Name: rs1242067
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.

rs1242067

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:143652765 (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 / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.264396 (69983/264690, TOPMED)
T=0.269330 (37243/138280, GnomAD)
T=0.37694 (10516/27898, 14KJPN) (+ 16 more)
T=0.28511 (5416/18996, ALFA)
T=0.35277 (5911/16756, 8.3KJPN)
T=0.3109 (1991/6404, 1000G_30x)
T=0.3145 (1575/5008, 1000G)
T=0.3324 (1489/4480, Estonian)
T=0.2896 (1116/3854, ALSPAC)
T=0.2953 (1095/3708, TWINSUK)
T=0.3485 (1021/2930, KOREAN)
T=0.3690 (676/1832, Korea1K)
T=0.296 (295/998, GoNL)
T=0.363 (218/600, NorthernSweden)
T=0.217 (110/506, SGDP_PRJ)
T=0.273 (90/330, HapMap)
T=0.227 (49/216, Qatari)
T=0.344 (73/212, Vietnamese)
T=0.24 (12/50, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC9A9 : Intron Variant
LOC102724120 : 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	18996	T=0.28511	C=0.71489
European	Sub	14370	T=0.31002	C=0.68998
African	Sub	2950	T=0.1502	C=0.8498
African Others	Sub	114	T=0.140	C=0.860
African American	Sub	2836	T=0.1506	C=0.8494
Asian	Sub	114	T=0.263	C=0.737
East Asian	Sub	88	T=0.26	C=0.74
Other Asian	Sub	26	T=0.27	C=0.73
Latin American 1	Sub	146	T=0.336	C=0.664
Latin American 2	Sub	610	T=0.339	C=0.661
South Asian	Sub	100	T=0.48	C=0.52
Other	Sub	706	T=0.261	C=0.739

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=0.264396	C=0.735604
gnomAD - Genomes	Global	Study-wide	138280	T=0.269330	C=0.730670
gnomAD - Genomes	European	Sub	75248	T=0.31198	C=0.68802
gnomAD - Genomes	African	Sub	41034	T=0.16009	C=0.83991
gnomAD - Genomes	American	Sub	13448	T=0.33247	C=0.66753
gnomAD - Genomes	Ashkenazi Jewish	Sub	3310	T=0.3224	C=0.6776
gnomAD - Genomes	East Asian	Sub	3106	T=0.3381	C=0.6619
gnomAD - Genomes	Other	Sub	2134	T=0.2858	C=0.7142
14KJPN	JAPANESE	Study-wide	27898	T=0.37694	C=0.62306
Allele Frequency Aggregator	Total	Global	18996	T=0.28511	C=0.71489
Allele Frequency Aggregator	European	Sub	14370	T=0.31002	C=0.68998
Allele Frequency Aggregator	African	Sub	2950	T=0.1502	C=0.8498
Allele Frequency Aggregator	Other	Sub	706	T=0.261	C=0.739
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.339	C=0.661
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.336	C=0.664
Allele Frequency Aggregator	Asian	Sub	114	T=0.263	C=0.737
Allele Frequency Aggregator	South Asian	Sub	100	T=0.48	C=0.52
8.3KJPN	JAPANESE	Study-wide	16756	T=0.35277	C=0.64723
1000Genomes_30x	Global	Study-wide	6404	T=0.3109	C=0.6891
1000Genomes_30x	African	Sub	1786	T=0.1540	C=0.8460
1000Genomes_30x	Europe	Sub	1266	T=0.3065	C=0.6935
1000Genomes_30x	South Asian	Sub	1202	T=0.4592	C=0.5408
1000Genomes_30x	East Asian	Sub	1170	T=0.3692	C=0.6308
1000Genomes_30x	American	Sub	980	T=0.351	C=0.649
1000Genomes	Global	Study-wide	5008	T=0.3145	C=0.6855
1000Genomes	African	Sub	1322	T=0.1505	C=0.8495
1000Genomes	East Asian	Sub	1008	T=0.3631	C=0.6369
1000Genomes	Europe	Sub	1006	T=0.3101	C=0.6899
1000Genomes	South Asian	Sub	978	T=0.461	C=0.539
1000Genomes	American	Sub	694	T=0.356	C=0.644
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.3324	C=0.6676
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.2896	C=0.7104
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.2953	C=0.7047
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3485	A=0.0000, C=0.6515, G=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	T=0.3690	C=0.6310
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.296	C=0.704
Northern Sweden	ACPOP	Study-wide	600	T=0.363	C=0.637
SGDP_PRJ	Global	Study-wide	506	T=0.217	C=0.783
HapMap	Global	Study-wide	330	T=0.273	C=0.727
HapMap	African	Sub	120	T=0.167	C=0.833
HapMap	American	Sub	120	T=0.300	C=0.700
HapMap	Asian	Sub	90	T=0.38	C=0.62
Qatari	Global	Study-wide	216	T=0.227	C=0.773
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.344	C=0.656
Siberian	Global	Study-wide	50	T=0.24	C=0.76

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 3	NC_000003.12:g.143652765T>A
GRCh38.p14 chr 3	NC_000003.12:g.143652765T>C
GRCh38.p14 chr 3	NC_000003.12:g.143652765T>G
GRCh37.p13 chr 3	NC_000003.11:g.143371607T>A
GRCh37.p13 chr 3	NC_000003.11:g.143371607T>C
GRCh37.p13 chr 3	NC_000003.11:g.143371607T>G
SLC9A9 RefSeqGene	NG_017077.2:g.200767A>T
SLC9A9 RefSeqGene	NG_017077.2:g.200767A>G
SLC9A9 RefSeqGene	NG_017077.2:g.200767A>C

Gene: SLC9A9, solute carrier family 9 member A9 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC9A9 transcript	NM_173653.4:c.650-405A>T	N/A	Intron Variant
SLC9A9 transcript variant X3	XM_011512703.4:c.2-405A>T	N/A	Intron Variant
SLC9A9 transcript variant X4	XM_011512704.4:c.650-405A… XM_011512704.4:c.650-405A>T	N/A	Intron Variant
SLC9A9 transcript variant X1	XM_017006202.3:c.650-405A… XM_017006202.3:c.650-405A>T	N/A	Intron Variant
SLC9A9 transcript variant X2	XM_017006203.2:c.299-405A… XM_017006203.2:c.299-405A>T	N/A	Intron Variant

Gene: LOC102724120, uncharacterized LOC102724120 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102724120 transcript variant X1	XR_001740940.2:n.	N/A	Intron 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	G
GRCh38.p14 chr 3	NC_000003.12:g.143652765=	NC_000003.12:g.143652765T>A	NC_000003.12:g.143652765T>C	NC_000003.12:g.143652765T>G
GRCh37.p13 chr 3	NC_000003.11:g.143371607=	NC_000003.11:g.143371607T>A	NC_000003.11:g.143371607T>C	NC_000003.11:g.143371607T>G
SLC9A9 RefSeqGene	NG_017077.2:g.200767=	NG_017077.2:g.200767A>T	NG_017077.2:g.200767A>G	NG_017077.2:g.200767A>C
SLC9A9 transcript	NM_173653.3:c.650-405=	NM_173653.3:c.650-405A>T	NM_173653.3:c.650-405A>G	NM_173653.3:c.650-405A>C
SLC9A9 transcript	NM_173653.4:c.650-405=	NM_173653.4:c.650-405A>T	NM_173653.4:c.650-405A>G	NM_173653.4:c.650-405A>C
SLC9A9 transcript variant X1	XM_005247375.1:c.2-405=	XM_005247375.1:c.2-405A>T	XM_005247375.1:c.2-405A>G	XM_005247375.1:c.2-405A>C
SLC9A9 transcript variant X3	XM_011512703.4:c.2-405=	XM_011512703.4:c.2-405A>T	XM_011512703.4:c.2-405A>G	XM_011512703.4:c.2-405A>C
SLC9A9 transcript variant X4	XM_011512704.4:c.650-405=	XM_011512704.4:c.650-405A>T	XM_011512704.4:c.650-405A>G	XM_011512704.4:c.650-405A>C
SLC9A9 transcript variant X1	XM_017006202.3:c.650-405=	XM_017006202.3:c.650-405A>T	XM_017006202.3:c.650-405A>G	XM_017006202.3:c.650-405A>C
SLC9A9 transcript variant X2	XM_017006203.2:c.299-405=	XM_017006203.2:c.299-405A>T	XM_017006203.2:c.299-405A>G	XM_017006203.2:c.299-405A>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#.

81 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1871753	Oct 18, 2000 (87)
2	TSC-CSHL	ss2375310	Oct 23, 2000 (94)
3	SC_JCM	ss3803034	Sep 28, 2001 (100)
4	TSC-CSHL	ss5554277	Oct 08, 2002 (108)
5	SC_JCM	ss5860716	Feb 20, 2003 (111)
6	CSHL-HAPMAP	ss17735985	Feb 27, 2004 (120)
7	SSAHASNP	ss21949465	Apr 05, 2004 (121)
8	PERLEGEN	ss23946257	Sep 20, 2004 (123)
9	HGSV	ss77131256	Dec 07, 2007 (129)
10	HGSV	ss81608378	Dec 14, 2007 (130)
11	BCMHGSC_JDW	ss92308383	Mar 24, 2008 (129)
12	HUMANGENOME_JCVI	ss99138311	Feb 04, 2009 (130)
13	BGI	ss106303023	Feb 04, 2009 (130)
14	1000GENOMES	ss111051181	Jan 25, 2009 (130)
15	1000GENOMES	ss112533809	Jan 25, 2009 (130)
16	ILLUMINA-UK	ss117303437	Feb 14, 2009 (130)
17	ENSEMBL	ss135483363	Dec 01, 2009 (131)
18	ENSEMBL	ss139200148	Dec 01, 2009 (131)
19	GMI	ss156287586	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss162680426	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss164472809	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss167276985	Jul 04, 2010 (132)
23	BUSHMAN	ss203287257	Jul 04, 2010 (132)
24	BCM-HGSC-SUB	ss206077937	Jul 04, 2010 (132)
25	1000GENOMES	ss220471435	Jul 14, 2010 (132)
26	1000GENOMES	ss232064314	Jul 14, 2010 (132)
27	1000GENOMES	ss239429370	Jul 15, 2010 (132)
28	BL	ss253562294	May 09, 2011 (134)
29	GMI	ss277381921	May 04, 2012 (137)
30	GMI	ss284763517	Apr 25, 2013 (138)
31	PJP	ss292929969	May 09, 2011 (134)
32	TISHKOFF	ss556996743	Apr 25, 2013 (138)
33	SSMP	ss650725104	Apr 25, 2013 (138)
34	EVA-GONL	ss979248852	Aug 21, 2014 (142)
35	JMKIDD_LAB	ss1070895673	Aug 21, 2014 (142)
36	1000GENOMES	ss1306503232	Aug 21, 2014 (142)
37	DDI	ss1429613066	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1608395634	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1651389667	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1800150856	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1922472209	Feb 12, 2016 (147)
42	GENOMED	ss1969541723	Jul 19, 2016 (147)
43	JJLAB	ss2021806298	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2149902764	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2256539891	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2625404979	Nov 08, 2017 (151)
47	GRF	ss2705315683	Nov 08, 2017 (151)
48	GNOMAD	ss2800117302	Nov 08, 2017 (151)
49	SWEGEN	ss2993334725	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3024670668	Nov 08, 2017 (151)
51	CSHL	ss3345305082	Nov 08, 2017 (151)
52	URBANLAB	ss3647544814	Oct 12, 2018 (152)
53	EGCUT_WGS	ss3661259730	Jul 13, 2019 (153)
54	EVA_DECODE	ss3710455563	Jul 13, 2019 (153)
55	ACPOP	ss3730423195	Jul 13, 2019 (153)
56	EVA	ss3760799192	Jul 13, 2019 (153)
57	PACBIO	ss3784486445	Jul 13, 2019 (153)
58	PACBIO	ss3789976400	Jul 13, 2019 (153)
59	PACBIO	ss3794850973	Jul 13, 2019 (153)
60	KHV_HUMAN_GENOMES	ss3803930867	Jul 13, 2019 (153)
61	EVA	ss3828116709	Apr 25, 2020 (154)
62	EVA	ss3837491234	Apr 25, 2020 (154)
63	EVA	ss3842922378	Apr 25, 2020 (154)
64	SGDP_PRJ	ss3857149482	Apr 25, 2020 (154)
65	KRGDB	ss3903185709	Apr 25, 2020 (154)
66	KOGIC	ss3952583269	Apr 25, 2020 (154)
67	TOPMED	ss4586635633	Apr 26, 2021 (155)
68	TOMMO_GENOMICS	ss5161975361	Apr 26, 2021 (155)
69	1000G_HIGH_COVERAGE	ss5256326529	Oct 12, 2022 (156)
70	EVA	ss5343822955	Oct 12, 2022 (156)
71	HUGCELL_USP	ss5455434510	Oct 12, 2022 (156)
72	EVA	ss5507233055	Oct 12, 2022 (156)
73	1000G_HIGH_COVERAGE	ss5535920915	Oct 12, 2022 (156)
74	SANFORD_IMAGENETICS	ss5633358124	Oct 12, 2022 (156)
75	TOMMO_GENOMICS	ss5694968727	Oct 12, 2022 (156)
76	YY_MCH	ss5804320509	Oct 12, 2022 (156)
77	EVA	ss5826594465	Oct 12, 2022 (156)
78	EVA	ss5853873239	Oct 12, 2022 (156)
79	EVA	ss5871348581	Oct 12, 2022 (156)
80	EVA	ss5961716264	Oct 12, 2022 (156)
81	EVA	ss5980178851	Oct 12, 2022 (156)
82	1000Genomes	NC_000003.11 - 143371607	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000003.12 - 143652765	Oct 12, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 143371607	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000003.11 - 143371607	Oct 12, 2018 (152)
86	gnomAD - Genomes	NC_000003.12 - 143652765	Apr 26, 2021 (155)
87	Genome of the Netherlands Release 5	NC_000003.11 - 143371607	Apr 25, 2020 (154)
88	HapMap	NC_000003.12 - 143652765	Apr 25, 2020 (154)
89	KOREAN population from KRGDB	NC_000003.11 - 143371607	Apr 25, 2020 (154)
90	Korean Genome Project	NC_000003.12 - 143652765	Apr 25, 2020 (154)
91	Northern Sweden	NC_000003.11 - 143371607	Jul 13, 2019 (153)
92	Qatari	NC_000003.11 - 143371607	Apr 25, 2020 (154)
93	SGDP_PRJ	NC_000003.11 - 143371607	Apr 25, 2020 (154)
94	Siberian	NC_000003.11 - 143371607	Apr 25, 2020 (154)
95	8.3KJPN	NC_000003.11 - 143371607	Apr 26, 2021 (155)
96	14KJPN	NC_000003.12 - 143652765	Oct 12, 2022 (156)
97	TopMed	NC_000003.12 - 143652765	Apr 26, 2021 (155)
98	UK 10K study - Twins	NC_000003.11 - 143371607	Oct 12, 2018 (152)
99	A Vietnamese Genetic Variation Database	NC_000003.11 - 143371607	Jul 13, 2019 (153)
100	ALFA	NC_000003.12 - 143652765	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)
rs1534156	Apr 12, 2001 (94)
rs58118484	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10363103, ss3903185709	NC_000003.11:143371606:T:A	NC_000003.12:143652764:T:A	(self)
ss77131256, ss81608378	NC_000003.9:144854304:T:C	NC_000003.12:143652764:T:C	(self)
ss92308383, ss111051181, ss112533809, ss117303437, ss162680426, ss164472809, ss167276985, ss203287257, ss206077937, ss253562294, ss277381921, ss284763517, ss292929969	NC_000003.10:144854296:T:C	NC_000003.12:143652764:T:C	(self)
17778352, 9901685, 6997978, 4348317, 10363103, 3708060, 4514139, 9166462, 2419118, 19944668, 9901685, 2158475, ss220471435, ss232064314, ss239429370, ss556996743, ss650725104, ss979248852, ss1070895673, ss1306503232, ss1429613066, ss1608395634, ss1651389667, ss1800150856, ss1922472209, ss1969541723, ss2021806298, ss2149902764, ss2625404979, ss2705315683, ss2800117302, ss2993334725, ss3345305082, ss3661259730, ss3730423195, ss3760799192, ss3784486445, ss3789976400, ss3794850973, ss3828116709, ss3837491234, ss3857149482, ss3903185709, ss5161975361, ss5343822955, ss5507233055, ss5633358124, ss5826594465, ss5961716264, ss5980178851	NC_000003.11:143371606:T:C	NC_000003.12:143652764:T:C	(self)
23446850, 126320156, 2473829, 8961270, 28805831, 424013188, 4766308927, ss2256539891, ss3024670668, ss3647544814, ss3710455563, ss3803930867, ss3842922378, ss3952583269, ss4586635633, ss5256326529, ss5455434510, ss5535920915, ss5694968727, ss5804320509, ss5853873239, ss5871348581	NC_000003.12:143652764:T:C	NC_000003.12:143652764:T:C	(self)
ss17735985, ss21949465	NT_005612.14:49866760:T:C	NC_000003.12:143652764:T:C	(self)
ss1871753, ss2375310, ss3803034, ss5554277, ss5860716, ss23946257, ss99138311, ss106303023, ss135483363, ss139200148, ss156287586	NT_005612.16:49866752:T:C	NC_000003.12:143652764:T:C	(self)
10363103, ss3903185709	NC_000003.11:143371606:T:G	NC_000003.12:143652764: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 rs1242067

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

rs1242067