Name: rs113542024
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.

rs113542024

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:31168000 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.080082 (21197/264690, TOPMED)
G=0.083319 (11676/140136, GnomAD)
G=0.04218 (1192/28258, 14KJPN) (+ 15 more)
G=0.08200 (1549/18890, ALFA)
G=0.04314 (723/16760, 8.3KJPN)
G=0.0776 (497/6404, 1000G_30x)
G=0.0767 (384/5008, 1000G)
G=0.0846 (379/4480, Estonian)
G=0.0664 (256/3854, ALSPAC)
G=0.0626 (232/3708, TWINSUK)
G=0.0664 (194/2922, KOREAN)
G=0.096 (96/998, GoNL)
G=0.062 (37/600, NorthernSweden)
G=0.065 (14/216, Qatari)
T=0.46 (42/92, SGDP_PRJ)
G=0.12 (5/40, GENOME_DK)
T=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: POU5F1 : Intron 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=0.91800	G=0.08200
European	Sub	14286	T=0.91565	G=0.08435
African	Sub	2946	T=0.9545	G=0.0455
African Others	Sub	114	T=0.921	G=0.079
African American	Sub	2832	T=0.9559	G=0.0441
Asian	Sub	112	T=0.929	G=0.071
East Asian	Sub	86	T=0.97	G=0.03
Other Asian	Sub	26	T=0.81	G=0.19
Latin American 1	Sub	146	T=0.856	G=0.144
Latin American 2	Sub	610	T=0.830	G=0.170
South Asian	Sub	98	T=0.93	G=0.07
Other	Sub	692	T=0.899	G=0.101

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=0.919918	G=0.080082
gnomAD - Genomes	Global	Study-wide	140136	T=0.916681	G=0.083319
gnomAD - Genomes	European	Sub	75874	T=0.90429	G=0.09571
gnomAD - Genomes	African	Sub	42022	T=0.95143	G=0.04857
gnomAD - Genomes	American	Sub	13640	T=0.88446	G=0.11554
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.8689	G=0.1311
gnomAD - Genomes	East Asian	Sub	3134	T=0.9528	G=0.0472
gnomAD - Genomes	Other	Sub	2148	T=0.9004	G=0.0996
14KJPN	JAPANESE	Study-wide	28258	T=0.95782	G=0.04218
Allele Frequency Aggregator	Total	Global	18890	T=0.91800	G=0.08200
Allele Frequency Aggregator	European	Sub	14286	T=0.91565	G=0.08435
Allele Frequency Aggregator	African	Sub	2946	T=0.9545	G=0.0455
Allele Frequency Aggregator	Other	Sub	692	T=0.899	G=0.101
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.830	G=0.170
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.856	G=0.144
Allele Frequency Aggregator	Asian	Sub	112	T=0.929	G=0.071
Allele Frequency Aggregator	South Asian	Sub	98	T=0.93	G=0.07
8.3KJPN	JAPANESE	Study-wide	16760	T=0.95686	G=0.04314
1000Genomes_30x	Global	Study-wide	6404	T=0.9224	G=0.0776
1000Genomes_30x	African	Sub	1786	T=0.9440	G=0.0560
1000Genomes_30x	Europe	Sub	1266	T=0.8878	G=0.1122
1000Genomes_30x	South Asian	Sub	1202	T=0.9301	G=0.0699
1000Genomes_30x	East Asian	Sub	1170	T=0.9650	G=0.0350
1000Genomes_30x	American	Sub	980	T=0.867	G=0.133
1000Genomes	Global	Study-wide	5008	T=0.9233	G=0.0767
1000Genomes	African	Sub	1322	T=0.9463	G=0.0537
1000Genomes	East Asian	Sub	1008	T=0.9653	G=0.0347
1000Genomes	Europe	Sub	1006	T=0.8877	G=0.1123
1000Genomes	South Asian	Sub	978	T=0.928	G=0.072
1000Genomes	American	Sub	694	T=0.863	G=0.137
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9154	G=0.0846
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9336	G=0.0664
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9374	G=0.0626
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9336	G=0.0664
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.904	G=0.096
Northern Sweden	ACPOP	Study-wide	600	T=0.938	G=0.062
Qatari	Global	Study-wide	216	T=0.935	G=0.065
SGDP_PRJ	Global	Study-wide	92	T=0.46	G=0.54
The Danish reference pan genome	Danish	Study-wide	40	T=0.88	G=0.12
Siberian	Global	Study-wide	16	T=0.50	G=0.50

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 6	NC_000006.12:g.31168000T>G
GRCh37.p13 chr 6	NC_000006.11:g.31135777T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2650440T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2650546T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2426049T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2431645T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.2427332T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.2432917T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2471432T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2470730T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2478517T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2484137T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.2512131T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.2517716T>G

Gene: POU5F1, POU class 5 homeobox 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
POU5F1 transcript variant 1	NM_002701.6:c.406-1953A>C	N/A	Intron Variant
POU5F1 transcript variant 3	NM_001173531.3:c.	N/A	Genic Upstream Transcript Variant
POU5F1 transcript variant 4	NM_001285986.2:c.	N/A	Genic Upstream Transcript Variant
POU5F1 transcript variant 2	NM_203289.6:c.	N/A	Genic Upstream Transcript 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=	G
GRCh38.p14 chr 6	NC_000006.12:g.31168000=	NC_000006.12:g.31168000T>G
GRCh37.p13 chr 6	NC_000006.11:g.31135777=	NC_000006.11:g.31135777T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.2650440=	NT_113891.3:g.2650440T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.2650546=	NT_113891.2:g.2650546T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.2426049=	NT_167248.2:g.2426049T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.2431645=	NT_167248.1:g.2431645T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.2427332=	NT_167245.2:g.2427332T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.2432917=	NT_167245.1:g.2432917T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.2471432=	NT_167249.2:g.2471432T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.2470730=	NT_167249.1:g.2470730T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.2478517=	NT_167246.2:g.2478517T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.2484137=	NT_167246.1:g.2484137T>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.2512131=	NT_167247.2:g.2512131T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.2517716=	NT_167247.1:g.2517716T>G
POU5F1 transcript variant 1	NM_002701.4:c.406-1953=	NM_002701.4:c.406-1953A>C
POU5F1 transcript variant 1	NM_002701.6:c.406-1953=	NM_002701.6:c.406-1953A>C

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#.

43 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM-HGSC-SUB	ss207844905	Jul 04, 2010 (132)
2	1000GENOMES	ss233391876	Jul 14, 2010 (137)
3	TISHKOFF	ss559108455	Apr 25, 2013 (138)
4	SSMP	ss653027067	Apr 25, 2013 (138)
5	EVA-GONL	ss982755943	Aug 21, 2014 (142)
6	JMKIDD_LAB	ss1073500206	Aug 21, 2014 (142)
7	1000GENOMES	ss1319541015	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1581601217	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1615268694	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1658262727	Apr 01, 2015 (144)
11	WEILL_CORNELL_DGM	ss1926007190	Feb 12, 2016 (147)
12	GENOMED	ss1970353232	Jul 19, 2016 (147)
13	JJLAB	ss2023633890	Sep 14, 2016 (149)
14	USC_VALOUEV	ss2151799503	Nov 08, 2017 (151)
15	HUMAN_LONGEVITY	ss2282926241	Dec 20, 2016 (150)
16	GRF	ss2707392283	Nov 08, 2017 (151)
17	GNOMAD	ss2837390491	Nov 08, 2017 (151)
18	BIOINF_KMB_FNS_UNIBA	ss3025602520	Nov 08, 2017 (151)
19	EGCUT_WGS	ss3666704031	Jul 13, 2019 (153)
20	ACPOP	ss3733350769	Jul 13, 2019 (153)
21	EVA	ss3764811868	Jul 13, 2019 (153)
22	PACBIO	ss3785420320	Jul 13, 2019 (153)
23	PACBIO	ss3790779871	Jul 13, 2019 (153)
24	PACBIO	ss3795657248	Jul 13, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3807966065	Jul 13, 2019 (153)
26	EVA	ss3829824178	Apr 26, 2020 (154)
27	SGDP_PRJ	ss3864238492	Apr 26, 2020 (154)
28	KRGDB	ss3911014173	Apr 26, 2020 (154)
29	TOPMED	ss4698315977	Apr 26, 2021 (155)
30	TOMMO_GENOMICS	ss5176815661	Apr 26, 2021 (155)
31	1000G_HIGH_COVERAGE	ss5267920254	Oct 17, 2022 (156)
32	EVA	ss5364703227	Oct 17, 2022 (156)
33	HUGCELL_USP	ss5465658227	Oct 17, 2022 (156)
34	EVA	ss5508420606	Oct 17, 2022 (156)
35	1000G_HIGH_COVERAGE	ss5553572807	Oct 17, 2022 (156)
36	SANFORD_IMAGENETICS	ss5640075203	Oct 17, 2022 (156)
37	TOMMO_GENOMICS	ss5714665601	Oct 17, 2022 (156)
38	YY_MCH	ss5807296144	Oct 17, 2022 (156)
39	EVA	ss5842014813	Oct 17, 2022 (156)
40	EVA	ss5855277421	Oct 17, 2022 (156)
41	EVA	ss5883228488	Oct 17, 2022 (156)
42	EVA	ss5968578767	Oct 17, 2022 (156)
43	EVA	ss5980355200	Oct 17, 2022 (156)
44	1000Genomes	NC_000006.11 - 31135777	Oct 12, 2018 (152)
45	1000Genomes_30x	NC_000006.12 - 31168000	Oct 17, 2022 (156)
46	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 31135777	Oct 12, 2018 (152)
47	Genetic variation in the Estonian population	NC_000006.11 - 31135777	Oct 12, 2018 (152)
48	The Danish reference pan genome	NC_000006.11 - 31135777	Apr 26, 2020 (154)
49	gnomAD - Genomes	NC_000006.12 - 31168000	Apr 26, 2021 (155)
50	Genome of the Netherlands Release 5	NC_000006.11 - 31135777	Apr 26, 2020 (154)
51	KOREAN population from KRGDB	NC_000006.11 - 31135777	Apr 26, 2020 (154)
52	Northern Sweden	NC_000006.11 - 31135777	Jul 13, 2019 (153)
53	Qatari	NC_000006.11 - 31135777	Apr 26, 2020 (154)
54	SGDP_PRJ	NC_000006.11 - 31135777	Apr 26, 2020 (154)
55	Siberian	NC_000006.11 - 31135777	Apr 26, 2020 (154)
56	8.3KJPN	NC_000006.11 - 31135777	Apr 26, 2021 (155)
57	14KJPN	NC_000006.12 - 31168000	Oct 17, 2022 (156)
58	TopMed	NC_000006.12 - 31168000	Apr 26, 2021 (155)
59	UK 10K study - Twins	NC_000006.11 - 31135777	Oct 12, 2018 (152)
60	ALFA	NC_000006.12 - 31168000	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)
rs116288471	May 04, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss207844905	NC_000006.10:31243755:T:G	NC_000006.12:31167999:T:G	(self)
31307713, 17457141, 12442279, 7766156, 7755433, 18191567, 6635634, 8049120, 16255472, 4315857, 34784968, 17457141, ss233391876, ss559108455, ss653027067, ss982755943, ss1073500206, ss1319541015, ss1581601217, ss1615268694, ss1658262727, ss1926007190, ss1970353232, ss2023633890, ss2151799503, ss2707392283, ss2837390491, ss3666704031, ss3733350769, ss3764811868, ss3785420320, ss3790779871, ss3795657248, ss3829824178, ss3864238492, ss3911014173, ss5176815661, ss5364703227, ss5508420606, ss5640075203, ss5842014813, ss5968578767, ss5980355200	NC_000006.11:31135776:T:G	NC_000006.12:31167999:T:G	(self)
41098742, 221140268, 48502705, 535693535, 6883199512, ss2282926241, ss3025602520, ss3807966065, ss4698315977, ss5267920254, ss5465658227, ss5553572807, ss5714665601, ss5807296144, ss5855277421, ss5883228488	NC_000006.12:31167999:T:G	NC_000006.12:31167999:T:G	(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 rs113542024

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs113542024