777/16758, 8.3KJPN)
A=0.13766 (1898/13788, ALFA) (+ 14 more)
A=0.2806 (1405/5008, 1000G)
A=0.2737 (1226/4480, Estonian)
A=0.2730 (1052/3854, ALSPAC)
A=0.2764 (1025/3708, TWINSUK)
A=0.2993 (877/2930, KOREAN)
A=0.3160 (579/1832, Korea1K)
A=0.274 (273/998, GoNL)
A=0.290 (174/600, NorthernSweden)
A=0.270 (88/326, HapMap)
G=0.409 (112/274, SGDP_PRJ)
A=0.157 (34/216, Qatari)
A=0.360 (77/214, Vietnamese)
A=0.30 (12/40, GENOME_DK)
G=0.42 (11/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OSBPL3 : 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 7 NC_000007.14:g.24911763G>A
GRCh38.p13 chr 7 NC_000007.14:g.24911763G>C
GRCh38.p13 chr 7 NC_000007.14:g.24911763G>T
GRCh37.p13 chr 7 NC_000007.13:g.24951382G>A
GRCh37.p13 chr 7 NC_000007.13:g.24951382G>C
GRCh37.p13 chr 7 NC_000007.13:g.24951382G>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.-149-19142C…

NM_015550.4:c.-149-19142C>T

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+628…

XM_005249698.3:c.-150+6284C>T

N/A Intron Variant
OSBPL3 transcript variant X3 XM_006715681.3:c.-149-191…

XM_006715681.3:c.-149-19142C>T

N/A Intron Variant
OSBPL3 transcript variant X4 XM_006715682.3:c.-149-191…

XM_006715682.3:c.-149-19142C>T

N/A Intron Variant
OSBPL3 transcript variant X7 XM_006715683.3:c.-149-191…

XM_006715683.3:c.-149-19142C>T

N/A Intron Variant
OSBPL3 transcript variant X15 XM_006715684.4:c.-1192-19…

XM_006715684.4:c.-1192-19142C>T

N/A Intron Variant
OSBPL3 transcript variant X1 XM_011515258.2:c.-150+619…

XM_011515258.2:c.-150+6194C>T

N/A Intron Variant
OSBPL3 transcript variant X5 XM_011515259.2:c.-628-191…

XM_011515259.2:c.-628-19142C>T

N/A Intron Variant
OSBPL3 transcript variant X6 XM_017011948.1:c.-491-191…

XM_017011948.1:c.-491-19142C>T

N/A Intron Variant
OSBPL3 transcript variant X8 XM_017011949.1:c.-628-191…

XM_017011949.1:c.-628-19142C>T

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 13788 G=0.86234 A=0.13766, C=0.00000, T=0.00000
European Sub 10718 G=0.83094 A=0.16906, C=0.00000, T=0.00000
African Sub 2114 G=0.9901 A=0.0099, C=0.0000, T=0.0000
African Others Sub 78 G=1.00 A=0.00, C=0.00, T=0.00
African American Sub 2036 G=0.9897 A=0.0103, C=0.0000, T=0.0000
Asian Sub 40 G=0.93 A=0.07, C=0.00, T=0.00
East Asian Sub 28 G=0.96 A=0.04, C=0.00, T=0.00
Other Asian Sub 12 G=0.83 A=0.17, C=0.00, T=0.00
Latin American 1 Sub 88 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 2 Sub 272 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 44 G=0.95 A=0.05, C=0.00, T=0.00
Other Sub 512 G=0.883 A=0.117, C=0.000, T=0.000


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
gnomAD - Genomes Global Study-wide 140054 G=0.758172 A=0.241828
gnomAD - Genomes European Sub 75838 G=0.73259 A=0.26741
gnomAD - Genomes African Sub 41968 G=0.83909 A=0.16091
gnomAD - Genomes American Sub 13642 G=0.69843 A=0.30157
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.6757 A=0.3243
gnomAD - Genomes East Asian Sub 3132 G=0.6370 A=0.3630
gnomAD - Genomes Other Sub 2150 G=0.7642 A=0.2358
8.3KJPN JAPANESE Study-wide 16758 G=0.65527 A=0.34473
1000Genomes Global Study-wide 5008 G=0.7194 A=0.2806
1000Genomes African Sub 1322 G=0.8684 A=0.1316
1000Genomes East Asian Sub 1008 G=0.6042 A=0.3958
1000Genomes Europe Sub 1006 G=0.7227 A=0.2773
1000Genomes South Asian Sub 978 G=0.654 A=0.346
1000Genomes American Sub 694 G=0.690 A=0.310
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7263 A=0.2737
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7270 A=0.2730
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7236 A=0.2764
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7007 A=0.2993
Korean Genome Project KOREAN Study-wide 1832 G=0.6840 A=0.3160
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.726 A=0.274
Northern Sweden ACPOP Study-wide 600 G=0.710 A=0.290
HapMap Global Study-wide 326 G=0.730 A=0.270
HapMap African Sub 120 G=0.875 A=0.125
HapMap American Sub 118 G=0.729 A=0.271
HapMap Asian Sub 88 G=0.53 A=0.47
SGDP_PRJ Global Study-wide 274 G=0.409 A=0.591
Qatari Global Study-wide 216 G=0.843 A=0.157
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.640 A=0.360
The Danish reference pan genome Danish Study-wide 40 G=0.70 A=0.30
Siberian Global Study-wide 26 G=0.42 A=0.58
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= A C T
GRCh38.p13 chr 7 NC_000007.14:g.24911763= NC_000007.14:g.24911763G>A NC_000007.14:g.24911763G>C NC_000007.14:g.24911763G>T
GRCh37.p13 chr 7 NC_000007.13:g.24951382= NC_000007.13:g.24951382G>A NC_000007.13:g.24951382G>C NC_000007.13:g.24951382G>T
OSBPL3 transcript variant 1 NM_015550.2:c.-149-19142= NM_015550.2:c.-149-19142C>T NM_015550.2:c.-149-19142C>G NM_015550.2:c.-149-19142C>A
OSBPL3 transcript variant 1 NM_015550.4:c.-149-19142= NM_015550.4:c.-149-19142C>T NM_015550.4:c.-149-19142C>G NM_015550.4:c.-149-19142C>A
OSBPL3 transcript variant 2 NM_145320.1:c.-149-19142= NM_145320.1:c.-149-19142C>T NM_145320.1:c.-149-19142C>G NM_145320.1:c.-149-19142C>A
OSBPL3 transcript variant 3 NM_145321.1:c.-149-19142= NM_145321.1:c.-149-19142C>T NM_145321.1:c.-149-19142C>G NM_145321.1:c.-149-19142C>A
OSBPL3 transcript variant 4 NM_145322.1:c.-149-19142= NM_145322.1:c.-149-19142C>T NM_145322.1:c.-149-19142C>G NM_145322.1:c.-149-19142C>A
OSBPL3 transcript variant X1 XM_005249698.1:c.-150+6284= XM_005249698.1:c.-150+6284C>T XM_005249698.1:c.-150+6284C>G XM_005249698.1:c.-150+6284C>A
OSBPL3 transcript variant X2 XM_005249698.3:c.-150+6284= XM_005249698.3:c.-150+6284C>T XM_005249698.3:c.-150+6284C>G XM_005249698.3:c.-150+6284C>A
OSBPL3 transcript variant X3 XM_006715681.3:c.-149-19142= XM_006715681.3:c.-149-19142C>T XM_006715681.3:c.-149-19142C>G XM_006715681.3:c.-149-19142C>A
OSBPL3 transcript variant X4 XM_006715682.3:c.-149-19142= XM_006715682.3:c.-149-19142C>T XM_006715682.3:c.-149-19142C>G XM_006715682.3:c.-149-19142C>A
OSBPL3 transcript variant X7 XM_006715683.3:c.-149-19142= XM_006715683.3:c.-149-19142C>T XM_006715683.3:c.-149-19142C>G XM_006715683.3:c.-149-19142C>A
OSBPL3 transcript variant X15 XM_006715684.4:c.-1192-19142= XM_006715684.4:c.-1192-19142C>T XM_006715684.4:c.-1192-19142C>G XM_006715684.4:c.-1192-19142C>A
OSBPL3 transcript variant X1 XM_011515258.2:c.-150+6194= XM_011515258.2:c.-150+6194C>T XM_011515258.2:c.-150+6194C>G XM_011515258.2:c.-150+6194C>A
OSBPL3 transcript variant X5 XM_011515259.2:c.-628-19142= XM_011515259.2:c.-628-19142C>T XM_011515259.2:c.-628-19142C>G XM_011515259.2:c.-628-19142C>A
OSBPL3 transcript variant X6 XM_017011948.1:c.-491-19142= XM_017011948.1:c.-491-19142C>T XM_017011948.1:c.-491-19142C>G XM_017011948.1:c.-491-19142C>A
OSBPL3 transcript variant X8 XM_017011949.1:c.-628-19142= XM_017011949.1:c.-628-19142C>T XM_017011949.1:c.-628-19142C>G XM_017011949.1:c.-628-19142C>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#.

50 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss134 Sep 19, 2000 (36)
2 CSHL-HAPMAP ss17193219 Feb 27, 2004 (120)
3 ABI ss44836599 Mar 14, 2006 (126)
4 ILLUMINA-UK ss115987565 Feb 14, 2009 (130)
5 GMI ss154528830 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss166294735 Jul 04, 2010 (132)
7 BUSHMAN ss203089248 Jul 04, 2010 (132)
8 1000GENOMES ss222968560 Jul 14, 2010 (132)
9 1000GENOMES ss233894375 Jul 15, 2010 (132)
10 1000GENOMES ss240865921 Jul 15, 2010 (132)
11 BL ss254127996 May 09, 2011 (134)
12 GMI ss279229041 May 04, 2012 (137)
13 TISHKOFF ss559875628 Apr 25, 2013 (138)
14 SSMP ss654228942 Apr 25, 2013 (138)
15 EVA-GONL ss984063993 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1074451303 Aug 21, 2014 (142)
17 1000GENOMES ss1324345814 Aug 21, 2014 (142)
18 DDI ss1431061170 Apr 01, 2015 (144)
19 EVA_GENOME_DK ss1582116604 Apr 01, 2015 (144)
20 EVA_DECODE ss1593632842 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1617794034 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1660788067 Apr 01, 2015 (144)
23 HAMMER_LAB ss1804916751 Sep 08, 2015 (146)
24 WEILL_CORNELL_DGM ss1927309034 Feb 12, 2016 (147)
25 GENOMED ss1970651550 Jul 19, 2016 (147)
26 JJLAB ss2024331586 Sep 14, 2016 (149)
27 USC_VALOUEV ss2152527730 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2292525509 Dec 20, 2016 (150)
29 TOPMED ss2461386289 Dec 20, 2016 (150)
30 SYSTEMSBIOZJU ss2626654735 Nov 08, 2017 (151)
31 GRF ss2708184558 Nov 08, 2017 (151)
32 GNOMAD ss2850928510 Nov 08, 2017 (151)
33 SWEGEN ss3000794020 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3025960085 Nov 08, 2017 (151)
35 CSHL ss3347488228 Nov 08, 2017 (151)
36 TOPMED ss3525172238 Nov 08, 2017 (151)
37 EGCUT_WGS ss3668722788 Jul 13, 2019 (153)
38 EVA_DECODE ss3719304246 Jul 13, 2019 (153)
39 ACPOP ss3734451752 Jul 13, 2019 (153)
40 EVA ss3766316676 Jul 13, 2019 (153)
41 KHV_HUMAN_GENOMES ss3809484098 Jul 13, 2019 (153)
42 EVA ss3830470501 Apr 26, 2020 (154)
43 EVA ss3838722503 Apr 26, 2020 (154)
44 EVA ss3844173760 Apr 26, 2020 (154)
45 SGDP_PRJ ss3866853039 Apr 26, 2020 (154)
46 KRGDB ss3913891341 Apr 26, 2020 (154)
47 KOGIC ss3961077470 Apr 26, 2020 (154)
48 TOPMED ss4739177077 Apr 26, 2021 (155)
49 TOPMED ss4739177078 Apr 26, 2021 (155)
50 TOMMO_GENOMICS ss5182269171 Apr 26, 2021 (155)
51 1000Genomes NC_000007.13 - 24951382 Oct 12, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 24951382 Oct 12, 2018 (152)
53 Genetic variation in the Estonian population NC_000007.13 - 24951382 Oct 12, 2018 (152)
54 The Danish reference pan genome NC_000007.13 - 24951382 Apr 26, 2020 (154)
55 gnomAD - Genomes NC_000007.14 - 24911763 Apr 26, 2021 (155)
56 Genome of the Netherlands Release 5 NC_000007.13 - 24951382 Apr 26, 2020 (154)
57 HapMap NC_000007.14 - 24911763 Apr 26, 2020 (154)
58 KOREAN population from KRGDB NC_000007.13 - 24951382 Apr 26, 2020 (154)
59 Korean Genome Project NC_000007.14 - 24911763 Apr 26, 2020 (154)
60 Northern Sweden NC_000007.13 - 24951382 Jul 13, 2019 (153)
61 Qatari NC_000007.13 - 24951382 Apr 26, 2020 (154)
62 SGDP_PRJ NC_000007.13 - 24951382 Apr 26, 2020 (154)
63 Siberian NC_000007.13 - 24951382 Apr 26, 2020 (154)
64 8.3KJPN NC_000007.13 - 24951382 Apr 26, 2021 (155)
65 TopMed

Submission ignored due to conflicting rows:
Row 576554636 (NC_000007.14:24911762:G:A 63613/264690)
Row 576554637 (NC_000007.14:24911762:G:C 1/264690)

- Apr 26, 2021 (155)
66 TopMed

Submission ignored due to conflicting rows:
Row 576554636 (NC_000007.14:24911762:G:A 63613/264690)
Row 576554637 (NC_000007.14:24911762:G:C 1/264690)

- Apr 26, 2021 (155)
67 UK 10K study - Twins NC_000007.13 - 24951382 Oct 12, 2018 (152)
68 A Vietnamese Genetic Variation Database NC_000007.13 - 24951382 Jul 13, 2019 (153)
69 ALFA NC_000007.14 - 24911763 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
ss115987565, ss166294735, ss203089248, ss254127996, ss279229041, ss1593632842 NC_000007.12:24917906:G:A NC_000007.14:24911762:G:A (self)
36287769, 20229935, 14461036, 8281543, 9019640, 21068735, 7736617, 9350964, 18870019, 5044084, 40238478, 20229935, 4507524, ss222968560, ss233894375, ss240865921, ss559875628, ss654228942, ss984063993, ss1074451303, ss1324345814, ss1431061170, ss1582116604, ss1617794034, ss1660788067, ss1804916751, ss1927309034, ss1970651550, ss2024331586, ss2152527730, ss2461386289, ss2626654735, ss2708184558, ss2850928510, ss3000794020, ss3347488228, ss3668722788, ss3734451752, ss3766316676, ss3830470501, ss3838722503, ss3866853039, ss3913891341, ss5182269171 NC_000007.13:24951381:G:A NC_000007.14:24911762:G:A (self)
255870088, 3358815, 17455471, 360669105, 10341708297, ss2292525509, ss3025960085, ss3525172238, ss3719304246, ss3809484098, ss3844173760, ss3961077470, ss4739177077 NC_000007.14:24911762:G:A NC_000007.14:24911762:G:A (self)
ss17193219 NT_007819.14:24244989:G:A NC_000007.14:24911762:G:A (self)
ss134, ss44836599, ss154528830 NT_007819.17:24941381:G:A NC_000007.14:24911762:G:A (self)
10341708297, ss4739177078 NC_000007.14:24911762:G:C NC_000007.14:24911762:G:C
10341708297 NC_000007.14:24911762:G:T NC_000007.14:24911762:G:T
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 rs134

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