Name: rs1673004
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.

rs1673004

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:35142599 (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=0.349647 (92548/264690, TOPMED)
G=0.363881 (50923/139944, GnomAD)
G=0.29041 (8204/28250, 14KJPN) (+ 17 more)
G=0.39280 (7911/20140, ALFA)
G=0.28877 (4838/16754, 8.3KJPN)
G=0.3812 (2441/6404, 1000G_30x)
G=0.3818 (1912/5008, 1000G)
G=0.4884 (2187/4478, Estonian)
G=0.3731 (1438/3854, ALSPAC)
G=0.3681 (1365/3708, TWINSUK)
G=0.2971 (870/2928, KOREAN)
G=0.3270 (599/1832, Korea1K)
G=0.402 (241/600, NorthernSweden)
G=0.144 (77/534, MGP)
G=0.336 (109/324, HapMap)
C=0.377 (114/302, SGDP_PRJ)
G=0.403 (87/216, Qatari)
G=0.419 (88/210, Vietnamese)
C=0.31 (15/48, Siberian)
G=0.42 (17/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FXYD1 : Intron Variant
FXYD7 : 2KB Upstream 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	20140	C=0.60720	G=0.39280
European	Sub	15484	C=0.59210	G=0.40790
African	Sub	2960	C=0.6598	G=0.3402
African Others	Sub	114	C=0.675	G=0.325
African American	Sub	2846	C=0.6592	G=0.3408
Asian	Sub	112	C=0.616	G=0.384
East Asian	Sub	86	C=0.64	G=0.36
Other Asian	Sub	26	C=0.54	G=0.46
Latin American 1	Sub	146	C=0.575	G=0.425
Latin American 2	Sub	610	C=0.723	G=0.277
South Asian	Sub	98	C=0.53	G=0.47
Other	Sub	730	C=0.633	G=0.367

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	C=0.650353	G=0.349647
gnomAD - Genomes	Global	Study-wide	139944	C=0.636119	G=0.363881
gnomAD - Genomes	European	Sub	75782	C=0.61859	G=0.38141
gnomAD - Genomes	African	Sub	41934	C=0.64385	G=0.35615
gnomAD - Genomes	American	Sub	13646	C=0.71134	G=0.28866
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.6249	G=0.3751
gnomAD - Genomes	East Asian	Sub	3112	C=0.6115	G=0.3885
gnomAD - Genomes	Other	Sub	2148	C=0.6788	G=0.3212
14KJPN	JAPANESE	Study-wide	28250	C=0.70959	G=0.29041
Allele Frequency Aggregator	Total	Global	20140	C=0.60720	G=0.39280
Allele Frequency Aggregator	European	Sub	15484	C=0.59210	G=0.40790
Allele Frequency Aggregator	African	Sub	2960	C=0.6598	G=0.3402
Allele Frequency Aggregator	Other	Sub	730	C=0.633	G=0.367
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.723	G=0.277
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.575	G=0.425
Allele Frequency Aggregator	Asian	Sub	112	C=0.616	G=0.384
Allele Frequency Aggregator	South Asian	Sub	98	C=0.53	G=0.47
8.3KJPN	JAPANESE	Study-wide	16754	C=0.71123	G=0.28877
1000Genomes_30x	Global	Study-wide	6404	C=0.6188	G=0.3812
1000Genomes_30x	African	Sub	1786	C=0.6657	G=0.3343
1000Genomes_30x	Europe	Sub	1266	C=0.6319	G=0.3681
1000Genomes_30x	South Asian	Sub	1202	C=0.4651	G=0.5349
1000Genomes_30x	East Asian	Sub	1170	C=0.5915	G=0.4085
1000Genomes_30x	American	Sub	980	C=0.738	G=0.262
1000Genomes	Global	Study-wide	5008	C=0.6182	G=0.3818
1000Genomes	African	Sub	1322	C=0.6717	G=0.3283
1000Genomes	East Asian	Sub	1008	C=0.6002	G=0.3998
1000Genomes	Europe	Sub	1006	C=0.6292	G=0.3708
1000Genomes	South Asian	Sub	978	C=0.468	G=0.532
1000Genomes	American	Sub	694	C=0.738	G=0.262
Genetic variation in the Estonian population	Estonian	Study-wide	4478	C=0.5116	G=0.4884
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6269	G=0.3731
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6319	G=0.3681
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.7029	G=0.2971
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6730	G=0.3270
Northern Sweden	ACPOP	Study-wide	600	C=0.598	G=0.402
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.856	G=0.144
HapMap	Global	Study-wide	324	C=0.664	G=0.336
HapMap	African	Sub	118	C=0.610	G=0.390
HapMap	American	Sub	118	C=0.593	G=0.407
HapMap	Asian	Sub	88	C=0.83	G=0.17
SGDP_PRJ	Global	Study-wide	302	C=0.377	G=0.623
Qatari	Global	Study-wide	216	C=0.597	G=0.403
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.581	G=0.419
Siberian	Global	Study-wide	48	C=0.31	G=0.69
The Danish reference pan genome	Danish	Study-wide	40	C=0.57	G=0.42

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 19	NC_000019.10:g.35142599C>G
GRCh37.p13 chr 19	NC_000019.9:g.35633503C>G

Gene: FXYD1, FXYD domain containing ion transport regulator 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FXYD1 transcript variant c	NM_001278717.2:c.256+78C>G	N/A	Intron Variant
FXYD1 transcript variant d	NM_001278718.2:c.256+78C>G	N/A	Intron Variant
FXYD1 transcript variant a	NM_005031.5:c.256+78C>G	N/A	Intron Variant
FXYD1 transcript variant b	NM_021902.4:c.256+78C>G	N/A	Intron Variant
FXYD1 transcript variant X2	XM_017026874.3:c.256+78C>G	N/A	Intron Variant
FXYD1 transcript variant X3	XM_017026875.3:c.310+78C>G	N/A	Intron Variant
FXYD1 transcript variant X4	XM_017026876.3:c.310+78C>G	N/A	Intron Variant
FXYD1 transcript variant X1	XM_047438938.1:c.256+78C>G	N/A	Intron Variant

Gene: FXYD7, FXYD domain containing ion transport regulator 7 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
FXYD7 transcript	NM_022006.2:c.	N/A	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	C=	G
GRCh38.p14 chr 19	NC_000019.10:g.35142599=	NC_000019.10:g.35142599C>G
GRCh37.p13 chr 19	NC_000019.9:g.35633503=	NC_000019.9:g.35633503C>G
FXYD1 transcript variant c	NM_001278717.1:c.256+78=	NM_001278717.1:c.256+78C>G
FXYD1 transcript variant c	NM_001278717.2:c.256+78=	NM_001278717.2:c.256+78C>G
FXYD1 transcript variant d	NM_001278718.1:c.256+78=	NM_001278718.1:c.256+78C>G
FXYD1 transcript variant d	NM_001278718.2:c.256+78=	NM_001278718.2:c.256+78C>G
FXYD1 transcript variant a	NM_005031.4:c.256+78=	NM_005031.4:c.256+78C>G
FXYD1 transcript variant a	NM_005031.5:c.256+78=	NM_005031.5:c.256+78C>G
FXYD1 transcript variant b	NM_021902.3:c.256+78=	NM_021902.3:c.256+78C>G
FXYD1 transcript variant b	NM_021902.4:c.256+78=	NM_021902.4:c.256+78C>G
FXYD1 transcript variant X1	XM_005258991.1:c.310+78=	XM_005258991.1:c.310+78C>G
FXYD1 transcript variant X2	XM_017026874.3:c.256+78=	XM_017026874.3:c.256+78C>G
FXYD1 transcript variant X3	XM_017026875.3:c.310+78=	XM_017026875.3:c.310+78C>G
FXYD1 transcript variant X4	XM_017026876.3:c.310+78=	XM_017026876.3:c.310+78C>G
FXYD1 transcript variant X1	XM_047438938.1:c.256+78=	XM_047438938.1:c.256+78C>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#.

84 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss2500181	Nov 09, 2000 (89)
2	YUSUKE	ss4932274	Aug 28, 2002 (108)
3	CSHL-HAPMAP	ss17624620	Feb 27, 2004 (120)
4	SSAHASNP	ss21521674	Apr 05, 2004 (121)
5	KYUGEN	ss28461771	Sep 20, 2004 (123)
6	ABI	ss44192294	Mar 14, 2006 (126)
7	HGSV	ss84663399	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss90962568	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss96303515	Feb 05, 2009 (130)
10	BGI	ss103436259	Dec 01, 2009 (131)
11	1000GENOMES	ss111338943	Jan 25, 2009 (130)
12	1000GENOMES	ss115090216	Jan 25, 2009 (130)
13	ENSEMBL	ss132757966	Dec 01, 2009 (131)
14	ENSEMBL	ss137659512	Dec 01, 2009 (131)
15	ILLUMINA	ss160382371	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss168149435	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss169642862	Jul 04, 2010 (132)
18	BUSHMAN	ss203743964	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss208517450	Jul 04, 2010 (132)
20	1000GENOMES	ss228126113	Jul 14, 2010 (132)
21	1000GENOMES	ss237666982	Jul 15, 2010 (132)
22	1000GENOMES	ss243874534	Jul 15, 2010 (132)
23	GMI	ss283197073	May 04, 2012 (137)
24	PJP	ss292244765	May 09, 2011 (134)
25	ILLUMINA	ss480746715	Sep 08, 2015 (146)
26	TISHKOFF	ss565963326	Apr 25, 2013 (138)
27	SSMP	ss661824957	Apr 25, 2013 (138)
28	EVA-GONL	ss994266628	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1081881942	Aug 21, 2014 (142)
30	1000GENOMES	ss1363037242	Aug 21, 2014 (142)
31	DDI	ss1428394715	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1578627685	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1637905800	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1680899833	Apr 01, 2015 (144)
35	EVA_DECODE	ss1698320229	Apr 01, 2015 (144)
36	EVA_MGP	ss1711509859	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1809292697	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1937760318	Feb 12, 2016 (147)
39	GENOMED	ss1968637925	Jul 19, 2016 (147)
40	JJLAB	ss2029657967	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2158196428	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2225512097	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2629326240	Nov 08, 2017 (151)
44	GRF	ss2702804797	Nov 08, 2017 (151)
45	GNOMAD	ss2962481139	Nov 08, 2017 (151)
46	SWEGEN	ss3017414035	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3028661584	Nov 08, 2017 (151)
48	CSHL	ss3352288040	Nov 08, 2017 (151)
49	ILLUMINA	ss3636421035	Oct 12, 2018 (152)
50	OMUKHERJEE_ADBS	ss3646534979	Oct 12, 2018 (152)
51	URBANLAB	ss3650910672	Oct 12, 2018 (152)
52	EGCUT_WGS	ss3684189433	Jul 13, 2019 (153)
53	EVA_DECODE	ss3702701964	Jul 13, 2019 (153)
54	ACPOP	ss3743010061	Jul 13, 2019 (153)
55	EVA	ss3756025426	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3821273426	Jul 13, 2019 (153)
57	EVA	ss3835445931	Apr 27, 2020 (154)
58	EVA	ss3841345404	Apr 27, 2020 (154)
59	EVA	ss3846851221	Apr 27, 2020 (154)
60	SGDP_PRJ	ss3888147124	Apr 27, 2020 (154)
61	KRGDB	ss3938239573	Apr 27, 2020 (154)
62	KOGIC	ss3981269005	Apr 27, 2020 (154)
63	FSA-LAB	ss3984151801	Apr 27, 2021 (155)
64	EVA	ss3986792366	Apr 27, 2021 (155)
65	TOPMED	ss5073723292	Apr 27, 2021 (155)
66	EVA	ss5142012221	Apr 27, 2021 (155)
67	TOMMO_GENOMICS	ss5227590792	Apr 27, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5307128757	Oct 16, 2022 (156)
69	EVA	ss5434636563	Oct 16, 2022 (156)
70	HUGCELL_USP	ss5499670134	Oct 16, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5612807054	Oct 16, 2022 (156)
72	EVA	ss5623977454	Oct 16, 2022 (156)
73	EVA	ss5624089200	Oct 16, 2022 (156)
74	SANFORD_IMAGENETICS	ss5662326498	Oct 16, 2022 (156)
75	TOMMO_GENOMICS	ss5786168707	Oct 16, 2022 (156)
76	EVA	ss5800221968	Oct 16, 2022 (156)
77	YY_MCH	ss5817570523	Oct 16, 2022 (156)
78	EVA	ss5840504663	Oct 16, 2022 (156)
79	EVA	ss5848489805	Oct 16, 2022 (156)
80	EVA	ss5852276358	Oct 16, 2022 (156)
81	EVA	ss5927977524	Oct 16, 2022 (156)
82	EVA	ss5936573573	Oct 16, 2022 (156)
83	EVA	ss5953742452	Oct 16, 2022 (156)
84	EVA	ss5981049441	Oct 16, 2022 (156)
85	1000Genomes	NC_000019.9 - 35633503	Oct 12, 2018 (152)
86	1000Genomes_30x	NC_000019.10 - 35142599	Oct 16, 2022 (156)
87	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 35633503	Oct 12, 2018 (152)
88	Genetic variation in the Estonian population	NC_000019.9 - 35633503	Oct 12, 2018 (152)
89	The Danish reference pan genome	NC_000019.9 - 35633503	Apr 27, 2020 (154)
90	gnomAD - Genomes	NC_000019.10 - 35142599	Apr 27, 2021 (155)
91	HapMap	NC_000019.10 - 35142599	Apr 27, 2020 (154)
92	KOREAN population from KRGDB	NC_000019.9 - 35633503	Apr 27, 2020 (154)
93	Korean Genome Project	NC_000019.10 - 35142599	Apr 27, 2020 (154)
94	Medical Genome Project healthy controls from Spanish population	NC_000019.9 - 35633503	Apr 27, 2020 (154)
95	Northern Sweden	NC_000019.9 - 35633503	Jul 13, 2019 (153)
96	Qatari	NC_000019.9 - 35633503	Apr 27, 2020 (154)
97	SGDP_PRJ	NC_000019.9 - 35633503	Apr 27, 2020 (154)
98	Siberian	NC_000019.9 - 35633503	Apr 27, 2020 (154)
99	8.3KJPN	NC_000019.9 - 35633503	Apr 27, 2021 (155)
100	14KJPN	NC_000019.10 - 35142599	Oct 16, 2022 (156)
101	TopMed	NC_000019.10 - 35142599	Apr 27, 2021 (155)
102	UK 10K study - Twins	NC_000019.9 - 35633503	Oct 12, 2018 (152)
103	A Vietnamese Genetic Variation Database	NC_000019.9 - 35633503	Jul 13, 2019 (153)
104	ALFA	NC_000019.10 - 35142599	Apr 27, 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)
rs3746252	Oct 09, 2002 (108)
rs59742235	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84663399, ss90962568, ss111338943, ss115090216, ss160382371, ss168149435, ss169642862, ss203743964, ss208517450, ss283197073, ss292244765, ss1698320229	NC_000019.8:40325342:C:G	NC_000019.10:35142598:C:G	(self)
76439644, 42340102, 29927681, 4810702, 45416967, 625619, 16294926, 19802240, 40164104, 10712782, 85560099, 42340102, 9353216, ss228126113, ss237666982, ss243874534, ss480746715, ss565963326, ss661824957, ss994266628, ss1081881942, ss1363037242, ss1428394715, ss1578627685, ss1637905800, ss1680899833, ss1711509859, ss1809292697, ss1937760318, ss1968637925, ss2029657967, ss2158196428, ss2629326240, ss2702804797, ss2962481139, ss3017414035, ss3352288040, ss3636421035, ss3646534979, ss3684189433, ss3743010061, ss3756025426, ss3835445931, ss3841345404, ss3888147124, ss3938239573, ss3984151801, ss3986792366, ss5227590792, ss5434636563, ss5623977454, ss5624089200, ss5662326498, ss5800221968, ss5840504663, ss5848489805, ss5936573573, ss5953742452, ss5981049441	NC_000019.9:35633502:C:G	NC_000019.10:35142598:C:G	(self)
100332989, 539090159, 1691564, 37647006, 120005811, 289268956, 10791971075, ss2225512097, ss3028661584, ss3650910672, ss3702701964, ss3821273426, ss3846851221, ss3981269005, ss5073723292, ss5142012221, ss5307128757, ss5499670134, ss5612807054, ss5786168707, ss5817570523, ss5852276358, ss5927977524	NC_000019.10:35142598:C:G	NC_000019.10:35142598:C:G	(self)
ss17624620, ss21521674	NT_011109.15:7901720:C:G	NC_000019.10:35142598:C:G	(self)
ss2500181, ss4932274, ss28461771, ss44192294, ss96303515, ss103436259, ss132757966, ss137659512	NT_011109.16:7901720:C:G	NC_000019.10:35142598:C: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 rs1673004

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

rs1673004