Name: rs1048200
Published: September 21, 2022
License: Open Access

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.

rs1048200

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:36679180 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.453670 (120082/264690, TOPMED)
T=0.451294 (62904/139386, GnomAD)
T=0.46603 (13169/28258, 14KJPN) (+ 15 more)
T=0.45193 (8537/18890, ALFA)
T=0.46951 (7869/16760, 8.3KJPN)
T=0.4282 (2742/6404, 1000G_30x)
T=0.4545 (2276/5008, 1000G)
T=0.3772 (1690/4480, Estonian)
A=0.4904 (1890/3854, ALSPAC)
A=0.4736 (1756/3708, TWINSUK)
T=0.4154 (1217/2930, KOREAN)
T=0.4241 (777/1832, Korea1K)
A=0.044 (44/998, GoNL)
T=0.377 (226/600, NorthernSweden)
T=0.257 (115/448, SGDP_PRJ)
T=0.468 (101/216, Qatari)
T=0.27 (12/44, Siberian)
T=0.45 (18/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC25A21 : Intron Variant
PAX9 : 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	18890	T=0.45193	A=0.54807
European	Sub	14286	T=0.46311	A=0.53689
African	Sub	2946	T=0.4172	A=0.5828
African Others	Sub	114	T=0.456	A=0.544
African American	Sub	2832	T=0.4156	A=0.5844
Asian	Sub	112	T=0.446	A=0.554
East Asian	Sub	86	T=0.47	A=0.53
Other Asian	Sub	26	T=0.38	A=0.62
Latin American 1	Sub	146	T=0.438	A=0.562
Latin American 2	Sub	610	T=0.338	A=0.662
South Asian	Sub	98	T=0.58	A=0.42
Other	Sub	692	T=0.455	A=0.545

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.453670	A=0.546330
gnomAD - Genomes	Global	Study-wide	139386	T=0.451294	A=0.548706
gnomAD - Genomes	European	Sub	75552	T=0.47637	A=0.52363
gnomAD - Genomes	African	Sub	41718	T=0.41486	A=0.58514
gnomAD - Genomes	American	Sub	13578	T=0.39247	A=0.60753
gnomAD - Genomes	Ashkenazi Jewish	Sub	3314	T=0.5238	A=0.4762
gnomAD - Genomes	East Asian	Sub	3084	T=0.4925	A=0.5075
gnomAD - Genomes	Other	Sub	2140	T=0.4776	A=0.5224
14KJPN	JAPANESE	Study-wide	28258	T=0.46603	A=0.53397
Allele Frequency Aggregator	Total	Global	18890	T=0.45193	A=0.54807
Allele Frequency Aggregator	European	Sub	14286	T=0.46311	A=0.53689
Allele Frequency Aggregator	African	Sub	2946	T=0.4172	A=0.5828
Allele Frequency Aggregator	Other	Sub	692	T=0.455	A=0.545
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.338	A=0.662
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.438	A=0.562
Allele Frequency Aggregator	Asian	Sub	112	T=0.446	A=0.554
Allele Frequency Aggregator	South Asian	Sub	98	T=0.58	A=0.42
8.3KJPN	JAPANESE	Study-wide	16760	T=0.46951	A=0.53049
1000Genomes_30x	Global	Study-wide	6404	T=0.4282	A=0.5718
1000Genomes_30x	African	Sub	1786	T=0.4054	A=0.5946
1000Genomes_30x	Europe	Sub	1266	T=0.4755	A=0.5245
1000Genomes_30x	South Asian	Sub	1202	T=0.4235	A=0.5765
1000Genomes_30x	East Asian	Sub	1170	T=0.4752	A=0.5248
1000Genomes_30x	American	Sub	980	T=0.358	A=0.642
1000Genomes	Global	Study-wide	5008	T=0.4545	A=0.5455
1000Genomes	African	Sub	1322	T=0.4259	A=0.5741
1000Genomes	East Asian	Sub	1008	T=0.5030	A=0.4970
1000Genomes	Europe	Sub	1006	T=0.4781	A=0.5219
1000Genomes	South Asian	Sub	978	T=0.453	A=0.547
1000Genomes	American	Sub	694	T=0.406	A=0.594
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.3772	A=0.6228
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5096	A=0.4904
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5264	A=0.4736
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.4154	A=0.5846
Korean Genome Project	KOREAN	Study-wide	1832	T=0.4241	A=0.5759
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.956	A=0.044
Northern Sweden	ACPOP	Study-wide	600	T=0.377	A=0.623
SGDP_PRJ	Global	Study-wide	448	T=0.257	A=0.743
Qatari	Global	Study-wide	216	T=0.468	A=0.532
Siberian	Global	Study-wide	44	T=0.27	A=0.73
The Danish reference pan genome	Danish	Study-wide	40	T=0.45	A=0.55

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 14	NC_000014.9:g.36679180T>A
GRCh38.p14 chr 14	NC_000014.9:g.36679180T>C
GRCh37.p13 chr 14	NC_000014.8:g.37148385T>A
GRCh37.p13 chr 14	NC_000014.8:g.37148385T>C
PAX9 RefSeqGene	NG_013357.1:g.26613T>A
PAX9 RefSeqGene	NG_013357.1:g.26613T>C

Gene: SLC25A21, solute carrier family 25 member 21 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC25A21 transcript variant 2	NM_001171170.2:c.897-696A… NM_001171170.2:c.897-696A>T	N/A	Intron Variant
SLC25A21 transcript variant 1	NM_030631.4:c.*1478=	N/A	3 Prime UTR Variant
SLC25A21 transcript variant X1	XM_047431871.1:c.*1478=	N/A	3 Prime UTR Variant
SLC25A21 transcript variant X2	XM_011537288.4:c.*1478=	N/A	3 Prime UTR Variant
SLC25A21 transcript variant X3	XM_011537289.4:c.*1478=	N/A	3 Prime UTR Variant

Gene: PAX9, paired box 9 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PAX9 transcript variant 1	NM_001372076.1:c.*2728=	N/A	3 Prime UTR Variant
PAX9 transcript variant 2	NM_006194.4:c.*2728=	N/A	3 Prime UTR Variant

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

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
GRCh38.p14 chr 14	NC_000014.9:g.36679180=	NC_000014.9:g.36679180T>A	NC_000014.9:g.36679180T>C
GRCh37.p13 chr 14	NC_000014.8:g.37148385=	NC_000014.8:g.37148385T>A	NC_000014.8:g.37148385T>C
PAX9 RefSeqGene	NG_013357.1:g.26613=	NG_013357.1:g.26613T>A	NG_013357.1:g.26613T>C
PAX9 transcript variant 2	NM_006194.4:c.*2728=	NM_006194.4:c.*2728T>A	NM_006194.4:c.*2728T>C
PAX9 transcript variant 1	NM_001372076.1:c.*2728=	NM_001372076.1:c.*2728T>A	NM_001372076.1:c.*2728T>C
SLC25A21 transcript variant 1	NM_030631.4:c.*1478=	NM_030631.4:c.*1478A>T	NM_030631.4:c.*1478A>G
SLC25A21 transcript variant 1	NM_030631.3:c.*1478=	NM_030631.3:c.*1478A>T	NM_030631.3:c.*1478A>G
SLC25A21 transcript variant X2	XM_011537288.4:c.*1478=	XM_011537288.4:c.*1478A>T	XM_011537288.4:c.*1478A>G
SLC25A21 transcript variant X2	XM_011537288.3:c.*1478=	XM_011537288.3:c.*1478A>T	XM_011537288.3:c.*1478A>G
SLC25A21 transcript variant X2	XM_011537288.1:c.*1478=	XM_011537288.1:c.*1478A>T	XM_011537288.1:c.*1478A>G
SLC25A21 transcript variant X3	XM_011537289.4:c.*1478=	XM_011537289.4:c.*1478A>T	XM_011537289.4:c.*1478A>G
SLC25A21 transcript variant X3	XM_011537289.3:c.*1478=	XM_011537289.3:c.*1478A>T	XM_011537289.3:c.*1478A>G
SLC25A21 transcript variant X3	XM_011537289.1:c.*1478=	XM_011537289.1:c.*1478A>T	XM_011537289.1:c.*1478A>G
SLC25A21 transcript variant X1	XM_047431871.1:c.*1478=	XM_047431871.1:c.*1478A>T	XM_047431871.1:c.*1478A>G
SLC25A21 transcript variant 2	NM_001171170.1:c.897-696=	NM_001171170.1:c.897-696A>T	NM_001171170.1:c.897-696A>G
SLC25A21 transcript variant 2	NM_001171170.2:c.897-696=	NM_001171170.2:c.897-696A>T	NM_001171170.2:c.897-696A>G

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#.

58 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	LEE	ss1520909	Oct 05, 2000 (86)
2	LEE	ss4393726	May 29, 2002 (106)
3	LEE	ss4412600	May 29, 2002 (106)
4	WI_SSAHASNP	ss12284188	Jul 11, 2003 (116)
5	SI_EXO	ss71646276	May 18, 2007 (137)
6	HGSV	ss78869609	Dec 06, 2007 (137)
7	HGSV	ss82781639	Dec 15, 2007 (137)
8	ILLUMINA-UK	ss118412195	Feb 14, 2009 (137)
9	ENSEMBL	ss133918421	Dec 01, 2009 (137)
10	1000GENOMES	ss226511135	Jul 14, 2010 (137)
11	1000GENOMES	ss236497952	Jul 15, 2010 (137)
12	1000GENOMES	ss242940834	Jul 15, 2010 (137)
13	GMI	ss281958460	May 04, 2012 (137)
14	GMI	ss286821233	Apr 25, 2013 (138)
15	PJP	ss291701821	May 09, 2011 (137)
16	SSMP	ss659692005	Apr 25, 2013 (138)
17	EVA-GONL	ss991027171	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1079563326	Aug 21, 2014 (142)
19	1000GENOMES	ss1350562937	Aug 21, 2014 (142)
20	DDI	ss1427388244	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1577176152	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1631505220	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1674499253	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1934403934	Feb 12, 2016 (147)
25	GENOMED	ss1967935490	Jul 19, 2016 (147)
26	JJLAB	ss2027977329	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2156350369	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2201067796	Dec 20, 2016 (150)
29	GRF	ss2700768063	Nov 08, 2017 (151)
30	GNOMAD	ss2926436427	Nov 08, 2017 (151)
31	SWEGEN	ss3012021527	Nov 08, 2017 (151)
32	CSHL	ss3350753038	Nov 08, 2017 (151)
33	EGCUT_WGS	ss3679264590	Jul 13, 2019 (153)
34	EVA_DECODE	ss3696462992	Jul 13, 2019 (153)
35	ACPOP	ss3740283128	Jul 13, 2019 (153)
36	EVA	ss3752187165	Jul 13, 2019 (153)
37	PACBIO	ss3787634815	Jul 13, 2019 (153)
38	PACBIO	ss3792678068	Jul 13, 2019 (153)
39	PACBIO	ss3797562180	Jul 13, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3817519183	Jul 13, 2019 (153)
41	EVA	ss3833860201	Apr 27, 2020 (154)
42	EVA	ss3846010740	Apr 27, 2020 (154)
43	SGDP_PRJ	ss3881270929	Apr 27, 2020 (154)
44	KRGDB	ss3930261260	Apr 27, 2020 (154)
45	KOGIC	ss3974716846	Apr 27, 2020 (154)
46	TOPMED	ss4966801703	Apr 26, 2021 (155)
47	TOMMO_GENOMICS	ss5212736922	Apr 26, 2021 (155)
48	1000G_HIGH_COVERAGE	ss5295833890	Oct 16, 2022 (156)
49	EVA	ss5414574322	Oct 16, 2022 (156)
50	HUGCELL_USP	ss5489927010	Oct 16, 2022 (156)
51	1000G_HIGH_COVERAGE	ss5595908582	Oct 16, 2022 (156)
52	SANFORD_IMAGENETICS	ss5655994878	Oct 16, 2022 (156)
53	TOMMO_GENOMICS	ss5765399687	Oct 16, 2022 (156)
54	YY_MCH	ss5814654351	Oct 16, 2022 (156)
55	EVA	ss5840954504	Oct 16, 2022 (156)
56	EVA	ss5850986590	Oct 16, 2022 (156)
57	EVA	ss5900900912	Oct 16, 2022 (156)
58	EVA	ss5947419046	Oct 16, 2022 (156)
59	1000Genomes	NC_000014.8 - 37148385	Oct 12, 2018 (152)
60	1000Genomes_30x	NC_000014.9 - 36679180	Oct 16, 2022 (156)
61	The Avon Longitudinal Study of Parents and Children	NC_000014.8 - 37148385	Oct 12, 2018 (152)
62	Genetic variation in the Estonian population	NC_000014.8 - 37148385	Oct 12, 2018 (152)
63	The Danish reference pan genome	NC_000014.8 - 37148385	Apr 27, 2020 (154)
64	gnomAD - Genomes	NC_000014.9 - 36679180	Apr 26, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000014.8 - 37148385	Apr 27, 2020 (154)
66	KOREAN population from KRGDB	NC_000014.8 - 37148385	Apr 27, 2020 (154)
67	Korean Genome Project	NC_000014.9 - 36679180	Apr 27, 2020 (154)
68	Northern Sweden	NC_000014.8 - 37148385	Jul 13, 2019 (153)
69	Qatari	NC_000014.8 - 37148385	Apr 27, 2020 (154)
70	SGDP_PRJ	NC_000014.8 - 37148385	Apr 27, 2020 (154)
71	Siberian	NC_000014.8 - 37148385	Apr 27, 2020 (154)
72	8.3KJPN	NC_000014.8 - 37148385	Apr 26, 2021 (155)
73	14KJPN	NC_000014.9 - 36679180	Oct 16, 2022 (156)
74	TopMed	NC_000014.9 - 36679180	Apr 26, 2021 (155)
75	UK 10K study - Twins	NC_000014.8 - 37148385	Oct 12, 2018 (152)
76	ALFA	NC_000014.9 - 36679180	Apr 26, 2021 (155)

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)
rs3168889	Jul 03, 2002 (106)
rs45626734	Jan 15, 2013 (137)
rs59667213	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78869609, ss82781639, ss118412195, ss281958460, ss286821233, ss291701821	NC_000014.7:36218135:T:A	NC_000014.9:36679179:T:A	(self)
63526239, 35290239, 25002838, 3555576, 15761464, 37438654, 13567993, 16445864, 33287909, 8866723, 70706229, 35290239, ss226511135, ss236497952, ss242940834, ss659692005, ss991027171, ss1079563326, ss1350562937, ss1427388244, ss1577176152, ss1631505220, ss1674499253, ss1934403934, ss1967935490, ss2027977329, ss2156350369, ss2700768063, ss2926436427, ss3012021527, ss3350753038, ss3679264590, ss3740283128, ss3752187165, ss3787634815, ss3792678068, ss3797562180, ss3833860201, ss3881270929, ss3930261260, ss5212736922, ss5414574322, ss5655994878, ss5840954504, ss5947419046	NC_000014.8:37148384:T:A	NC_000014.9:36679179:T:A	(self)
83434517, 447968819, 31094847, 99236791, 182347362, 3762548666, ss2201067796, ss3696462992, ss3817519183, ss3846010740, ss3974716846, ss4966801703, ss5295833890, ss5489927010, ss5595908582, ss5765399687, ss5814654351, ss5850986590, ss5900900912	NC_000014.9:36679179:T:A	NC_000014.9:36679179:T:A	(self)
ss12284188	NT_026437.10:17068423:T:A	NC_000014.9:36679179:T:A	(self)
ss1520909, ss4393726, ss4412600, ss71646276, ss133918421	NT_026437.12:18148384:T:A	NC_000014.9:36679179:T:A	(self)
ss2201067796	NC_000014.9:36679179:T:C	NC_000014.9:36679179:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1048200

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1048200