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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.

rs980085

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:20893960 (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
T=0.269538 (71344/264690, TOPMED)
T=0.25703 (4622/17982, ALFA)
T=0.32631 (5469/16760, 8.3KJPN) (+ 15 more)
T=0.2933 (1469/5008, 1000G)
T=0.2616 (1172/4480, Estonian)
T=0.1619 (624/3854, ALSPAC)
T=0.1570 (582/3708, TWINSUK)
T=0.3515 (1030/2930, KOREAN)
T=0.3370 (637/1890, HapMap)
T=0.3286 (602/1832, Korea1K)
T=0.1387 (157/1132, Daghestan)
T=0.145 (145/998, GoNL)
T=0.230 (138/600, NorthernSweden)
T=0.169 (85/504, SGDP_PRJ)
T=0.185 (40/216, Qatari)
T=0.369 (79/214, Vietnamese)
T=0.29 (14/48, Siberian)
T=0.20 (8/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLCO1B3 : Intron Variant
SLCO1B3-SLCO1B7 : 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 12 NC_000012.12:g.20893960T>A
GRCh38.p13 chr 12 NC_000012.12:g.20893960T>C
GRCh38.p13 chr 12 NC_000012.12:g.20893960T>G
GRCh37.p13 chr 12 NC_000012.11:g.21046894T>A
GRCh37.p13 chr 12 NC_000012.11:g.21046894T>C
GRCh37.p13 chr 12 NC_000012.11:g.21046894T>G
SLCO1B3 RefSeqGene NG_032071.1:g.88257T>A
SLCO1B3 RefSeqGene NG_032071.1:g.88257T>C
SLCO1B3 RefSeqGene NG_032071.1:g.88257T>G
Gene: SLCO1B3, solute carrier organic anion transporter family member 1B3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLCO1B3 transcript variant 2 NM_001349920.2:c.1599-447…

NM_001349920.2:c.1599-4476T>A

N/A Intron Variant
SLCO1B3 transcript variant 1 NM_019844.4:c.1683-4476T>A N/A Intron Variant
Gene: SLCO1B3-SLCO1B7, SLCO1B3-SLCO1B7 readthrough (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLCO1B3-SLCO1B7 transcript NM_001371097.1:c.1683-447…

NM_001371097.1:c.1683-4476T>A

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 17982 T=0.25703 A=0.00000, C=0.00000, G=0.74297
European Sub 14432 T=0.20482 A=0.00000, C=0.00000, G=0.79518
African Sub 2086 T=0.6218 A=0.0000, C=0.0000, G=0.3782
African Others Sub 90 T=0.67 A=0.00, C=0.00, G=0.33
African American Sub 1996 T=0.6197 A=0.0000, C=0.0000, G=0.3803
Asian Sub 42 T=0.52 A=0.00, C=0.00, G=0.48
East Asian Sub 32 T=0.56 A=0.00, C=0.00, G=0.44
Other Asian Sub 10 T=0.4 A=0.0, C=0.0, G=0.6
Latin American 1 Sub 114 T=0.254 A=0.000, C=0.000, G=0.746
Latin American 2 Sub 634 T=0.262 A=0.000, C=0.000, G=0.738
South Asian Sub 30 T=0.23 A=0.00, C=0.00, G=0.77
Other Sub 644 T=0.225 A=0.000, C=0.000, G=0.775


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=0.269538 G=0.730462
8.3KJPN JAPANESE Study-wide 16760 T=0.32631 G=0.67369
1000Genomes Global Study-wide 5008 T=0.2933 G=0.7067
1000Genomes African Sub 1322 T=0.5477 G=0.4523
1000Genomes East Asian Sub 1008 T=0.3571 G=0.6429
1000Genomes Europe Sub 1006 T=0.1710 G=0.8290
1000Genomes South Asian Sub 978 T=0.080 G=0.920
1000Genomes American Sub 694 T=0.195 G=0.805
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.2616 G=0.7384
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.1619 G=0.8381
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.1570 G=0.8430
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.3515 G=0.6485
HapMap Global Study-wide 1890 T=0.3370 G=0.6630
HapMap American Sub 770 T=0.197 G=0.803
HapMap African Sub 690 T=0.539 G=0.461
HapMap Asian Sub 254 T=0.350 G=0.650
HapMap Europe Sub 176 T=0.136 G=0.864
Korean Genome Project KOREAN Study-wide 1832 T=0.3286 G=0.6714
Genome-wide autozygosity in Daghestan Global Study-wide 1132 T=0.1387 G=0.8613
Genome-wide autozygosity in Daghestan Daghestan Sub 626 T=0.128 G=0.872
Genome-wide autozygosity in Daghestan Near_East Sub 144 T=0.201 G=0.799
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=0.180 G=0.820
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.148 G=0.852
Genome-wide autozygosity in Daghestan South Asian Sub 96 T=0.08 G=0.92
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.06 G=0.94
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.145 G=0.855
Northern Sweden ACPOP Study-wide 600 T=0.230 G=0.770
SGDP_PRJ Global Study-wide 504 T=0.169 G=0.831
Qatari Global Study-wide 216 T=0.185 G=0.815
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.369 G=0.631
Siberian Global Study-wide 48 T=0.29 G=0.71
The Danish reference pan genome Danish Study-wide 40 T=0.20 G=0.80
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 12 NC_000012.12:g.20893960= NC_000012.12:g.20893960T>A NC_000012.12:g.20893960T>C NC_000012.12:g.20893960T>G
GRCh37.p13 chr 12 NC_000012.11:g.21046894= NC_000012.11:g.21046894T>A NC_000012.11:g.21046894T>C NC_000012.11:g.21046894T>G
SLCO1B3 RefSeqGene NG_032071.1:g.88257= NG_032071.1:g.88257T>A NG_032071.1:g.88257T>C NG_032071.1:g.88257T>G
SLCO1B3 transcript variant 2 NM_001349920.2:c.1599-4476= NM_001349920.2:c.1599-4476T>A NM_001349920.2:c.1599-4476T>C NM_001349920.2:c.1599-4476T>G
SLCO1B3-SLCO1B7 transcript NM_001371097.1:c.1683-4476= NM_001371097.1:c.1683-4476T>A NM_001371097.1:c.1683-4476T>C NM_001371097.1:c.1683-4476T>G
SLCO1B3 transcript variant 1 NM_019844.3:c.1683-4476= NM_019844.3:c.1683-4476T>A NM_019844.3:c.1683-4476T>C NM_019844.3:c.1683-4476T>G
SLCO1B3 transcript variant 1 NM_019844.4:c.1683-4476= NM_019844.4:c.1683-4476T>A NM_019844.4:c.1683-4476T>C NM_019844.4:c.1683-4476T>G
SLCO1B3 transcript variant X1 XM_005253347.1:c.1683-4476= XM_005253347.1:c.1683-4476T>A XM_005253347.1:c.1683-4476T>C XM_005253347.1:c.1683-4476T>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#.

79 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1433058 Oct 05, 2000 (86)
2 RIKENSNPRC ss5603564 Dec 12, 2002 (110)
3 SC_SNP ss15818004 Feb 27, 2004 (120)
4 PERLEGEN ss23433295 Sep 20, 2004 (123)
5 ILLUMINA ss75213538 Dec 06, 2007 (129)
6 HGSV ss84294931 Dec 14, 2007 (130)
7 BCMHGSC_JDW ss89017915 Mar 24, 2008 (129)
8 BGI ss103030415 Dec 01, 2009 (131)
9 1000GENOMES ss111608751 Jan 25, 2009 (130)
10 ILLUMINA-UK ss118627339 Feb 14, 2009 (130)
11 KRIBB_YJKIM ss119376576 Dec 01, 2009 (131)
12 ENSEMBL ss133043198 Dec 01, 2009 (131)
13 ILLUMINA ss152536432 Dec 01, 2009 (131)
14 GMI ss157204945 Dec 01, 2009 (131)
15 ILLUMINA ss159102637 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss167930080 Jul 04, 2010 (132)
17 ILLUMINA ss168870969 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss170542100 Jul 04, 2010 (132)
19 ILLUMINA ss174897707 Jul 04, 2010 (132)
20 BUSHMAN ss203630994 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss208339818 Jul 04, 2010 (132)
22 1000GENOMES ss225643804 Jul 14, 2010 (132)
23 1000GENOMES ss235853399 Jul 15, 2010 (132)
24 1000GENOMES ss242426203 Jul 15, 2010 (132)
25 BL ss254937977 May 09, 2011 (134)
26 GMI ss281303640 May 04, 2012 (137)
27 GMI ss286520841 Apr 25, 2013 (138)
28 PJP ss291396627 May 09, 2011 (134)
29 ILLUMINA ss537627663 Sep 08, 2015 (146)
30 TISHKOFF ss563037986 Apr 25, 2013 (138)
31 SSMP ss658573800 Apr 25, 2013 (138)
32 ILLUMINA ss832615433 Jul 13, 2019 (153)
33 EVA-GONL ss989314576 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1078303364 Aug 21, 2014 (142)
35 1000GENOMES ss1344196465 Aug 21, 2014 (142)
36 HAMMER_LAB ss1397628212 Sep 08, 2015 (146)
37 DDI ss1426867114 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1576154393 Apr 01, 2015 (144)
39 EVA_DECODE ss1598987165 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1628162299 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1671156332 Apr 01, 2015 (144)
42 EVA_SVP ss1713312472 Apr 01, 2015 (144)
43 HAMMER_LAB ss1807152128 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1932679119 Feb 12, 2016 (147)
45 GENOMED ss1967541967 Jul 19, 2016 (147)
46 JJLAB ss2027086754 Sep 14, 2016 (149)
47 USC_VALOUEV ss2155412414 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2188357069 Dec 20, 2016 (150)
49 TOPMED ss2352013157 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2628022846 Nov 08, 2017 (151)
51 GRF ss2699740606 Nov 08, 2017 (151)
52 GNOMAD ss2908149327 Nov 08, 2017 (151)
53 SWEGEN ss3009326444 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3027349603 Nov 08, 2017 (151)
55 TOPMED ss3164811867 Nov 08, 2017 (151)
56 TOPMED ss3164811868 Nov 08, 2017 (151)
57 TOPMED ss3164811869 Nov 08, 2017 (151)
58 CSHL ss3349959583 Nov 08, 2017 (151)
59 ILLUMINA ss3626832916 Oct 12, 2018 (152)
60 ILLUMINA ss3637951315 Oct 12, 2018 (152)
61 ILLUMINA ss3637951316 Oct 12, 2018 (152)
62 ILLUMINA ss3642945902 Oct 12, 2018 (152)
63 URBANLAB ss3649785894 Oct 12, 2018 (152)
64 EGCUT_WGS ss3676641963 Jul 13, 2019 (153)
65 EVA_DECODE ss3693255369 Jul 13, 2019 (153)
66 ACPOP ss3738834864 Jul 13, 2019 (153)
67 EVA ss3750227692 Jul 13, 2019 (153)
68 PACBIO ss3787166688 Jul 13, 2019 (153)
69 PACBIO ss3792277478 Jul 13, 2019 (153)
70 PACBIO ss3797160169 Jul 13, 2019 (153)
71 KHV_HUMAN_GENOMES ss3815545236 Jul 13, 2019 (153)
72 EVA ss3833013114 Apr 26, 2020 (154)
73 EVA ss3840074457 Apr 26, 2020 (154)
74 EVA ss3845558294 Apr 26, 2020 (154)
75 SGDP_PRJ ss3877839973 Apr 26, 2020 (154)
76 KRGDB ss3926371784 Apr 26, 2020 (154)
77 KOGIC ss3971414784 Apr 26, 2020 (154)
78 TOPMED ss4911130010 Apr 26, 2021 (155)
79 TOMMO_GENOMICS ss5205384851 Apr 26, 2021 (155)
80 1000Genomes NC_000012.11 - 21046894 Oct 12, 2018 (152)
81 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 21046894 Oct 12, 2018 (152)
82 Genome-wide autozygosity in Daghestan NC_000012.10 - 20938161 Apr 26, 2020 (154)
83 Genetic variation in the Estonian population NC_000012.11 - 21046894 Oct 12, 2018 (152)
84 The Danish reference pan genome NC_000012.11 - 21046894 Apr 26, 2020 (154)
85 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 401316035 (NC_000012.12:20893959:T:A 1/140020)
Row 401316036 (NC_000012.12:20893959:T:G 100872/139980)

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

Submission ignored due to conflicting rows:
Row 401316035 (NC_000012.12:20893959:T:A 1/140020)
Row 401316036 (NC_000012.12:20893959:T:G 100872/139980)

- Apr 26, 2021 (155)
87 Genome of the Netherlands Release 5 NC_000012.11 - 21046894 Apr 26, 2020 (154)
88 HapMap NC_000012.12 - 20893960 Apr 26, 2020 (154)
89 KOREAN population from KRGDB NC_000012.11 - 21046894 Apr 26, 2020 (154)
90 Korean Genome Project NC_000012.12 - 20893960 Apr 26, 2020 (154)
91 Northern Sweden NC_000012.11 - 21046894 Jul 13, 2019 (153)
92 Qatari NC_000012.11 - 21046894 Apr 26, 2020 (154)
93 SGDP_PRJ NC_000012.11 - 21046894 Apr 26, 2020 (154)
94 Siberian NC_000012.11 - 21046894 Apr 26, 2020 (154)
95 8.3KJPN NC_000012.11 - 21046894 Apr 26, 2021 (155)
96 TopMed NC_000012.12 - 20893960 Apr 26, 2021 (155)
97 UK 10K study - Twins NC_000012.11 - 21046894 Oct 12, 2018 (152)
98 A Vietnamese Genetic Variation Database NC_000012.11 - 21046894 Jul 13, 2019 (153)
99 ALFA NC_000012.12 - 20893960 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)
rs57331118 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
3761132490, ss3164811867 NC_000012.12:20893959:T:A NC_000012.12:20893959:T:A (self)
3761132490, ss3164811868 NC_000012.12:20893959:T:C NC_000012.12:20893959:T:C (self)
ss84294931 NC_000012.9:20938160:T:G NC_000012.12:20893959:T:G (self)
99187, ss89017915, ss111608751, ss118627339, ss167930080, ss170542100, ss203630994, ss208339818, ss254937977, ss281303640, ss286520841, ss291396627, ss1397628212, ss1598987165, ss1713312472, ss3642945902 NC_000012.10:20938160:T:G NC_000012.12:20893959:T:G (self)
56914798, 31602391, 22380211, 2874554, 14100997, 33549178, 12119729, 14721049, 29856953, 7928768, 63354158, 31602391, 7012060, ss225643804, ss235853399, ss242426203, ss537627663, ss563037986, ss658573800, ss832615433, ss989314576, ss1078303364, ss1344196465, ss1426867114, ss1576154393, ss1628162299, ss1671156332, ss1807152128, ss1932679119, ss1967541967, ss2027086754, ss2155412414, ss2352013157, ss2628022846, ss2699740606, ss2908149327, ss3009326444, ss3349959583, ss3626832916, ss3637951315, ss3637951316, ss3676641963, ss3738834864, ss3750227692, ss3787166688, ss3792277478, ss3797160169, ss3833013114, ss3840074457, ss3877839973, ss3926371784, ss5205384851 NC_000012.11:21046893:T:G NC_000012.12:20893959:T:G (self)
770629, 27792785, 79375031, 126675667, 3761132490, ss2188357069, ss3027349603, ss3164811869, ss3649785894, ss3693255369, ss3815545236, ss3845558294, ss3971414784, ss4911130010 NC_000012.12:20893959:T:G NC_000012.12:20893959:T:G (self)
ss15818004 NT_009714.16:13805867:T:G NC_000012.12:20893959:T:G (self)
ss1433058, ss5603564, ss23433295, ss75213538, ss103030415, ss119376576, ss133043198, ss152536432, ss157204945, ss159102637, ss168870969, ss174897707 NT_009714.17:13807017:T:G NC_000012.12:20893959:T: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 rs980085

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