Name: rs234757
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.

rs234757

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:42998542 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.107684 (28503/264690, TOPMED)
T=0.097277 (13637/140188, GnomAD)
T=0.28066 (7931/28258, 14KJPN) (+ 16 more)
T=0.08025 (1516/18890, ALFA)
T=0.27947 (4684/16760, 8.3KJPN)
T=0.1490 (954/6404, 1000G_30x)
T=0.1476 (739/5008, 1000G)
T=0.0337 (151/4480, Estonian)
T=0.0924 (356/3854, ALSPAC)
T=0.0952 (353/3708, TWINSUK)
T=0.2362 (692/2930, KOREAN)
T=0.2331 (427/1832, Korea1K)
T=0.088 (88/998, GoNL)
T=0.077 (46/600, NorthernSweden)
T=0.114 (60/528, SGDP_PRJ)
T=0.102 (22/216, Qatari)
T=0.245 (52/212, Vietnamese)
T=0.07 (4/56, Siberian)
T=0.10 (4/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PKNOX1 : 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=0.08025	C=0.91975
European	Sub	14286	T=0.07350	C=0.92650
African	Sub	2946	T=0.0767	C=0.9233
African Others	Sub	114	T=0.088	C=0.912
African American	Sub	2832	T=0.0763	C=0.9237
Asian	Sub	112	T=0.223	C=0.777
East Asian	Sub	86	T=0.24	C=0.76
Other Asian	Sub	26	T=0.15	C=0.85
Latin American 1	Sub	146	T=0.110	C=0.890
Latin American 2	Sub	610	T=0.207	C=0.793
South Asian	Sub	98	T=0.09	C=0.91
Other	Sub	692	T=0.092	C=0.908

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	T=0.107684	C=0.892316
gnomAD - Genomes	Global	Study-wide	140188	T=0.097277	C=0.902723
gnomAD - Genomes	European	Sub	75934	T=0.08690	C=0.91310
gnomAD - Genomes	African	Sub	42018	T=0.08484	C=0.91516
gnomAD - Genomes	American	Sub	13638	T=0.15010	C=0.84990
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.1309	C=0.8691
gnomAD - Genomes	East Asian	Sub	3122	T=0.2297	C=0.7703
gnomAD - Genomes	Other	Sub	2152	T=0.1273	C=0.8727
14KJPN	JAPANESE	Study-wide	28258	T=0.28066	C=0.71934
Allele Frequency Aggregator	Total	Global	18890	T=0.08025	C=0.91975
Allele Frequency Aggregator	European	Sub	14286	T=0.07350	C=0.92650
Allele Frequency Aggregator	African	Sub	2946	T=0.0767	C=0.9233
Allele Frequency Aggregator	Other	Sub	692	T=0.092	C=0.908
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.207	C=0.793
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.110	C=0.890
Allele Frequency Aggregator	Asian	Sub	112	T=0.223	C=0.777
Allele Frequency Aggregator	South Asian	Sub	98	T=0.09	C=0.91
8.3KJPN	JAPANESE	Study-wide	16760	T=0.27947	C=0.72053
1000Genomes_30x	Global	Study-wide	6404	T=0.1490	C=0.8510
1000Genomes_30x	African	Sub	1786	T=0.0823	C=0.9177
1000Genomes_30x	Europe	Sub	1266	T=0.1288	C=0.8712
1000Genomes_30x	South Asian	Sub	1202	T=0.1389	C=0.8611
1000Genomes_30x	East Asian	Sub	1170	T=0.2274	C=0.7726
1000Genomes_30x	American	Sub	980	T=0.215	C=0.785
1000Genomes	Global	Study-wide	5008	T=0.1476	C=0.8524
1000Genomes	African	Sub	1322	T=0.0809	C=0.9191
1000Genomes	East Asian	Sub	1008	T=0.2292	C=0.7708
1000Genomes	Europe	Sub	1006	T=0.1183	C=0.8817
1000Genomes	South Asian	Sub	978	T=0.135	C=0.865
1000Genomes	American	Sub	694	T=0.216	C=0.784
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.0337	C=0.9663
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0924	C=0.9076
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0952	C=0.9048
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2362	C=0.7638
Korean Genome Project	KOREAN	Study-wide	1832	T=0.2331	C=0.7669
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.088	C=0.912
Northern Sweden	ACPOP	Study-wide	600	T=0.077	C=0.923
SGDP_PRJ	Global	Study-wide	528	T=0.114	C=0.886
Qatari	Global	Study-wide	216	T=0.102	C=0.898
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.245	C=0.755
Siberian	Global	Study-wide	56	T=0.07	C=0.93
The Danish reference pan genome	Danish	Study-wide	40	T=0.10	C=0.90

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 21	NC_000021.9:g.42998542T>C
GRCh37.p13 chr 21	NC_000021.8:g.44418652T>C

Gene: PKNOX1, PBX/knotted 1 homeobox 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PKNOX1 transcript variant 2	NM_001286258.2:c.-235-578… NM_001286258.2:c.-235-5784T>C	N/A	Intron Variant
PKNOX1 transcript variant 3	NM_001320694.2:c.-56-5784… NM_001320694.2:c.-56-5784T>C	N/A	Intron Variant
PKNOX1 transcript variant 1	NM_004571.5:c.-56-5784T>C	N/A	Intron Variant
PKNOX1 transcript variant X1	XM_047440826.1:c.-56-5784… XM_047440826.1:c.-56-5784T>C	N/A	Intron Variant
PKNOX1 transcript variant X3	XM_047440828.1:c.-56-5784… XM_047440828.1:c.-56-5784T>C	N/A	Intron Variant
PKNOX1 transcript variant X4	XM_047440829.1:c.-56-5784… XM_047440829.1:c.-56-5784T>C	N/A	Intron Variant
PKNOX1 transcript variant X5	XM_047440830.1:c.-56-5784… XM_047440830.1:c.-56-5784T>C	N/A	Intron Variant
PKNOX1 transcript variant X2	XM_047440827.1:c.-2469=	N/A	5 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=	C
GRCh38.p14 chr 21	NC_000021.9:g.42998542=	NC_000021.9:g.42998542T>C
GRCh37.p13 chr 21	NC_000021.8:g.44418652=	NC_000021.8:g.44418652T>C
PKNOX1 transcript variant X2	XM_047440827.1:c.-2469=	XM_047440827.1:c.-2469T>C
PKNOX1 transcript variant 2	NM_001286258.2:c.-235-5784=	NM_001286258.2:c.-235-5784T>C
PKNOX1 transcript variant 3	NM_001320694.2:c.-56-5784=	NM_001320694.2:c.-56-5784T>C
PKNOX1 transcript	NM_004571.3:c.-56-5784=	NM_004571.3:c.-56-5784T>C
PKNOX1 transcript variant 1	NM_004571.5:c.-56-5784=	NM_004571.5:c.-56-5784T>C
PKNOX1 transcript variant X1	XM_047440826.1:c.-56-5784=	XM_047440826.1:c.-56-5784T>C
PKNOX1 transcript variant X3	XM_047440828.1:c.-56-5784=	XM_047440828.1:c.-56-5784T>C
PKNOX1 transcript variant X4	XM_047440829.1:c.-56-5784=	XM_047440829.1:c.-56-5784T>C
PKNOX1 transcript variant X5	XM_047440830.1:c.-56-5784=	XM_047440830.1:c.-56-5784T>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#.

74 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss303120	Jul 12, 2000 (79)
2	KWOK	ss1243927	Oct 04, 2000 (86)
3	KWOK	ss1840818	Oct 18, 2000 (87)
4	SC_JCM	ss5890375	Feb 20, 2003 (117)
5	BCM_SSAHASNP	ss10979903	Jul 11, 2003 (116)
6	BCM_SSAHASNP	ss14274501	Dec 05, 2003 (126)
7	WUGSC_SSAHASNP	ss14435626	Dec 05, 2003 (126)
8	SC_SNP	ss14833043	Dec 05, 2003 (119)
9	SSAHASNP	ss21822258	Apr 05, 2004 (121)
10	AFFY	ss76479590	Dec 06, 2007 (142)
11	HGSV	ss77538980	Dec 07, 2007 (129)
12	BCMHGSC_JDW	ss91853276	Mar 24, 2008 (129)
13	ILLUMINA-UK	ss117542134	Dec 01, 2009 (142)
14	COMPLETE_GENOMICS	ss168126753	Jul 04, 2010 (142)
15	COMPLETE_GENOMICS	ss169637344	Jul 04, 2010 (142)
16	COMPLETE_GENOMICS	ss172084544	Jul 04, 2010 (142)
17	BUSHMAN	ss204031378	Jul 04, 2010 (142)
18	BCM-HGSC-SUB	ss208792666	Aug 21, 2014 (142)
19	BL	ss255996352	May 09, 2011 (134)
20	GMI	ss283558467	May 04, 2012 (137)
21	GMI	ss287539287	Apr 25, 2013 (138)
22	PJP	ss292719326	May 09, 2011 (134)
23	1000GENOMES	ss341044984	May 09, 2011 (134)
24	TISHKOFF	ss566525445	Apr 25, 2013 (138)
25	SSMP	ss662436821	Apr 25, 2013 (138)
26	EVA-GONL	ss995163993	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1082534048	Aug 21, 2014 (142)
28	1000GENOMES	ss1366454083	Aug 21, 2014 (142)
29	DDI	ss1429198504	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1579681634	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1639651621	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1682645654	Apr 01, 2015 (144)
33	EVA_DECODE	ss1699235491	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1809708349	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1938714642	Feb 12, 2016 (147)
36	GENOMED	ss1969235748	Jul 19, 2016 (147)
37	JJLAB	ss2030132246	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2158737423	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2246113850	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2629565041	Nov 08, 2017 (151)
41	GRF	ss2704468284	Nov 08, 2017 (151)
42	GNOMAD	ss2972248350	Nov 08, 2017 (151)
43	SWEGEN	ss3018961339	Nov 08, 2017 (151)
44	BIOINF_KMB_FNS_UNIBA	ss3028905998	Nov 08, 2017 (151)
45	CSHL	ss3352740855	Nov 08, 2017 (151)
46	URBANLAB	ss3651126034	Oct 12, 2018 (152)
47	EGCUT_WGS	ss3685538259	Jul 13, 2019 (153)
48	EVA_DECODE	ss3707818980	Jul 13, 2019 (153)
49	ACPOP	ss3743771245	Jul 13, 2019 (153)
50	EVA	ss3759161406	Jul 13, 2019 (153)
51	PACBIO	ss3788776186	Jul 13, 2019 (153)
52	PACBIO	ss3793649011	Jul 13, 2019 (153)
53	PACBIO	ss3798535321	Jul 13, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3822327331	Jul 13, 2019 (153)
55	EVA	ss3835898452	Apr 27, 2020 (154)
56	EVA	ss3841577027	Apr 27, 2020 (154)
57	EVA	ss3847090756	Apr 27, 2020 (154)
58	SGDP_PRJ	ss3890095328	Apr 27, 2020 (154)
59	KRGDB	ss3940441276	Apr 27, 2020 (154)
60	KOGIC	ss3983177220	Apr 27, 2020 (154)
61	TOPMED	ss5103004488	Apr 26, 2021 (155)
62	TOMMO_GENOMICS	ss5231717079	Apr 26, 2021 (155)
63	1000G_HIGH_COVERAGE	ss5310365202	Oct 16, 2022 (156)
64	HUGCELL_USP	ss5502399366	Oct 16, 2022 (156)
65	EVA	ss5512335654	Oct 16, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5617574296	Oct 16, 2022 (156)
67	SANFORD_IMAGENETICS	ss5664099998	Oct 16, 2022 (156)
68	TOMMO_GENOMICS	ss5792284111	Oct 16, 2022 (156)
69	YY_MCH	ss5818481406	Oct 16, 2022 (156)
70	EVA	ss5839101268	Oct 16, 2022 (156)
71	EVA	ss5853324671	Oct 16, 2022 (156)
72	EVA	ss5892527522	Oct 16, 2022 (156)
73	EVA	ss5958999260	Oct 16, 2022 (156)
74	EVA	ss5981118306	Oct 16, 2022 (156)
75	1000Genomes	NC_000021.8 - 44418652	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000021.9 - 42998542	Oct 16, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000021.8 - 44418652	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000021.8 - 44418652	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000021.8 - 44418652	Apr 27, 2020 (154)
80	gnomAD - Genomes	NC_000021.9 - 42998542	Apr 26, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000021.8 - 44418652	Apr 27, 2020 (154)
82	KOREAN population from KRGDB	NC_000021.8 - 44418652	Apr 27, 2020 (154)
83	Korean Genome Project	NC_000021.9 - 42998542	Apr 27, 2020 (154)
84	Northern Sweden	NC_000021.8 - 44418652	Jul 13, 2019 (153)
85	Qatari	NC_000021.8 - 44418652	Apr 27, 2020 (154)
86	SGDP_PRJ	NC_000021.8 - 44418652	Apr 27, 2020 (154)
87	Siberian	NC_000021.8 - 44418652	Apr 27, 2020 (154)
88	8.3KJPN	NC_000021.8 - 44418652	Apr 26, 2021 (155)
89	14KJPN	NC_000021.9 - 42998542	Oct 16, 2022 (156)
90	TopMed	NC_000021.9 - 42998542	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000021.8 - 44418652	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000021.8 - 44418652	Jul 13, 2019 (153)
93	ALFA	NC_000021.9 - 42998542	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)
rs1672114	Aug 27, 2003 (117)
rs2212837	Feb 20, 2003 (111)
rs3921063	Feb 20, 2003 (111)
rs4405844	Aug 27, 2003 (117)
rs10299677	Mar 10, 2006 (126)
rs10319169	Mar 10, 2006 (126)
rs55838866	Aug 21, 2014 (142)
rs77100180	Aug 21, 2014 (142)
rs113685113	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss76479590, ss77538980, ss91853276, ss117542134, ss168126753, ss169637344, ss172084544, ss204031378, ss208792666, ss255996352, ss283558467, ss287539287, ss292719326, ss1699235491	NC_000021.7:43291720:T:C	NC_000021.9:42998541:T:C	(self)
79980306, 44268657, 31276507, 5846573, 19720455, 47618670, 17056110, 20756564, 42112308, 11253777, 89686386, 44268657, 9767902, ss341044984, ss566525445, ss662436821, ss995163993, ss1082534048, ss1366454083, ss1429198504, ss1579681634, ss1639651621, ss1682645654, ss1809708349, ss1938714642, ss1969235748, ss2030132246, ss2158737423, ss2629565041, ss2704468284, ss2972248350, ss3018961339, ss3352740855, ss3685538259, ss3743771245, ss3759161406, ss3788776186, ss3793649011, ss3798535321, ss3835898452, ss3841577027, ss3890095328, ss3940441276, ss5231717079, ss5512335654, ss5664099998, ss5839101268, ss5958999260, ss5981118306	NC_000021.8:44418651:T:C	NC_000021.9:42998541:T:C	(self)
105100231, 564332139, 39555221, 126121215, 378113434, 3682948638, ss2246113850, ss3028905998, ss3651126034, ss3707818980, ss3822327331, ss3847090756, ss3983177220, ss5103004488, ss5310365202, ss5502399366, ss5617574296, ss5792284111, ss5818481406, ss5853324671, ss5892527522	NC_000021.9:42998541:T:C	NC_000021.9:42998541:T:C	(self)
ss303120, ss1243927, ss1840818	NT_011515.12:1413092:T:C	NC_000021.9:42998541:T:C	(self)
ss5890375, ss10979903	NT_030188.2:1167977:T:C	NC_000021.9:42998541:T:C	(self)
ss14274501, ss14435626, ss14833043, ss21822258	NT_030188.3:1167977:T:C	NC_000021.9:42998541: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 rs234757

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

rs234757