Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs12455253

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr18:26943867 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.149122 (39471/264690, TOPMED)
G=0.154572 (21650/140064, GnomAD)
G=0.16392 (3683/22468, ALFA) (+ 15 more)
G=0.36181 (6064/16760, 8.3KJPN)
G=0.1336 (669/5008, 1000G)
G=0.1980 (887/4480, Estonian)
G=0.1627 (627/3854, ALSPAC)
G=0.1726 (640/3708, TWINSUK)
G=0.2939 (861/2930, KOREAN)
G=0.2713 (497/1832, Korea1K)
G=0.164 (164/998, GoNL)
G=0.135 (81/600, NorthernSweden)
G=0.131 (43/328, HapMap)
G=0.102 (22/216, Qatari)
G=0.206 (44/214, Vietnamese)
C=0.438 (63/144, SGDP_PRJ)
G=0.12 (5/40, GENOME_DK)
C=0.46 (11/24, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHST9 : 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 18 NC_000018.10:g.26943867C>A
GRCh38.p13 chr 18 NC_000018.10:g.26943867C>G
GRCh38.p13 chr 18 NC_000018.10:g.26943867C>T
GRCh37.p13 chr 18 NC_000018.9:g.24523831C>A
GRCh37.p13 chr 18 NC_000018.9:g.24523831C>G
GRCh37.p13 chr 18 NC_000018.9:g.24523831C>T
CHST9 RefSeqGene NG_029856.1:g.246459G>T
CHST9 RefSeqGene NG_029856.1:g.246459G>C
CHST9 RefSeqGene NG_029856.1:g.246459G>A
Gene: CHST9, carbohydrate sulfotransferase 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CHST9 transcript variant 3 NM_001256316.2:c.203-2651…

NM_001256316.2:c.203-26517G>T

N/A Intron Variant
CHST9 transcript variant 1 NM_031422.6:c.240+462G>T N/A Intron Variant
CHST9 transcript variant X4 XM_006722555.4:c.240+462G…

XM_006722555.4:c.240+462G>T

N/A Intron Variant
CHST9 transcript variant X1 XM_017026033.1:c.240+462G…

XM_017026033.1:c.240+462G>T

N/A Intron Variant
CHST9 transcript variant X2 XM_017026034.1:c.69+462G>T N/A Intron Variant
CHST9 transcript variant X3 XM_005258362.4:c. N/A Genic Upstream Transcript 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 22468 C=0.83608 G=0.16392
European Sub 17728 C=0.82339 G=0.17661
African Sub 2976 C=0.9099 G=0.0901
African Others Sub 114 C=0.947 G=0.053
African American Sub 2862 C=0.9085 G=0.0915
Asian Sub 114 C=0.728 G=0.272
East Asian Sub 88 C=0.69 G=0.31
Other Asian Sub 26 C=0.85 G=0.15
Latin American 1 Sub 150 C=0.867 G=0.133
Latin American 2 Sub 626 C=0.827 G=0.173
South Asian Sub 98 C=0.94 G=0.06
Other Sub 776 C=0.847 G=0.153


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 C=0.850878 G=0.149122
gnomAD - Genomes Global Study-wide 140064 C=0.845428 G=0.154572
gnomAD - Genomes European Sub 75848 C=0.81752 G=0.18248
gnomAD - Genomes African Sub 41988 C=0.90766 G=0.09234
gnomAD - Genomes American Sub 13636 C=0.83265 G=0.16735
gnomAD - Genomes Ashkenazi Jewish Sub 3316 C=0.8197 G=0.1803
gnomAD - Genomes East Asian Sub 3128 C=0.7708 G=0.2292
gnomAD - Genomes Other Sub 2148 C=0.8440 G=0.1560
8.3KJPN JAPANESE Study-wide 16760 C=0.63819 G=0.36181
1000Genomes Global Study-wide 5008 C=0.8664 G=0.1336
1000Genomes African Sub 1322 C=0.9349 G=0.0651
1000Genomes East Asian Sub 1008 C=0.7966 G=0.2034
1000Genomes Europe Sub 1006 C=0.8201 G=0.1799
1000Genomes South Asian Sub 978 C=0.907 G=0.093
1000Genomes American Sub 694 C=0.847 G=0.153
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8020 G=0.1980
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8373 G=0.1627
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8274 G=0.1726
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.7061 A=0.0000, G=0.2939, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 C=0.7287 G=0.2713
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.836 G=0.164
Northern Sweden ACPOP Study-wide 600 C=0.865 G=0.135
HapMap Global Study-wide 328 C=0.869 G=0.131
HapMap African Sub 120 C=0.983 G=0.017
HapMap American Sub 120 C=0.883 G=0.117
HapMap Asian Sub 88 C=0.69 G=0.31
Qatari Global Study-wide 216 C=0.898 G=0.102
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.794 G=0.206
SGDP_PRJ Global Study-wide 144 C=0.438 G=0.562
The Danish reference pan genome Danish Study-wide 40 C=0.88 G=0.12
Siberian Global Study-wide 24 C=0.46 G=0.54
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 C= A G T
GRCh38.p13 chr 18 NC_000018.10:g.26943867= NC_000018.10:g.26943867C>A NC_000018.10:g.26943867C>G NC_000018.10:g.26943867C>T
GRCh37.p13 chr 18 NC_000018.9:g.24523831= NC_000018.9:g.24523831C>A NC_000018.9:g.24523831C>G NC_000018.9:g.24523831C>T
CHST9 RefSeqGene NG_029856.1:g.246459= NG_029856.1:g.246459G>T NG_029856.1:g.246459G>C NG_029856.1:g.246459G>A
CHST9 transcript variant 3 NM_001256316.1:c.203-26517= NM_001256316.1:c.203-26517G>T NM_001256316.1:c.203-26517G>C NM_001256316.1:c.203-26517G>A
CHST9 transcript variant 3 NM_001256316.2:c.203-26517= NM_001256316.2:c.203-26517G>T NM_001256316.2:c.203-26517G>C NM_001256316.2:c.203-26517G>A
CHST9 transcript variant 1 NM_031422.5:c.240+462= NM_031422.5:c.240+462G>T NM_031422.5:c.240+462G>C NM_031422.5:c.240+462G>A
CHST9 transcript variant 1 NM_031422.6:c.240+462= NM_031422.6:c.240+462G>T NM_031422.6:c.240+462G>C NM_031422.6:c.240+462G>A
CHST9 transcript variant X2 XM_005258363.1:c.-15-26517= XM_005258363.1:c.-15-26517G>T XM_005258363.1:c.-15-26517G>C XM_005258363.1:c.-15-26517G>A
CHST9 transcript variant X4 XM_006722555.4:c.240+462= XM_006722555.4:c.240+462G>T XM_006722555.4:c.240+462G>C XM_006722555.4:c.240+462G>A
CHST9 transcript variant X1 XM_017026033.1:c.240+462= XM_017026033.1:c.240+462G>T XM_017026033.1:c.240+462G>C XM_017026033.1:c.240+462G>A
CHST9 transcript variant X2 XM_017026034.1:c.69+462= XM_017026034.1:c.69+462G>T XM_017026034.1:c.69+462G>C XM_017026034.1:c.69+462G>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#.

77 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19379524 Feb 28, 2004 (120)
2 PERLEGEN ss24030661 Sep 20, 2004 (123)
3 ABI ss44061896 Mar 14, 2006 (126)
4 ILLUMINA ss75243445 Dec 07, 2007 (129)
5 HUMANGENOME_JCVI ss96499516 Feb 04, 2009 (130)
6 BGI ss103382869 Dec 01, 2009 (131)
7 KRIBB_YJKIM ss119782469 Dec 01, 2009 (131)
8 ENSEMBL ss136458048 Dec 01, 2009 (131)
9 ILLUMINA ss160272566 Dec 01, 2009 (131)
10 ILLUMINA ss172093659 Jul 04, 2010 (132)
11 1000GENOMES ss227780090 Jul 14, 2010 (132)
12 1000GENOMES ss237409053 Jul 15, 2010 (132)
13 1000GENOMES ss243671727 Jul 15, 2010 (132)
14 GMI ss282937370 May 04, 2012 (137)
15 PJP ss292143724 May 09, 2011 (134)
16 ILLUMINA ss479744073 May 04, 2012 (137)
17 ILLUMINA ss479749900 May 04, 2012 (137)
18 ILLUMINA ss480306816 Sep 08, 2015 (146)
19 ILLUMINA ss484670338 May 04, 2012 (137)
20 ILLUMINA ss536783475 Sep 08, 2015 (146)
21 TISHKOFF ss565553657 Apr 25, 2013 (138)
22 SSMP ss661381186 Apr 25, 2013 (138)
23 ILLUMINA ss778342345 Aug 21, 2014 (142)
24 ILLUMINA ss782782023 Aug 21, 2014 (142)
25 ILLUMINA ss783747943 Aug 21, 2014 (142)
26 ILLUMINA ss832034609 Apr 01, 2015 (144)
27 ILLUMINA ss833796956 Aug 21, 2014 (142)
28 EVA-GONL ss993573751 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1081385906 Aug 21, 2014 (142)
30 1000GENOMES ss1360443146 Aug 21, 2014 (142)
31 DDI ss1428172670 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1578342172 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1636560597 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1679554630 Apr 01, 2015 (144)
35 EVA_DECODE ss1697627550 Apr 01, 2015 (144)
36 ILLUMINA ss1752250290 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1937049401 Feb 12, 2016 (147)
38 GENOMED ss1968488563 Jul 19, 2016 (147)
39 JJLAB ss2029293135 Sep 14, 2016 (149)
40 USC_VALOUEV ss2157795248 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2220342215 Dec 20, 2016 (150)
42 TOPMED ss2385719424 Dec 20, 2016 (150)
43 ILLUMINA ss2633456019 Nov 08, 2017 (151)
44 GRF ss2702378557 Nov 08, 2017 (151)
45 GNOMAD ss2955029987 Nov 08, 2017 (151)
46 SWEGEN ss3016299740 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3028472723 Nov 08, 2017 (151)
48 TOPMED ss3275481360 Nov 08, 2017 (151)
49 CSHL ss3351958427 Nov 08, 2017 (151)
50 ILLUMINA ss3627777369 Oct 12, 2018 (152)
51 ILLUMINA ss3631433359 Oct 12, 2018 (152)
52 ILLUMINA ss3633157318 Oct 12, 2018 (152)
53 ILLUMINA ss3633865913 Oct 12, 2018 (152)
54 ILLUMINA ss3634699729 Oct 12, 2018 (152)
55 ILLUMINA ss3635553300 Oct 12, 2018 (152)
56 ILLUMINA ss3636388494 Oct 12, 2018 (152)
57 ILLUMINA ss3637304892 Oct 12, 2018 (152)
58 ILLUMINA ss3638188042 Oct 12, 2018 (152)
59 ILLUMINA ss3640407037 Oct 12, 2018 (152)
60 ILLUMINA ss3643164380 Oct 12, 2018 (152)
61 URBANLAB ss3650762059 Oct 12, 2018 (152)
62 EGCUT_WGS ss3683124688 Jul 13, 2019 (153)
63 EVA_DECODE ss3701381190 Jul 13, 2019 (153)
64 ACPOP ss3742419944 Jul 13, 2019 (153)
65 ILLUMINA ss3744999883 Jul 13, 2019 (153)
66 EVA ss3755211692 Jul 13, 2019 (153)
67 ILLUMINA ss3772497434 Jul 13, 2019 (153)
68 KHV_HUMAN_GENOMES ss3820480695 Jul 13, 2019 (153)
69 EVA ss3835099443 Apr 27, 2020 (154)
70 EVA ss3841165216 Apr 27, 2020 (154)
71 EVA ss3846666559 Apr 27, 2020 (154)
72 SGDP_PRJ ss3886721876 Apr 27, 2020 (154)
73 KRGDB ss3936565564 Apr 27, 2020 (154)
74 KOGIC ss3979881393 Apr 27, 2020 (154)
75 EVA ss4017790476 Apr 27, 2021 (155)
76 TOPMED ss5051447187 Apr 27, 2021 (155)
77 TOMMO_GENOMICS ss5224529343 Apr 27, 2021 (155)
78 1000Genomes NC_000018.9 - 24523831 Oct 12, 2018 (152)
79 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 24523831 Oct 12, 2018 (152)
80 Genetic variation in the Estonian population NC_000018.9 - 24523831 Oct 12, 2018 (152)
81 The Danish reference pan genome NC_000018.9 - 24523831 Apr 27, 2020 (154)
82 gnomAD - Genomes NC_000018.10 - 26943867 Apr 27, 2021 (155)
83 Genome of the Netherlands Release 5 NC_000018.9 - 24523831 Apr 27, 2020 (154)
84 HapMap NC_000018.10 - 26943867 Apr 27, 2020 (154)
85 KOREAN population from KRGDB NC_000018.9 - 24523831 Apr 27, 2020 (154)
86 Korean Genome Project NC_000018.10 - 26943867 Apr 27, 2020 (154)
87 Northern Sweden NC_000018.9 - 24523831 Jul 13, 2019 (153)
88 Qatari NC_000018.9 - 24523831 Apr 27, 2020 (154)
89 SGDP_PRJ NC_000018.9 - 24523831 Apr 27, 2020 (154)
90 Siberian NC_000018.9 - 24523831 Apr 27, 2020 (154)
91 8.3KJPN NC_000018.9 - 24523831 Apr 27, 2021 (155)
92 TopMed NC_000018.10 - 26943867 Apr 27, 2021 (155)
93 UK 10K study - Twins NC_000018.9 - 24523831 Oct 12, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000018.9 - 24523831 Jul 13, 2019 (153)
95 ALFA NC_000018.10 - 26943867 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
43742958, ss3936565564 NC_000018.9:24523830:C:A NC_000018.10:26943866:C:A (self)
ss160272566, ss282937370, ss292143724, ss479744073, ss1697627550, ss3643164380 NC_000018.8:22777828:C:G NC_000018.10:26943866:C:G (self)
73752272, 40854120, 28862936, 4536771, 18204287, 43742958, 15704809, 19091323, 38738856, 10311602, 82498650, 40854120, 9029384, ss227780090, ss237409053, ss243671727, ss479749900, ss480306816, ss484670338, ss536783475, ss565553657, ss661381186, ss778342345, ss782782023, ss783747943, ss832034609, ss833796956, ss993573751, ss1081385906, ss1360443146, ss1428172670, ss1578342172, ss1636560597, ss1679554630, ss1752250290, ss1937049401, ss1968488563, ss2029293135, ss2157795248, ss2385719424, ss2633456019, ss2702378557, ss2955029987, ss3016299740, ss3351958427, ss3627777369, ss3631433359, ss3633157318, ss3633865913, ss3634699729, ss3635553300, ss3636388494, ss3637304892, ss3638188042, ss3640407037, ss3683124688, ss3742419944, ss3744999883, ss3755211692, ss3772497434, ss3835099443, ss3841165216, ss3886721876, ss3936565564, ss4017790476, ss5224529343 NC_000018.9:24523830:C:G NC_000018.10:26943866:C:G (self)
520279562, 1568766, 36259394, 166589009, 266992850, 9865618464, ss2220342215, ss3028472723, ss3275481360, ss3650762059, ss3701381190, ss3820480695, ss3846666559, ss3979881393, ss5051447187 NC_000018.10:26943866:C:G NC_000018.10:26943866:C:G (self)
ss19379524 NT_010966.13:6012932:C:G NC_000018.10:26943866:C:G (self)
ss24030661, ss44061896, ss75243445, ss96499516, ss103382869, ss119782469, ss136458048, ss172093659 NT_010966.14:6012932:C:G NC_000018.10:26943866:C:G (self)
43742958, ss3936565564 NC_000018.9:24523830:C:T NC_000018.10:26943866:C:T (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 rs12455253

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