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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.

rs132

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:24905138 (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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.274430 (72639/264690, TOPMED)
C=0.21835 (5451/24964, ALFA)
C=0.35458 (5942/16758, 8.3KJPN) (+ 12 more)
C=0.3189 (1597/5008, 1000G)
C=0.2976 (1147/3854, ALSPAC)
C=0.3007 (1115/3708, TWINSUK)
C=0.3204 (938/2928, KOREAN)
C=0.303 (302/998, GoNL)
C=0.310 (186/600, NorthernSweden)
C=0.322 (105/326, HapMap)
T=0.397 (116/292, SGDP_PRJ)
C=0.245 (53/216, Qatari)
C=0.374 (80/214, Vietnamese)
C=0.30 (12/40, GENOME_DK)
T=0.39 (11/28, 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.24905138T>A
GRCh38.p13 chr 7 NC_000007.14:g.24905138T>C
GRCh38.p13 chr 7 NC_000007.14:g.24905138T>G
GRCh37.p13 chr 7 NC_000007.13:g.24944757T>A
GRCh37.p13 chr 7 NC_000007.13:g.24944757T>C
GRCh37.p13 chr 7 NC_000007.13:g.24944757T>G
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.-149-12517A…

NM_015550.4:c.-149-12517A>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.-149-125…

XM_005249698.3:c.-149-12517A>T

N/A Intron Variant
OSBPL3 transcript variant X3 XM_006715681.3:c.-149-125…

XM_006715681.3:c.-149-12517A>T

N/A Intron Variant
OSBPL3 transcript variant X4 XM_006715682.3:c.-149-125…

XM_006715682.3:c.-149-12517A>T

N/A Intron Variant
OSBPL3 transcript variant X7 XM_006715683.3:c.-149-125…

XM_006715683.3:c.-149-12517A>T

N/A Intron Variant
OSBPL3 transcript variant X15 XM_006715684.4:c.-1192-12…

XM_006715684.4:c.-1192-12517A>T

N/A Intron Variant
OSBPL3 transcript variant X1 XM_011515258.2:c.-149-125…

XM_011515258.2:c.-149-12517A>T

N/A Intron Variant
OSBPL3 transcript variant X5 XM_011515259.2:c.-628-125…

XM_011515259.2:c.-628-12517A>T

N/A Intron Variant
OSBPL3 transcript variant X6 XM_017011948.1:c.-491-125…

XM_017011948.1:c.-491-12517A>T

N/A Intron Variant
OSBPL3 transcript variant X8 XM_017011949.1:c.-628-125…

XM_017011949.1:c.-628-12517A>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 24964 T=0.78165 A=0.00000, C=0.21835, G=0.00000
European Sub 20828 T=0.76210 A=0.00000, C=0.23790, G=0.00000
African Sub 2036 T=0.9740 A=0.0000, C=0.0260, G=0.0000
African Others Sub 80 T=1.00 A=0.00, C=0.00, G=0.00
African American Sub 1956 T=0.9729 A=0.0000, C=0.0271, G=0.0000
Asian Sub 54 T=0.80 A=0.00, C=0.20, G=0.00
East Asian Sub 40 T=0.82 A=0.00, C=0.17, G=0.00
Other Asian Sub 14 T=0.71 A=0.00, C=0.29, G=0.00
Latin American 1 Sub 106 T=0.953 A=0.000, C=0.047, G=0.000
Latin American 2 Sub 352 T=0.909 A=0.000, C=0.091, G=0.000
South Asian Sub 56 T=0.82 A=0.00, C=0.18, G=0.00
Other Sub 1532 T=0.7487 A=0.0000, C=0.2513, G=0.0000


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=0.725570 C=0.274430
8.3KJPN JAPANESE Study-wide 16758 T=0.64542 C=0.35458
1000Genomes Global Study-wide 5008 T=0.6811 C=0.3189
1000Genomes African Sub 1322 T=0.7927 C=0.2073
1000Genomes East Asian Sub 1008 T=0.5923 C=0.4077
1000Genomes Europe Sub 1006 T=0.6938 C=0.3062
1000Genomes South Asian Sub 978 T=0.621 C=0.379
1000Genomes American Sub 694 T=0.664 C=0.336
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7024 C=0.2976
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6993 C=0.3007
KOREAN population from KRGDB KOREAN Study-wide 2928 T=0.6796 C=0.3204
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.697 C=0.303
Northern Sweden ACPOP Study-wide 600 T=0.690 C=0.310
HapMap Global Study-wide 326 T=0.678 C=0.322
HapMap African Sub 118 T=0.746 C=0.254
HapMap American Sub 118 T=0.720 C=0.280
HapMap Asian Sub 90 T=0.53 C=0.47
SGDP_PRJ Global Study-wide 292 T=0.397 C=0.603
Qatari Global Study-wide 216 T=0.755 C=0.245
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.626 C=0.374
The Danish reference pan genome Danish Study-wide 40 T=0.70 C=0.30
Siberian Global Study-wide 28 T=0.39 C=0.61
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 G
GRCh38.p13 chr 7 NC_000007.14:g.24905138= NC_000007.14:g.24905138T>A NC_000007.14:g.24905138T>C NC_000007.14:g.24905138T>G
GRCh37.p13 chr 7 NC_000007.13:g.24944757= NC_000007.13:g.24944757T>A NC_000007.13:g.24944757T>C NC_000007.13:g.24944757T>G
OSBPL3 transcript variant 1 NM_015550.2:c.-149-12517= NM_015550.2:c.-149-12517A>T NM_015550.2:c.-149-12517A>G NM_015550.2:c.-149-12517A>C
OSBPL3 transcript variant 1 NM_015550.4:c.-149-12517= NM_015550.4:c.-149-12517A>T NM_015550.4:c.-149-12517A>G NM_015550.4:c.-149-12517A>C
OSBPL3 transcript variant 2 NM_145320.1:c.-149-12517= NM_145320.1:c.-149-12517A>T NM_145320.1:c.-149-12517A>G NM_145320.1:c.-149-12517A>C
OSBPL3 transcript variant 3 NM_145321.1:c.-149-12517= NM_145321.1:c.-149-12517A>T NM_145321.1:c.-149-12517A>G NM_145321.1:c.-149-12517A>C
OSBPL3 transcript variant 4 NM_145322.1:c.-149-12517= NM_145322.1:c.-149-12517A>T NM_145322.1:c.-149-12517A>G NM_145322.1:c.-149-12517A>C
OSBPL3 transcript variant X1 XM_005249698.1:c.-149-12517= XM_005249698.1:c.-149-12517A>T XM_005249698.1:c.-149-12517A>G XM_005249698.1:c.-149-12517A>C
OSBPL3 transcript variant X2 XM_005249698.3:c.-149-12517= XM_005249698.3:c.-149-12517A>T XM_005249698.3:c.-149-12517A>G XM_005249698.3:c.-149-12517A>C
OSBPL3 transcript variant X3 XM_006715681.3:c.-149-12517= XM_006715681.3:c.-149-12517A>T XM_006715681.3:c.-149-12517A>G XM_006715681.3:c.-149-12517A>C
OSBPL3 transcript variant X4 XM_006715682.3:c.-149-12517= XM_006715682.3:c.-149-12517A>T XM_006715682.3:c.-149-12517A>G XM_006715682.3:c.-149-12517A>C
OSBPL3 transcript variant X7 XM_006715683.3:c.-149-12517= XM_006715683.3:c.-149-12517A>T XM_006715683.3:c.-149-12517A>G XM_006715683.3:c.-149-12517A>C
OSBPL3 transcript variant X15 XM_006715684.4:c.-1192-12517= XM_006715684.4:c.-1192-12517A>T XM_006715684.4:c.-1192-12517A>G XM_006715684.4:c.-1192-12517A>C
OSBPL3 transcript variant X1 XM_011515258.2:c.-149-12517= XM_011515258.2:c.-149-12517A>T XM_011515258.2:c.-149-12517A>G XM_011515258.2:c.-149-12517A>C
OSBPL3 transcript variant X5 XM_011515259.2:c.-628-12517= XM_011515259.2:c.-628-12517A>T XM_011515259.2:c.-628-12517A>G XM_011515259.2:c.-628-12517A>C
OSBPL3 transcript variant X6 XM_017011948.1:c.-491-12517= XM_017011948.1:c.-491-12517A>T XM_017011948.1:c.-491-12517A>G XM_017011948.1:c.-491-12517A>C
OSBPL3 transcript variant X8 XM_017011949.1:c.-628-12517= XM_017011949.1:c.-628-12517A>T XM_017011949.1:c.-628-12517A>G XM_017011949.1:c.-628-12517A>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#.

59 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss132 Sep 19, 2000 (36)
2 TSC-CSHL ss3156955 Jun 15, 2001 (96)
3 PERLEGEN ss23983703 Sep 20, 2004 (123)
4 ILLUMINA-UK ss115987551 Feb 14, 2009 (130)
5 GMI ss154528781 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss166294612 Jul 04, 2010 (132)
7 BUSHMAN ss203089172 Jul 04, 2010 (132)
8 1000GENOMES ss212009546 Jul 14, 2010 (132)
9 1000GENOMES ss222968539 Jul 14, 2010 (132)
10 1000GENOMES ss233894353 Jul 15, 2010 (132)
11 1000GENOMES ss240865909 Jul 15, 2010 (132)
12 BL ss254127950 May 09, 2011 (134)
13 GMI ss279229031 May 04, 2012 (137)
14 ILLUMINA ss484109388 May 04, 2012 (137)
15 ILLUMINA ss485409142 May 04, 2012 (137)
16 ILLUMINA ss536299624 Sep 08, 2015 (146)
17 TISHKOFF ss559875605 Apr 25, 2013 (138)
18 SSMP ss654228911 Apr 25, 2013 (138)
19 ILLUMINA ss780530001 Sep 08, 2015 (146)
20 ILLUMINA ss782499945 Sep 08, 2015 (146)
21 ILLUMINA ss836021602 Sep 08, 2015 (146)
22 EVA-GONL ss984063942 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1074451273 Aug 21, 2014 (142)
24 1000GENOMES ss1324345630 Aug 21, 2014 (142)
25 DDI ss1431061155 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1582116583 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1617793913 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1660787946 Apr 01, 2015 (144)
29 HAMMER_LAB ss1804916733 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1927308985 Feb 12, 2016 (147)
31 GENOMED ss1970651537 Jul 19, 2016 (147)
32 JJLAB ss2024331558 Sep 14, 2016 (149)
33 USC_VALOUEV ss2152527701 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2292525115 Dec 20, 2016 (150)
35 TOPMED ss2461385896 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2626654722 Nov 08, 2017 (151)
37 ILLUMINA ss2634581251 Nov 08, 2017 (151)
38 GRF ss2708184536 Nov 08, 2017 (151)
39 GNOMAD ss2850927991 Nov 08, 2017 (151)
40 SWEGEN ss3000793946 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3025960075 Nov 08, 2017 (151)
42 CSHL ss3347488203 Nov 08, 2017 (151)
43 TOPMED ss3525170974 Nov 08, 2017 (151)
44 TOPMED ss3525170975 Nov 08, 2017 (151)
45 ILLUMINA ss3629774436 Oct 12, 2018 (152)
46 ILLUMINA ss3632490030 Oct 12, 2018 (152)
47 ILLUMINA ss3642551652 Oct 12, 2018 (152)
48 EVA_DECODE ss3719304140 Jul 13, 2019 (153)
49 EVA_DECODE ss3719304141 Jul 13, 2019 (153)
50 ACPOP ss3734451709 Jul 13, 2019 (153)
51 EVA ss3766316620 Jul 13, 2019 (153)
52 KHV_HUMAN_GENOMES ss3809484050 Jul 13, 2019 (153)
53 EVA ss3830470479 Apr 26, 2020 (154)
54 EVA ss3838722492 Apr 26, 2020 (154)
55 EVA ss3844173748 Apr 26, 2020 (154)
56 SGDP_PRJ ss3866852942 Apr 26, 2020 (154)
57 KRGDB ss3913891247 Apr 26, 2020 (154)
58 TOPMED ss4739175379 Apr 26, 2021 (155)
59 TOMMO_GENOMICS ss5182268988 Apr 26, 2021 (155)
60 1000Genomes NC_000007.13 - 24944757 Oct 12, 2018 (152)
61 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 24944757 Oct 12, 2018 (152)
62 The Danish reference pan genome NC_000007.13 - 24944757 Apr 26, 2020 (154)
63 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 255868693 (NC_000007.14:24905137:T:A 6/133398)
Row 255868694 (NC_000007.14:24905137:T:C 38250/133408)
Row 255868695 (NC_000007.14:24905137:T:G 1/133466)

- Apr 26, 2021 (155)
64 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 255868693 (NC_000007.14:24905137:T:A 6/133398)
Row 255868694 (NC_000007.14:24905137:T:C 38250/133408)
Row 255868695 (NC_000007.14:24905137:T:G 1/133466)

- Apr 26, 2021 (155)
65 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 255868693 (NC_000007.14:24905137:T:A 6/133398)
Row 255868694 (NC_000007.14:24905137:T:C 38250/133408)
Row 255868695 (NC_000007.14:24905137:T:G 1/133466)

- Apr 26, 2021 (155)
66 Genome of the Netherlands Release 5 NC_000007.13 - 24944757 Apr 26, 2020 (154)
67 HapMap NC_000007.14 - 24905138 Apr 26, 2020 (154)
68 KOREAN population from KRGDB NC_000007.13 - 24944757 Apr 26, 2020 (154)
69 Northern Sweden NC_000007.13 - 24944757 Jul 13, 2019 (153)
70 Qatari NC_000007.13 - 24944757 Apr 26, 2020 (154)
71 SGDP_PRJ NC_000007.13 - 24944757 Apr 26, 2020 (154)
72 Siberian NC_000007.13 - 24944757 Apr 26, 2020 (154)
73 8.3KJPN NC_000007.13 - 24944757 Apr 26, 2021 (155)
74 TopMed NC_000007.14 - 24905138 Apr 26, 2021 (155)
75 UK 10K study - Twins NC_000007.13 - 24944757 Oct 12, 2018 (152)
76 A Vietnamese Genetic Variation Database NC_000007.13 - 24944757 Jul 13, 2019 (153)
77 ALFA NC_000007.14 - 24905138 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)
rs17150500 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2850927991 NC_000007.13:24944756:T:A NC_000007.14:24905137:T:A (self)
12098908889, ss3525170974, ss3719304140 NC_000007.14:24905137:T:A NC_000007.14:24905137:T:A (self)
ss115987551, ss166294612, ss203089172, ss212009546, ss254127950, ss279229031, ss485409142 NC_000007.12:24911281:T:C NC_000007.14:24905137:T:C (self)
36287578, 20229798, 8281522, 9019589, 21068641, 7736574, 9350915, 18869922, 5044055, 40238295, 20229798, 4507504, ss222968539, ss233894353, ss240865909, ss484109388, ss536299624, ss559875605, ss654228911, ss780530001, ss782499945, ss836021602, ss984063942, ss1074451273, ss1324345630, ss1431061155, ss1582116583, ss1617793913, ss1660787946, ss1804916733, ss1927308985, ss1970651537, ss2024331558, ss2152527701, ss2461385896, ss2626654722, ss2634581251, ss2708184536, ss2850927991, ss3000793946, ss3347488203, ss3629774436, ss3632490030, ss3642551652, ss3734451709, ss3766316620, ss3830470479, ss3838722492, ss3866852942, ss3913891247, ss5182268988 NC_000007.13:24944756:T:C NC_000007.14:24905137:T:C (self)
3358801, 360668026, 576552938, 12098908889, ss2292525115, ss3025960075, ss3525170975, ss3719304141, ss3809484050, ss3844173748, ss4739175379 NC_000007.14:24905137:T:C NC_000007.14:24905137:T:C (self)
ss132, ss3156955, ss23983703, ss154528781 NT_007819.17:24934756:T:C NC_000007.14:24905137:T:C (self)
12098908889 NC_000007.14:24905137:T:G NC_000007.14:24905137:T:G
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 rs132

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