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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.

rs2238357

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr15:92142136 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.324527 (85899/264690, TOPMED)
C=0.321481 (45035/140086, GnomAD)
C=0.41605 (6973/16760, 8.3KJPN) (+ 15 more)
C=0.20387 (3253/15956, ALFA)
C=0.3403 (1704/5008, 1000G)
C=0.3085 (1382/4480, Estonian)
C=0.2994 (1154/3854, ALSPAC)
C=0.3042 (1128/3708, TWINSUK)
C=0.3744 (1097/2930, KOREAN)
C=0.3963 (726/1832, Korea1K)
C=0.3496 (625/1788, HapMap)
C=0.306 (305/998, GoNL)
C=0.300 (180/600, NorthernSweden)
G=0.420 (115/274, SGDP_PRJ)
C=0.264 (57/216, Qatari)
C=0.411 (88/214, Vietnamese)
C=0.45 (18/40, GENOME_DK)
G=0.37 (11/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLCO3A1 : 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 15 NC_000015.10:g.92142136G>A
GRCh38.p13 chr 15 NC_000015.10:g.92142136G>C
GRCh37.p13 chr 15 NC_000015.9:g.92685366G>A
GRCh37.p13 chr 15 NC_000015.9:g.92685366G>C
Gene: SLCO3A1, solute carrier organic anion transporter family member 3A1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLCO3A1 transcript variant 2 NM_001145044.1:c.1513-484…

NM_001145044.1:c.1513-4848G>A

N/A Intron Variant
SLCO3A1 transcript variant 1 NM_013272.4:c.1513-4848G>A N/A Intron Variant
SLCO3A1 transcript variant 3 NR_135775.2:n. N/A Intron Variant
SLCO3A1 transcript variant X1 XM_005254889.1:c.1513-484…

XM_005254889.1:c.1513-4848G>A

N/A Intron Variant
SLCO3A1 transcript variant X3 XM_005254891.3:c.1168-484…

XM_005254891.3:c.1168-4848G>A

N/A Intron Variant
SLCO3A1 transcript variant X2 XM_011521456.2:c.1339-484…

XM_011521456.2:c.1339-4848G>A

N/A Intron Variant
SLCO3A1 transcript variant X4 XR_931795.1:n. N/A Intron Variant
SLCO3A1 transcript variant X5 XR_931796.2: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 15956 G=0.79613 A=0.00000, C=0.20387
European Sub 13740 G=0.77460 A=0.00000, C=0.22540
African Sub 1258 G=0.9595 A=0.0000, C=0.0405
African Others Sub 64 G=0.97 A=0.00, C=0.03
African American Sub 1194 G=0.9590 A=0.0000, C=0.0410
Asian Sub 50 G=0.98 A=0.00, C=0.02
East Asian Sub 36 G=0.97 A=0.00, C=0.03
Other Asian Sub 14 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 74 G=1.00 A=0.00, C=0.00
Latin American 2 Sub 288 G=1.000 A=0.000, C=0.000
South Asian Sub 48 G=0.96 A=0.00, C=0.04
Other Sub 498 G=0.795 A=0.000, C=0.205


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=0.675473 C=0.324527
gnomAD - Genomes Global Study-wide 140086 G=0.678519 C=0.321481
gnomAD - Genomes European Sub 75860 G=0.69098 C=0.30902
gnomAD - Genomes African Sub 41982 G=0.65011 C=0.34989
gnomAD - Genomes American Sub 13646 G=0.71559 C=0.28441
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.7011 C=0.2989
gnomAD - Genomes East Asian Sub 3124 G=0.5714 C=0.4286
gnomAD - Genomes Other Sub 2152 G=0.6789 C=0.3211
8.3KJPN JAPANESE Study-wide 16760 G=0.58395 C=0.41605
1000Genomes Global Study-wide 5008 G=0.6597 C=0.3403
1000Genomes African Sub 1322 G=0.6203 C=0.3797
1000Genomes East Asian Sub 1008 G=0.5694 C=0.4306
1000Genomes Europe Sub 1006 G=0.6918 C=0.3082
1000Genomes South Asian Sub 978 G=0.738 C=0.262
1000Genomes American Sub 694 G=0.709 C=0.291
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6915 C=0.3085
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7006 C=0.2994
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6958 C=0.3042
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6256 C=0.3744
Korean Genome Project KOREAN Study-wide 1832 G=0.6037 C=0.3963
HapMap Global Study-wide 1788 G=0.6504 C=0.3496
HapMap African Sub 690 G=0.645 C=0.355
HapMap American Sub 668 G=0.662 C=0.338
HapMap Asian Sub 254 G=0.606 C=0.394
HapMap Europe Sub 176 G=0.693 C=0.307
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.694 C=0.306
Northern Sweden ACPOP Study-wide 600 G=0.700 C=0.300
SGDP_PRJ Global Study-wide 274 G=0.420 C=0.580
Qatari Global Study-wide 216 G=0.736 C=0.264
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.589 C=0.411
The Danish reference pan genome Danish Study-wide 40 G=0.55 C=0.45
Siberian Global Study-wide 30 G=0.37 C=0.63
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
GRCh38.p13 chr 15 NC_000015.10:g.92142136= NC_000015.10:g.92142136G>A NC_000015.10:g.92142136G>C
GRCh37.p13 chr 15 NC_000015.9:g.92685366= NC_000015.9:g.92685366G>A NC_000015.9:g.92685366G>C
SLCO3A1 transcript variant 2 NM_001145044.1:c.1513-4848= NM_001145044.1:c.1513-4848G>A NM_001145044.1:c.1513-4848G>C
SLCO3A1 transcript variant 1 NM_013272.3:c.1513-4848= NM_013272.3:c.1513-4848G>A NM_013272.3:c.1513-4848G>C
SLCO3A1 transcript variant 1 NM_013272.4:c.1513-4848= NM_013272.4:c.1513-4848G>A NM_013272.4:c.1513-4848G>C
SLCO3A1 transcript variant X1 XM_005254889.1:c.1513-4848= XM_005254889.1:c.1513-4848G>A XM_005254889.1:c.1513-4848G>C
SLCO3A1 transcript variant X2 XM_005254890.1:c.1339-4848= XM_005254890.1:c.1339-4848G>A XM_005254890.1:c.1339-4848G>C
SLCO3A1 transcript variant X4 XM_005254891.1:c.1168-4848= XM_005254891.1:c.1168-4848G>A XM_005254891.1:c.1168-4848G>C
SLCO3A1 transcript variant X3 XM_005254891.3:c.1168-4848= XM_005254891.3:c.1168-4848G>A XM_005254891.3:c.1168-4848G>C
SLCO3A1 transcript variant X2 XM_011521456.2:c.1339-4848= XM_011521456.2:c.1339-4848G>A XM_011521456.2:c.1339-4848G>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#.

88 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3193276 Aug 15, 2001 (98)
2 PERLEGEN ss23738860 Sep 20, 2004 (123)
3 ABI ss43793261 Mar 15, 2006 (126)
4 AFFY ss66271120 Dec 01, 2006 (127)
5 AFFY ss76415750 Dec 08, 2007 (130)
6 HGSV ss78074435 Dec 07, 2007 (129)
7 HGSV ss81210711 Dec 15, 2007 (130)
8 KRIBB_YJKIM ss81733231 Dec 14, 2007 (130)
9 BGI ss103262751 Dec 01, 2009 (131)
10 1000GENOMES ss109039114 Jan 23, 2009 (130)
11 1000GENOMES ss114554416 Jan 25, 2009 (130)
12 ILLUMINA-UK ss118330378 Feb 14, 2009 (130)
13 GMI ss156863663 Dec 01, 2009 (131)
14 ILLUMINA ss160519333 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss170221766 Jul 04, 2010 (132)
16 ILLUMINA ss173202786 Jul 04, 2010 (132)
17 BUSHMAN ss201188274 Jul 04, 2010 (132)
18 1000GENOMES ss227039236 Jul 14, 2010 (132)
19 1000GENOMES ss236880769 Jul 15, 2010 (132)
20 1000GENOMES ss243248851 Jul 15, 2010 (132)
21 BL ss255203035 May 09, 2011 (134)
22 GMI ss282364775 May 04, 2012 (137)
23 ILLUMINA ss480477628 May 04, 2012 (137)
24 ILLUMINA ss480491988 May 04, 2012 (137)
25 ILLUMINA ss481291672 Sep 08, 2015 (146)
26 ILLUMINA ss485036305 May 04, 2012 (137)
27 ILLUMINA ss537059451 Sep 08, 2015 (146)
28 TISHKOFF ss564654510 Apr 25, 2013 (138)
29 SSMP ss660397243 Apr 25, 2013 (138)
30 ILLUMINA ss778342342 Sep 08, 2015 (146)
31 ILLUMINA ss782964394 Sep 08, 2015 (146)
32 ILLUMINA ss783926304 Sep 08, 2015 (146)
33 ILLUMINA ss832220651 Sep 08, 2015 (146)
34 ILLUMINA ss833796953 Sep 08, 2015 (146)
35 EVA-GONL ss992086473 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1080342964 Aug 21, 2014 (142)
37 1000GENOMES ss1354632749 Aug 21, 2014 (142)
38 DDI ss1427717066 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1577753496 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1633622564 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1676616597 Apr 01, 2015 (144)
42 EVA_DECODE ss1696115907 Apr 01, 2015 (144)
43 EVA_SVP ss1713511744 Apr 01, 2015 (144)
44 ILLUMINA ss1752177892 Sep 08, 2015 (146)
45 HAMMER_LAB ss1808330752 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1935488887 Feb 12, 2016 (147)
47 JJLAB ss2028528096 Sep 14, 2016 (149)
48 USC_VALOUEV ss2156937094 Nov 08, 2017 (151)
49 HUMAN_LONGEVITY ss2209143423 Dec 20, 2016 (150)
50 TOPMED ss2373699042 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2628758967 Nov 08, 2017 (151)
52 ILLUMINA ss2633267528 Nov 08, 2017 (151)
53 GRF ss2701424934 Nov 08, 2017 (151)
54 ILLUMINA ss2710823628 Nov 08, 2017 (151)
55 GNOMAD ss2938250959 Nov 08, 2017 (151)
56 SWEGEN ss3013759874 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3028087881 Nov 08, 2017 (151)
58 TOPMED ss3235344294 Nov 08, 2017 (151)
59 TOPMED ss3235344295 Nov 08, 2017 (151)
60 CSHL ss3351244577 Nov 08, 2017 (151)
61 ILLUMINA ss3627431650 Oct 12, 2018 (152)
62 ILLUMINA ss3631257759 Oct 12, 2018 (152)
63 ILLUMINA ss3633107297 Oct 12, 2018 (152)
64 ILLUMINA ss3633812406 Oct 12, 2018 (152)
65 ILLUMINA ss3634621567 Oct 12, 2018 (152)
66 ILLUMINA ss3635501087 Oct 12, 2018 (152)
67 ILLUMINA ss3636312084 Oct 12, 2018 (152)
68 ILLUMINA ss3637252414 Oct 12, 2018 (152)
69 ILLUMINA ss3638102791 Oct 12, 2018 (152)
70 ILLUMINA ss3640328887 Oct 12, 2018 (152)
71 EGCUT_WGS ss3680889903 Jul 13, 2019 (153)
72 EVA_DECODE ss3698468987 Jul 13, 2019 (153)
73 ACPOP ss3741172749 Jul 13, 2019 (153)
74 ILLUMINA ss3744922090 Jul 13, 2019 (153)
75 EVA ss3753450659 Jul 13, 2019 (153)
76 ILLUMINA ss3772420568 Jul 13, 2019 (153)
77 PACBIO ss3787928050 Jul 13, 2019 (153)
78 PACBIO ss3792927008 Jul 13, 2019 (153)
79 PACBIO ss3797811642 Jul 13, 2019 (153)
80 KHV_HUMAN_GENOMES ss3818752790 Jul 13, 2019 (153)
81 EVA ss3834377978 Apr 27, 2020 (154)
82 EVA ss3840791672 Apr 27, 2020 (154)
83 EVA ss3846281796 Apr 27, 2020 (154)
84 SGDP_PRJ ss3883534585 Apr 27, 2020 (154)
85 KRGDB ss3932787870 Apr 27, 2020 (154)
86 KOGIC ss3976748782 Apr 27, 2020 (154)
87 TOPMED ss5001612656 Apr 27, 2021 (155)
88 TOMMO_GENOMICS ss5217565044 Apr 27, 2021 (155)
89 1000Genomes NC_000015.9 - 92685366 Oct 12, 2018 (152)
90 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 92685366 Oct 12, 2018 (152)
91 Genetic variation in the Estonian population NC_000015.9 - 92685366 Oct 12, 2018 (152)
92 The Danish reference pan genome NC_000015.9 - 92685366 Apr 27, 2020 (154)
93 gnomAD - Genomes NC_000015.10 - 92142136 Apr 27, 2021 (155)
94 Genome of the Netherlands Release 5 NC_000015.9 - 92685366 Apr 27, 2020 (154)
95 HapMap NC_000015.10 - 92142136 Apr 27, 2020 (154)
96 KOREAN population from KRGDB NC_000015.9 - 92685366 Apr 27, 2020 (154)
97 Korean Genome Project NC_000015.10 - 92142136 Apr 27, 2020 (154)
98 Northern Sweden NC_000015.9 - 92685366 Jul 13, 2019 (153)
99 Qatari NC_000015.9 - 92685366 Apr 27, 2020 (154)
100 SGDP_PRJ NC_000015.9 - 92685366 Apr 27, 2020 (154)
101 Siberian NC_000015.9 - 92685366 Apr 27, 2020 (154)
102 8.3KJPN NC_000015.9 - 92685366 Apr 27, 2021 (155)
103 TopMed NC_000015.10 - 92142136 Apr 27, 2021 (155)
104 UK 10K study - Twins NC_000015.9 - 92685366 Oct 12, 2018 (152)
105 A Vietnamese Genetic Variation Database NC_000015.9 - 92685366 Jul 13, 2019 (153)
106 ALFA NC_000015.10 - 92142136 Apr 27, 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)
rs56602858 May 25, 2008 (130)
rs56977915 Feb 27, 2009 (130)
rs59796846 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
5772258996, ss3235344294 NC_000015.10:92142135:G:A NC_000015.10:92142135:G:A (self)
ss66271120, ss76415750, ss78074435, ss81210711, ss109039114, ss114554416, ss118330378, ss160519333, ss170221766, ss201188274, ss255203035, ss282364775, ss480477628, ss1696115907, ss1713511744 NC_000015.8:90486369:G:C NC_000015.10:92142135:G:C (self)
67745882, 37623234, 26628151, 3972520, 16785618, 39965264, 14457614, 17530809, 35551565, 9453448, 75534351, 37623234, 8362270, ss227039236, ss236880769, ss243248851, ss480491988, ss481291672, ss485036305, ss537059451, ss564654510, ss660397243, ss778342342, ss782964394, ss783926304, ss832220651, ss833796953, ss992086473, ss1080342964, ss1354632749, ss1427717066, ss1577753496, ss1633622564, ss1676616597, ss1752177892, ss1808330752, ss1935488887, ss2028528096, ss2156937094, ss2373699042, ss2628758967, ss2633267528, ss2701424934, ss2710823628, ss2938250959, ss3013759874, ss3351244577, ss3627431650, ss3631257759, ss3633107297, ss3633812406, ss3634621567, ss3635501087, ss3636312084, ss3637252414, ss3638102791, ss3640328887, ss3680889903, ss3741172749, ss3744922090, ss3753450659, ss3772420568, ss3787928050, ss3792927008, ss3797811642, ss3834377978, ss3840791672, ss3883534585, ss3932787870, ss5217565044 NC_000015.9:92685365:G:C NC_000015.10:92142135:G:C (self)
477607838, 1317180, 33126783, 135780215, 217158316, 5772258996, ss2209143423, ss3028087881, ss3235344295, ss3698468987, ss3818752790, ss3846281796, ss3976748782, ss5001612656 NC_000015.10:92142135:G:C NC_000015.10:92142135:G:C (self)
ss3193276, ss23738860, ss43793261, ss81733231, ss103262751, ss156863663, ss173202786 NT_010274.17:7650892:G:C NC_000015.10:92142135:G:C (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 rs2238357

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