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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.

rs4148942

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:72009601 (GRCh38.p14) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.004518 (1196/264690, TOPMED)
G=0.003695 (518/140198, GnomAD)
G=0.00476 (401/84314, ALFA) (+ 17 more)
G=0.00680 (535/78680, PAGE_STUDY)
G=0.03284 (928/28258, 14KJPN)
G=0.03413 (572/16760, 8.3KJPN)
G=0.0039 (25/6404, 1000G_30x)
G=0.0044 (22/5008, 1000G)
G=0.0013 (6/4480, Estonian)
G=0.0039 (15/3854, ALSPAC)
G=0.0043 (16/3708, TWINSUK)
G=0.0113 (33/2922, KOREAN)
G=0.002 (2/998, GoNL)
G=0.004 (3/788, PRJEB37584)
G=0.009 (2/216, Qatari)
G=0.014 (3/214, Vietnamese)
C=0.5 (3/6, SGDP_PRJ)
G=0.5 (3/6, SGDP_PRJ)
C=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHST3 : 3 Prime UTR Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 84314 C=0.99524 G=0.00476
European Sub 73980 C=0.99540 G=0.00460
African Sub 3746 C=0.9992 G=0.0008
African Others Sub 166 C=1.000 G=0.000
African American Sub 3580 C=0.9992 G=0.0008
Asian Sub 3274 C=0.9878 G=0.0122
East Asian Sub 2648 C=0.9902 G=0.0098
Other Asian Sub 626 C=0.978 G=0.022
Latin American 1 Sub 436 C=0.995 G=0.005
Latin American 2 Sub 928 C=0.998 G=0.002
South Asian Sub 274 C=0.996 G=0.004
Other Sub 1676 C=0.9922 G=0.0078


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=0.995482 G=0.004518
gnomAD - Genomes Global Study-wide 140198 C=0.996305 G=0.003695
gnomAD - Genomes European Sub 75928 C=0.99561 G=0.00439
gnomAD - Genomes African Sub 42026 C=0.99838 G=0.00162
gnomAD - Genomes American Sub 13644 C=0.99678 G=0.00322
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.9910 G=0.0090
gnomAD - Genomes East Asian Sub 3128 C=0.9914 G=0.0086
gnomAD - Genomes Other Sub 2152 C=0.9926 G=0.0074
Allele Frequency Aggregator Total Global 84314 C=0.99524 G=0.00476
Allele Frequency Aggregator European Sub 73980 C=0.99540 G=0.00460
Allele Frequency Aggregator African Sub 3746 C=0.9992 G=0.0008
Allele Frequency Aggregator Asian Sub 3274 C=0.9878 G=0.0122
Allele Frequency Aggregator Other Sub 1676 C=0.9922 G=0.0078
Allele Frequency Aggregator Latin American 2 Sub 928 C=0.998 G=0.002
Allele Frequency Aggregator Latin American 1 Sub 436 C=0.995 G=0.005
Allele Frequency Aggregator South Asian Sub 274 C=0.996 G=0.004
The PAGE Study Global Study-wide 78680 C=0.99320 G=0.00680
The PAGE Study AfricanAmerican Sub 32510 C=0.99862 G=0.00138
The PAGE Study Mexican Sub 10808 C=0.99325 G=0.00675
The PAGE Study Asian Sub 8316 C=0.9693 G=0.0307
The PAGE Study PuertoRican Sub 7916 C=0.9995 G=0.0005
The PAGE Study NativeHawaiian Sub 4532 C=0.9898 G=0.0102
The PAGE Study Cuban Sub 4226 C=0.9934 G=0.0066
The PAGE Study Dominican Sub 3826 C=0.9838 G=0.0162
The PAGE Study CentralAmerican Sub 2448 C=0.9975 G=0.0025
The PAGE Study SouthAmerican Sub 1982 C=0.9960 G=0.0040
The PAGE Study NativeAmerican Sub 1260 C=0.9960 G=0.0040
The PAGE Study SouthAsian Sub 856 C=0.996 G=0.004
14KJPN JAPANESE Study-wide 28258 C=0.96716 G=0.03284
8.3KJPN JAPANESE Study-wide 16760 C=0.96587 G=0.03413
1000Genomes_30x Global Study-wide 6404 C=0.9961 G=0.0039
1000Genomes_30x African Sub 1786 C=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9945 G=0.0055
1000Genomes_30x South Asian Sub 1202 C=0.9983 G=0.0017
1000Genomes_30x East Asian Sub 1170 C=0.9889 G=0.0111
1000Genomes_30x American Sub 980 C=0.997 G=0.003
1000Genomes Global Study-wide 5008 C=0.9956 G=0.0044
1000Genomes African Sub 1322 C=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 C=0.9881 G=0.0119
1000Genomes Europe Sub 1006 C=0.9940 G=0.0060
1000Genomes South Asian Sub 978 C=0.998 G=0.002
1000Genomes American Sub 694 C=0.997 G=0.003
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9987 G=0.0013
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9961 G=0.0039
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9957 G=0.0043
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9887 G=0.0113
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.998 G=0.002
CNV burdens in cranial meningiomas Global Study-wide 788 C=0.996 G=0.004
CNV burdens in cranial meningiomas CRM Sub 788 C=0.996 G=0.004
Qatari Global Study-wide 216 C=0.991 G=0.009
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.986 G=0.014
SGDP_PRJ Global Study-wide 6 C=0.5 G=0.5
Siberian Global Study-wide 2 C=0.5 G=0.5
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.p14 chr 10 NC_000010.11:g.72009601C>G
GRCh37.p13 chr 10 NC_000010.10:g.73769359C>G
CHST3 RefSeqGene NG_012635.1:g.50240C>G
Gene: CHST3, carbohydrate sulfotransferase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHST3 transcript NM_004273.5:c.*1130= N/A 3 Prime UTR Variant
CHST3 transcript variant X1 XM_006718075.5:c.*1130= N/A 3 Prime UTR Variant
CHST3 transcript variant X2 XM_011540369.3:c.*1130= N/A 3 Prime UTR Variant
CHST3 transcript variant X3 XM_047426022.1:c.*1130= N/A 3 Prime UTR 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.

Allele: G (allele ID: 316148 )
ClinVar Accession Disease Names Clinical Significance
RCV000278403.3 Spondyloepiphyseal dysplasia with congenital joint dislocations Uncertain-Significance
RCV000318256.3 Spondyloepiphyseal dysplasia congenita Uncertain-Significance
RCV000335862.3 Larsen syndrome Uncertain-Significance
RCV000375155.3 Skeletal dysplasia Uncertain-Significance
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= G
GRCh38.p14 chr 10 NC_000010.11:g.72009601= NC_000010.11:g.72009601C>G
GRCh37.p13 chr 10 NC_000010.10:g.73769359= NC_000010.10:g.73769359C>G
CHST3 RefSeqGene NG_012635.1:g.50240= NG_012635.1:g.50240C>G
CHST3 transcript NM_004273.5:c.*1130= NM_004273.5:c.*1130C>G
CHST3 transcript NM_004273.4:c.*1130= NM_004273.4:c.*1130C>G
CHST3 transcript variant X1 XM_006718075.5:c.*1130= XM_006718075.5:c.*1130C>G
CHST3 transcript variant X2 XM_006718075.4:c.*1130= XM_006718075.4:c.*1130C>G
CHST3 transcript variant X2 XM_006718075.3:c.*1130= XM_006718075.3:c.*1130C>G
CHST3 transcript variant X2 XM_006718075.2:c.*1130= XM_006718075.2:c.*1130C>G
CHST3 transcript variant X1 XM_006718075.1:c.*1130= XM_006718075.1:c.*1130C>G
CHST3 transcript variant X2 XM_011540369.3:c.*1130= XM_011540369.3:c.*1130C>G
CHST3 transcript variant X1 XM_011540369.2:c.*1130= XM_011540369.2:c.*1130C>G
CHST3 transcript variant X1 XM_011540369.1:c.*1130= XM_011540369.1:c.*1130C>G
CHST3 transcript variant X3 XM_047426022.1:c.*1130= XM_047426022.1:c.*1130C>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#.

49 SubSNP, 18 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 RIKENSNPRC ss5603288 Dec 16, 2002 (110)
2 1000GENOMES ss336218210 May 09, 2011 (134)
3 ILLUMINA ss535996632 Sep 08, 2015 (146)
4 SSMP ss656955969 Apr 25, 2013 (138)
5 EVA-GONL ss987638078 Aug 21, 2014 (142)
6 JMKIDD_LAB ss1077099273 Aug 21, 2014 (142)
7 1000GENOMES ss1337994655 Aug 21, 2014 (142)
8 EVA_DECODE ss1597310077 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1624862600 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1667856633 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1931003957 Feb 12, 2016 (147)
12 ILLUMINA ss1946285827 Feb 12, 2016 (147)
13 ILLUMINA ss1959273274 Feb 12, 2016 (147)
14 USC_VALOUEV ss2154504101 Dec 20, 2016 (150)
15 HUMAN_LONGEVITY ss2175888519 Dec 20, 2016 (150)
16 ILLUMINA ss2632729138 Nov 08, 2017 (151)
17 GRF ss2698749110 Nov 08, 2017 (151)
18 GNOMAD ss2890334966 Nov 08, 2017 (151)
19 AFFY ss2984915641 Nov 08, 2017 (151)
20 AFFY ss2985561693 Nov 08, 2017 (151)
21 SWEGEN ss3006707480 Nov 08, 2017 (151)
22 ILLUMINA ss3021252051 Nov 08, 2017 (151)
23 ILLUMINA ss3625581958 Oct 12, 2018 (152)
24 ILLUMINA ss3626476654 Oct 12, 2018 (152)
25 ILLUMINA ss3644538528 Oct 12, 2018 (152)
26 ILLUMINA ss3651608280 Oct 12, 2018 (152)
27 ILLUMINA ss3653686377 Oct 12, 2018 (152)
28 EGCUT_WGS ss3674124115 Jul 13, 2019 (153)
29 ILLUMINA ss3725168002 Jul 13, 2019 (153)
30 EVA ss3748274205 Jul 13, 2019 (153)
31 PAGE_CC ss3771566512 Jul 13, 2019 (153)
32 KHV_HUMAN_GENOMES ss3813647497 Jul 13, 2019 (153)
33 SGDP_PRJ ss3874498967 Apr 26, 2020 (154)
34 KRGDB ss3922587667 Apr 26, 2020 (154)
35 EVA ss3984636555 Apr 26, 2021 (155)
36 TOPMED ss4857158656 Apr 26, 2021 (155)
37 TOMMO_GENOMICS ss5198254613 Apr 26, 2021 (155)
38 1000G_HIGH_COVERAGE ss5284537515 Oct 16, 2022 (156)
39 EVA ss5394331818 Oct 16, 2022 (156)
40 HUGCELL_USP ss5480066542 Oct 16, 2022 (156)
41 1000G_HIGH_COVERAGE ss5578729251 Oct 16, 2022 (156)
42 SANFORD_IMAGENETICS ss5649570659 Oct 16, 2022 (156)
43 TOMMO_GENOMICS ss5744265110 Oct 16, 2022 (156)
44 YY_MCH ss5811655726 Oct 16, 2022 (156)
45 EVA ss5824592477 Oct 16, 2022 (156)
46 EVA ss5847600217 Oct 16, 2022 (156)
47 EVA ss5849630133 Oct 16, 2022 (156)
48 EVA ss5879461996 Oct 16, 2022 (156)
49 EVA ss5940848082 Oct 16, 2022 (156)
50 1000Genomes NC_000010.10 - 73769359 Oct 12, 2018 (152)
51 1000Genomes_30x NC_000010.11 - 72009601 Oct 16, 2022 (156)
52 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 73769359 Oct 12, 2018 (152)
53 Genetic variation in the Estonian population NC_000010.10 - 73769359 Oct 12, 2018 (152)
54 gnomAD - Genomes NC_000010.11 - 72009601 Apr 26, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000010.10 - 73769359 Apr 26, 2020 (154)
56 KOREAN population from KRGDB NC_000010.10 - 73769359 Apr 26, 2020 (154)
57 The PAGE Study NC_000010.11 - 72009601 Jul 13, 2019 (153)
58 CNV burdens in cranial meningiomas NC_000010.10 - 73769359 Apr 26, 2021 (155)
59 Qatari NC_000010.10 - 73769359 Apr 26, 2020 (154)
60 SGDP_PRJ NC_000010.10 - 73769359 Apr 26, 2020 (154)
61 Siberian NC_000010.10 - 73769359 Apr 26, 2020 (154)
62 8.3KJPN NC_000010.10 - 73769359 Apr 26, 2021 (155)
63 14KJPN NC_000010.11 - 72009601 Oct 16, 2022 (156)
64 TopMed NC_000010.11 - 72009601 Apr 26, 2021 (155)
65 UK 10K study - Twins NC_000010.10 - 73769359 Oct 12, 2018 (152)
66 A Vietnamese Genetic Variation Database NC_000010.10 - 73769359 Jul 13, 2019 (153)
67 ALFA NC_000010.11 - 72009601 Apr 26, 2021 (155)
68 ClinVar RCV000278403.3 Oct 16, 2022 (156)
69 ClinVar RCV000318256.3 Oct 16, 2022 (156)
70 ClinVar RCV000335862.3 Oct 16, 2022 (156)
71 ClinVar RCV000375155.3 Oct 16, 2022 (156)
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
ss1597310077 NC_000010.9:73439364:C:G NC_000010.11:72009600:C:G (self)
50403158, 27979333, 19862363, 12477762, 29765061, 186017, 13045887, 26515947, 7020455, 56223920, 27979333, 6215307, ss336218210, ss535996632, ss656955969, ss987638078, ss1077099273, ss1337994655, ss1624862600, ss1667856633, ss1931003957, ss1946285827, ss1959273274, ss2154504101, ss2632729138, ss2698749110, ss2890334966, ss2984915641, ss2985561693, ss3006707480, ss3021252051, ss3625581958, ss3626476654, ss3644538528, ss3651608280, ss3653686377, ss3674124115, ss3748274205, ss3874498967, ss3922587667, ss3984636555, ss5198254613, ss5394331818, ss5649570659, ss5824592477, ss5847600217, ss5940848082 NC_000010.10:73769358:C:G NC_000010.11:72009600:C:G (self)
RCV000278403.3, RCV000318256.3, RCV000335862.3, RCV000375155.3, 66255186, 356180456, 787981, 78102214, 72704311, 9302033668, ss2175888519, ss3725168002, ss3771566512, ss3813647497, ss4857158656, ss5284537515, ss5480066542, ss5578729251, ss5744265110, ss5811655726, ss5849630133, ss5879461996 NC_000010.11:72009600:C:G NC_000010.11:72009600:C:G (self)
ss5603288 NT_030059.13:24573822:C:G NC_000010.11:72009600:C: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 rs4148942

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.post761+d5e8e07