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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.

rs137

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:24926112 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.279739 (74044/264690, TOPMED)
G=0.278400 (38981/140018, GnomAD)
G=0.28411 (6810/23970, ALFA) (+ 16 more)
G=0.37224 (6238/16758, 8.3KJPN)
G=0.3225 (1615/5008, 1000G)
G=0.2703 (1211/4480, Estonian)
G=0.2927 (1128/3854, ALSPAC)
G=0.2972 (1102/3708, TWINSUK)
G=0.3372 (988/2930, KOREAN)
G=0.2945 (556/1888, HapMap)
G=0.3373 (618/1832, Korea1K)
G=0.296 (295/998, GoNL)
G=0.358 (224/626, Chileans)
G=0.270 (162/600, NorthernSweden)
A=0.407 (122/300, SGDP_PRJ)
G=0.222 (48/216, Qatari)
G=0.349 (74/212, Vietnamese)
G=0.33 (13/40, GENOME_DK)
A=0.42 (11/26, 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.24926112A>G
GRCh37.p13 chr 7 NC_000007.13:g.24965731A>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.-149-33491T…

NM_015550.4:c.-149-33491T>C

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 X3 XM_006715681.3:c.-149-334…

XM_006715681.3:c.-149-33491T>C

N/A Intron Variant
OSBPL3 transcript variant X4 XM_006715682.3:c.-149-334…

XM_006715682.3:c.-149-33491T>C

N/A Intron Variant
OSBPL3 transcript variant X7 XM_006715683.3:c.-149-334…

XM_006715683.3:c.-149-33491T>C

N/A Intron Variant
OSBPL3 transcript variant X15 XM_006715684.4:c.-1192-33…

XM_006715684.4:c.-1192-33491T>C

N/A Intron Variant
OSBPL3 transcript variant X5 XM_011515259.2:c.-628-334…

XM_011515259.2:c.-628-33491T>C

N/A Intron Variant
OSBPL3 transcript variant X6 XM_017011948.1:c.-491-334…

XM_017011948.1:c.-491-33491T>C

N/A Intron Variant
OSBPL3 transcript variant X8 XM_017011949.1:c.-628-334…

XM_017011949.1:c.-628-33491T>C

N/A Intron Variant
OSBPL3 transcript variant X2 XM_005249698.3:c. N/A Genic Upstream Transcript Variant
OSBPL3 transcript variant X1 XM_011515258.2:c. N/A Genic Upstream Transcript 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 (New)
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 23970 A=0.71589 G=0.28411
European Sub 15668 A=0.71675 G=0.28325
African Sub 3624 A=0.7608 G=0.2392
African Others Sub 126 A=0.754 G=0.246
African American Sub 3498 A=0.7610 G=0.2390
Asian Sub 160 A=0.594 G=0.406
East Asian Sub 102 A=0.618 G=0.382
Other Asian Sub 58 A=0.55 G=0.45
Latin American 1 Sub 292 A=0.753 G=0.247
Latin American 2 Sub 2770 A=0.6700 G=0.3300
South Asian Sub 110 A=0.573 G=0.427
Other Sub 1346 A=0.6976 G=0.3024


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=0.720261 G=0.279739
gnomAD - Genomes Global Study-wide 140018 A=0.721600 G=0.278400
gnomAD - Genomes European Sub 75846 A=0.71873 G=0.28127
gnomAD - Genomes African Sub 41926 A=0.75865 G=0.24135
gnomAD - Genomes American Sub 13652 A=0.66488 G=0.33512
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.6304 G=0.3696
gnomAD - Genomes East Asian Sub 3122 A=0.6304 G=0.3696
gnomAD - Genomes Other Sub 2152 A=0.7337 G=0.2663
8.3KJPN JAPANESE Study-wide 16758 A=0.62776 G=0.37224
1000Genomes Global Study-wide 5008 A=0.6775 G=0.3225
1000Genomes African Sub 1322 A=0.7655 G=0.2345
1000Genomes East Asian Sub 1008 A=0.6022 G=0.3978
1000Genomes Europe Sub 1006 A=0.7038 G=0.2962
1000Genomes South Asian Sub 978 A=0.625 G=0.375
1000Genomes American Sub 694 A=0.656 G=0.344
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7297 G=0.2703
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7073 G=0.2927
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.7028 G=0.2972
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6628 G=0.3372
HapMap Global Study-wide 1888 A=0.7055 G=0.2945
HapMap American Sub 770 A=0.682 G=0.318
HapMap African Sub 690 A=0.772 G=0.228
HapMap Asian Sub 252 A=0.567 G=0.433
HapMap Europe Sub 176 A=0.744 G=0.256
Korean Genome Project KOREAN Study-wide 1832 A=0.6627 G=0.3373
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.704 G=0.296
Chileans Chilean Study-wide 626 A=0.642 G=0.358
Northern Sweden ACPOP Study-wide 600 A=0.730 G=0.270
SGDP_PRJ Global Study-wide 300 A=0.407 G=0.593
Qatari Global Study-wide 216 A=0.778 G=0.222
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.651 G=0.349
The Danish reference pan genome Danish Study-wide 40 A=0.68 G=0.33
Siberian Global Study-wide 26 A=0.42 G=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 A= G
GRCh38.p13 chr 7 NC_000007.14:g.24926112= NC_000007.14:g.24926112A>G
GRCh37.p13 chr 7 NC_000007.13:g.24965731= NC_000007.13:g.24965731A>G
OSBPL3 transcript variant 1 NM_015550.2:c.-149-33491= NM_015550.2:c.-149-33491T>C
OSBPL3 transcript variant 1 NM_015550.4:c.-149-33491= NM_015550.4:c.-149-33491T>C
OSBPL3 transcript variant 2 NM_145320.1:c.-149-33491= NM_145320.1:c.-149-33491T>C
OSBPL3 transcript variant 3 NM_145321.1:c.-149-33491= NM_145321.1:c.-149-33491T>C
OSBPL3 transcript variant 4 NM_145322.1:c.-149-33491= NM_145322.1:c.-149-33491T>C
OSBPL3 transcript variant X3 XM_006715681.3:c.-149-33491= XM_006715681.3:c.-149-33491T>C
OSBPL3 transcript variant X4 XM_006715682.3:c.-149-33491= XM_006715682.3:c.-149-33491T>C
OSBPL3 transcript variant X7 XM_006715683.3:c.-149-33491= XM_006715683.3:c.-149-33491T>C
OSBPL3 transcript variant X15 XM_006715684.4:c.-1192-33491= XM_006715684.4:c.-1192-33491T>C
OSBPL3 transcript variant X5 XM_011515259.2:c.-628-33491= XM_011515259.2:c.-628-33491T>C
OSBPL3 transcript variant X6 XM_017011948.1:c.-491-33491= XM_017011948.1:c.-491-33491T>C
OSBPL3 transcript variant X8 XM_017011949.1:c.-628-33491= XM_017011949.1:c.-628-33491T>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#.

52 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss137 Sep 19, 2000 (36)
2 TSC-CSHL ss1307065 Oct 05, 2000 (92)
3 ABI ss44788518 Mar 15, 2006 (126)
4 AFFY ss76473383 Dec 08, 2007 (129)
5 KRIBB_YJKIM ss104807672 Feb 05, 2009 (130)
6 ILLUMINA-UK ss115987654 Feb 14, 2009 (130)
7 GMI ss154529015 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss166295015 Jul 04, 2010 (132)
9 BUSHMAN ss203089432 Jul 04, 2010 (132)
10 1000GENOMES ss212009575 Jul 14, 2010 (132)
11 1000GENOMES ss222968637 Jul 14, 2010 (132)
12 1000GENOMES ss233894432 Jul 15, 2010 (132)
13 1000GENOMES ss240865972 Jul 15, 2010 (132)
14 GMI ss279229095 May 04, 2012 (137)
15 TISHKOFF ss559875701 Apr 25, 2013 (138)
16 SSMP ss654229020 Apr 25, 2013 (138)
17 EVA-GONL ss984064101 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1074451401 Aug 21, 2014 (142)
19 1000GENOMES ss1324346239 Aug 21, 2014 (142)
20 DDI ss1431061209 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1582116659 Apr 01, 2015 (144)
22 EVA_DECODE ss1593632968 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1617794264 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1660788297 Apr 01, 2015 (144)
25 EVA_SVP ss1712939939 Apr 01, 2015 (144)
26 HAMMER_LAB ss1804916810 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1927309161 Feb 12, 2016 (147)
28 GENOMED ss1970651584 Jul 19, 2016 (147)
29 JJLAB ss2024331655 Sep 14, 2016 (149)
30 USC_VALOUEV ss2152527804 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2292526360 Dec 20, 2016 (150)
32 TOPMED ss2461387115 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2626654781 Nov 08, 2017 (151)
34 GRF ss2708184635 Nov 08, 2017 (151)
35 GNOMAD ss2850929606 Nov 08, 2017 (151)
36 SWEGEN ss3000794179 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3025960124 Nov 08, 2017 (151)
38 CSHL ss3347488278 Nov 08, 2017 (151)
39 TOPMED ss3525174807 Nov 08, 2017 (151)
40 EGCUT_WGS ss3668722954 Jul 13, 2019 (153)
41 EVA_DECODE ss3719304470 Jul 13, 2019 (153)
42 ACPOP ss3734451869 Jul 13, 2019 (153)
43 EVA ss3766316812 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3809484248 Jul 13, 2019 (153)
45 EVA ss3830470561 Apr 26, 2020 (154)
46 EVA ss3838722549 Apr 26, 2020 (154)
47 EVA ss3844173805 Apr 26, 2020 (154)
48 SGDP_PRJ ss3866853268 Apr 26, 2020 (154)
49 KRGDB ss3913891568 Apr 26, 2020 (154)
50 KOGIC ss3961077702 Apr 26, 2020 (154)
51 TOPMED ss4739180484 Apr 26, 2021 (155)
52 TOMMO_GENOMICS ss5182269641 Apr 26, 2021 (155)
53 1000Genomes NC_000007.13 - 24965731 Oct 12, 2018 (152)
54 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 24965731 Oct 12, 2018 (152)
55 Chileans NC_000007.13 - 24965731 Apr 26, 2020 (154)
56 Genetic variation in the Estonian population NC_000007.13 - 24965731 Oct 12, 2018 (152)
57 The Danish reference pan genome NC_000007.13 - 24965731 Apr 26, 2020 (154)
58 gnomAD - Genomes NC_000007.14 - 24926112 Apr 26, 2021 (155)
59 Genome of the Netherlands Release 5 NC_000007.13 - 24965731 Apr 26, 2020 (154)
60 HapMap NC_000007.14 - 24926112 Apr 26, 2020 (154)
61 KOREAN population from KRGDB NC_000007.13 - 24965731 Apr 26, 2020 (154)
62 Korean Genome Project NC_000007.14 - 24926112 Apr 26, 2020 (154)
63 Northern Sweden NC_000007.13 - 24965731 Jul 13, 2019 (153)
64 Qatari NC_000007.13 - 24965731 Apr 26, 2020 (154)
65 SGDP_PRJ NC_000007.13 - 24965731 Apr 26, 2020 (154)
66 Siberian NC_000007.13 - 24965731 Apr 26, 2020 (154)
67 8.3KJPN NC_000007.13 - 24965731 Apr 26, 2021 (155)
68 TopMed NC_000007.14 - 24926112 Apr 26, 2021 (155)
69 UK 10K study - Twins NC_000007.13 - 24965731 Oct 12, 2018 (152)
70 A Vietnamese Genetic Variation Database NC_000007.13 - 24965731 Jul 13, 2019 (153)
71 ALFA NC_000007.14 - 24926112 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)
rs880780 Jan 18, 2001 (92)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss115987654, ss166295015, ss203089432, ss212009575, ss279229095, ss1593632968, ss1712939939 NC_000007.12:24932255:A:G NC_000007.14:24926111:A:G (self)
36288204, 20230185, 404144, 14461202, 8281598, 9019747, 21068962, 7736734, 9351091, 18870248, 5044158, 40238948, 20230185, 4507596, ss222968637, ss233894432, ss240865972, ss559875701, ss654229020, ss984064101, ss1074451401, ss1324346239, ss1431061209, ss1582116659, ss1617794264, ss1660788297, ss1804916810, ss1927309161, ss1970651584, ss2024331655, ss2152527804, ss2461387115, ss2626654781, ss2708184635, ss2850929606, ss3000794179, ss3347488278, ss3668722954, ss3734451869, ss3766316812, ss3830470561, ss3838722549, ss3866853268, ss3913891568, ss5182269641 NC_000007.13:24965730:A:G NC_000007.14:24926111:A:G (self)
255873176, 3358839, 17455703, 360671278, 576558043, 6960042529, ss2292526360, ss3025960124, ss3525174807, ss3719304470, ss3809484248, ss3844173805, ss3961077702, ss4739180484 NC_000007.14:24926111:A:G NC_000007.14:24926111:A:G (self)
ss137, ss1307065, ss44788518, ss76473383, ss104807672, ss154529015 NT_007819.17:24955730:A:G NC_000007.14:24926111: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.

1 citation for rs137
PMID Title Author Year Journal
26656845 Fine-mapping cellular QTLs with RASQUAL and ATAC-seq. Kumasaka N et al. 2016 Nature genetics
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