Name: rs6665822
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.

rs6665822

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:155130671 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.443511 (117393/264690, TOPMED)
A=0.42586 (12039/28270, ALFA)
C=0.06373 (1800/28244, 14KJPN) (+ 16 more)
C=0.06235 (1045/16760, 8.3KJPN)
C=0.3648 (2336/6404, 1000G_30x)
C=0.3608 (1807/5008, 1000G)
A=0.4518 (2024/4480, Estonian)
A=0.4883 (1882/3854, ALSPAC)
A=0.4617 (1712/3708, TWINSUK)
C=0.0829 (243/2930, KOREAN)
C=0.3451 (653/1892, HapMap)
A=0.460 (459/998, GoNL)
A=0.458 (275/600, NorthernSweden)
C=0.235 (107/456, SGDP_PRJ)
A=0.366 (79/216, Qatari)
C=0.173 (37/214, Vietnamese)
C=0.29 (14/48, Siberian)
C=0.50 (20/40, GENOME_DK)
A=0.50 (20/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: EFNA1 : 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	28364	C=0.57435	A=0.42565, G=0.00000, T=0.00000
European	Sub	25644	C=0.57249	A=0.42751, G=0.00000, T=0.00000
African	Sub	698	C=0.670	A=0.330, G=0.000, T=0.000
African Others	Sub	22	C=0.55	A=0.45, G=0.00, T=0.00
African American	Sub	676	C=0.675	A=0.325, G=0.000, T=0.000
Asian	Sub	22	C=0.23	A=0.77, G=0.00, T=0.00
East Asian	Sub	16	C=0.06	A=0.94, G=0.00, T=0.00
Other Asian	Sub	6	C=0.7	A=0.3, G=0.0, T=0.0
Latin American 1	Sub	56	C=0.80	A=0.20, G=0.00, T=0.00
Latin American 2	Sub	148	C=0.649	A=0.351, G=0.000, T=0.000
South Asian	Sub	52	C=0.85	A=0.15, G=0.00, T=0.00
Other	Sub	1744	C=0.5459	A=0.4541, G=0.0000, T=0.0000

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	C=0.443511	A=0.556489
Allele Frequency Aggregator	Total	Global	28270	C=0.57414	A=0.42586, G=0.00000, T=0.00000
Allele Frequency Aggregator	European	Sub	25568	C=0.57236	A=0.42764, G=0.00000, T=0.00000
Allele Frequency Aggregator	Other	Sub	1726	C=0.5440	A=0.4560, G=0.0000, T=0.0000
Allele Frequency Aggregator	African	Sub	698	C=0.670	A=0.330, G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	148	C=0.649	A=0.351, G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	56	C=0.80	A=0.20, G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	52	C=0.85	A=0.15, G=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	22	C=0.23	A=0.77, G=0.00, T=0.00
14KJPN	JAPANESE	Study-wide	28244	C=0.06373	A=0.93627
8.3KJPN	JAPANESE	Study-wide	16760	C=0.06235	A=0.93765
1000Genomes_30x	Global	Study-wide	6404	C=0.3648	A=0.6352
1000Genomes_30x	African	Sub	1786	C=0.3544	A=0.6456
1000Genomes_30x	Europe	Sub	1266	C=0.5387	A=0.4613
1000Genomes_30x	South Asian	Sub	1202	C=0.4676	A=0.5324
1000Genomes_30x	East Asian	Sub	1170	C=0.0863	A=0.9137
1000Genomes_30x	American	Sub	980	C=0.365	A=0.635
1000Genomes	Global	Study-wide	5008	C=0.3608	A=0.6392
1000Genomes	African	Sub	1322	C=0.3616	A=0.6384
1000Genomes	East Asian	Sub	1008	C=0.0863	A=0.9137
1000Genomes	Europe	Sub	1006	C=0.5308	A=0.4692
1000Genomes	South Asian	Sub	978	C=0.467	A=0.533
1000Genomes	American	Sub	694	C=0.362	A=0.638
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5482	A=0.4518
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5117	A=0.4883
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5383	A=0.4617
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0829	A=0.9171, G=0.0000
HapMap	Global	Study-wide	1892	C=0.3451	A=0.6549
HapMap	American	Sub	770	C=0.401	A=0.599
HapMap	African	Sub	692	C=0.325	A=0.675
HapMap	Asian	Sub	254	C=0.067	A=0.933
HapMap	Europe	Sub	176	C=0.580	A=0.420
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.540	A=0.460
Northern Sweden	ACPOP	Study-wide	600	C=0.542	A=0.458
SGDP_PRJ	Global	Study-wide	456	C=0.235	A=0.765
Qatari	Global	Study-wide	216	C=0.634	A=0.366
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.173	A=0.827
Siberian	Global	Study-wide	48	C=0.29	A=0.71
The Danish reference pan genome	Danish	Study-wide	40	C=0.50	A=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 1	NC_000001.11:g.155130671C>A
GRCh38.p14 chr 1	NC_000001.11:g.155130671C>G
GRCh38.p14 chr 1	NC_000001.11:g.155130671C>T
GRCh37.p13 chr 1	NC_000001.10:g.155103147C>A
GRCh37.p13 chr 1	NC_000001.10:g.155103147C>G
GRCh37.p13 chr 1	NC_000001.10:g.155103147C>T

Gene: EFNA1, ephrin A1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EFNA1 transcript variant 1	NM_004428.3:c.93-668C>A	N/A	Intron Variant
EFNA1 transcript variant 2	NM_182685.2:c.93-668C>A	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	C=	A	G	T
GRCh38.p14 chr 1	NC_000001.11:g.155130671=	NC_000001.11:g.155130671C>A	NC_000001.11:g.155130671C>G	NC_000001.11:g.155130671C>T
GRCh37.p13 chr 1	NC_000001.10:g.155103147=	NC_000001.10:g.155103147C>A	NC_000001.10:g.155103147C>G	NC_000001.10:g.155103147C>T
EFNA1 transcript variant 1	NM_004428.2:c.93-668=	NM_004428.2:c.93-668C>A	NM_004428.2:c.93-668C>G	NM_004428.2:c.93-668C>T
EFNA1 transcript variant 1	NM_004428.3:c.93-668=	NM_004428.3:c.93-668C>A	NM_004428.3:c.93-668C>G	NM_004428.3:c.93-668C>T
EFNA1 transcript variant 2	NM_182685.1:c.93-668=	NM_182685.1:c.93-668C>A	NM_182685.1:c.93-668C>G	NM_182685.1:c.93-668C>T
EFNA1 transcript variant 2	NM_182685.2:c.93-668=	NM_182685.2:c.93-668C>A	NM_182685.2:c.93-668C>G	NM_182685.2:c.93-668C>T

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#.

89 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9827330	Jul 11, 2003 (116)
2	CSHL-HAPMAP	ss19834163	Feb 27, 2004 (120)
3	SSAHASNP	ss20506554	Apr 05, 2004 (121)
4	ILLUMINA	ss75034430	Dec 06, 2007 (129)
5	BCMHGSC_JDW	ss87825815	Mar 23, 2008 (129)
6	HUMANGENOME_JCVI	ss99251426	Feb 06, 2009 (130)
7	BGI	ss102785949	Dec 01, 2009 (131)
8	1000GENOMES	ss108602163	Jan 23, 2009 (130)
9	1000GENOMES	ss111159362	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss119034268	Feb 15, 2009 (130)
11	KRIBB_YJKIM	ss119519821	Dec 01, 2009 (131)
12	ENSEMBL	ss139415865	Dec 01, 2009 (131)
13	GMI	ss155757244	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss164127277	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss165226341	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss167138148	Jul 04, 2010 (132)
17	BUSHMAN	ss199090714	Jul 04, 2010 (132)
18	1000GENOMES	ss218652944	Jul 14, 2010 (132)
19	1000GENOMES	ss230733204	Jul 14, 2010 (132)
20	1000GENOMES	ss238380748	Jul 15, 2010 (132)
21	GMI	ss276052338	May 04, 2012 (137)
22	GMI	ss284153275	Apr 25, 2013 (138)
23	PJP	ss290637767	May 09, 2011 (134)
24	ILLUMINA	ss482107784	May 04, 2012 (137)
25	ILLUMINA	ss484266993	May 04, 2012 (137)
26	ILLUMINA	ss536451998	Sep 08, 2015 (146)
27	TISHKOFF	ss554699787	Apr 25, 2013 (138)
28	SSMP	ss648416106	Apr 25, 2013 (138)
29	ILLUMINA	ss780589488	Sep 08, 2015 (146)
30	ILLUMINA	ss782579537	Sep 08, 2015 (146)
31	ILLUMINA	ss836082351	Sep 08, 2015 (146)
32	EVA-GONL	ss975686017	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1068271913	Aug 21, 2014 (142)
34	1000GENOMES	ss1292939744	Aug 21, 2014 (142)
35	DDI	ss1425979935	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1574394153	Apr 01, 2015 (144)
37	EVA_DECODE	ss1585067673	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1601221617	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1644215650	Apr 01, 2015 (144)
40	EVA_SVP	ss1712371242	Apr 01, 2015 (144)
41	HAMMER_LAB	ss1795097205	Sep 08, 2015 (146)
42	WEILL_CORNELL_DGM	ss1918919931	Feb 12, 2016 (147)
43	GENOMED	ss1966868218	Jul 19, 2016 (147)
44	JJLAB	ss2019975437	Sep 14, 2016 (149)
45	ILLUMINA	ss2094848755	Dec 20, 2016 (150)
46	ILLUMINA	ss2094976661	Dec 20, 2016 (150)
47	USC_VALOUEV	ss2148000243	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2166572228	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2624495674	Nov 08, 2017 (151)
50	ILLUMINA	ss2632576652	Nov 08, 2017 (151)
51	GRF	ss2697973066	Nov 08, 2017 (151)
52	GNOMAD	ss2761358091	Nov 08, 2017 (151)
53	AFFY	ss2984879621	Nov 08, 2017 (151)
54	AFFY	ss2985525260	Nov 08, 2017 (151)
55	SWEGEN	ss2987757691	Nov 08, 2017 (151)
56	BIOINF_KMB_FNS_UNIBA	ss3023744926	Nov 08, 2017 (151)
57	CSHL	ss3343712084	Nov 08, 2017 (151)
58	ILLUMINA	ss3626209530	Oct 11, 2018 (152)
59	ILLUMINA	ss3630609516	Oct 11, 2018 (152)
60	ILLUMINA	ss3641616917	Oct 11, 2018 (152)
61	ILLUMINA	ss3642796872	Oct 11, 2018 (152)
62	URBANLAB	ss3646791992	Oct 11, 2018 (152)
63	ILLUMINA	ss3651471344	Oct 11, 2018 (152)
64	ILLUMINA	ss3653648830	Oct 11, 2018 (152)
65	EGCUT_WGS	ss3655698259	Jul 12, 2019 (153)
66	EVA_DECODE	ss3687789708	Jul 12, 2019 (153)
67	ACPOP	ss3727488478	Jul 12, 2019 (153)
68	EVA	ss3746812512	Jul 12, 2019 (153)
69	PACBIO	ss3783567274	Jul 12, 2019 (153)
70	PACBIO	ss3789198625	Jul 12, 2019 (153)
71	PACBIO	ss3794070632	Jul 12, 2019 (153)
72	KHV_HUMAN_GENOMES	ss3799813598	Jul 12, 2019 (153)
73	EVA	ss3826425853	Apr 25, 2020 (154)
74	SGDP_PRJ	ss3850013449	Apr 25, 2020 (154)
75	KRGDB	ss3895221604	Apr 25, 2020 (154)
76	TOPMED	ss4468435002	Apr 25, 2021 (155)
77	TOMMO_GENOMICS	ss5146500458	Apr 25, 2021 (155)
78	1000G_HIGH_COVERAGE	ss5244305147	Oct 12, 2022 (156)
79	EVA	ss5314651331	Oct 12, 2022 (156)
80	EVA	ss5322073377	Oct 12, 2022 (156)
81	HUGCELL_USP	ss5444897457	Oct 12, 2022 (156)
82	1000G_HIGH_COVERAGE	ss5517639752	Oct 12, 2022 (156)
83	SANFORD_IMAGENETICS	ss5626598085	Oct 12, 2022 (156)
84	TOMMO_GENOMICS	ss5673701726	Oct 12, 2022 (156)
85	YY_MCH	ss5801263052	Oct 12, 2022 (156)
86	EVA	ss5832670140	Oct 12, 2022 (156)
87	EVA	ss5849110097	Oct 12, 2022 (156)
88	EVA	ss5910260006	Oct 12, 2022 (156)
89	EVA	ss5938392334	Oct 12, 2022 (156)
90	1000Genomes	NC_000001.10 - 155103147	Oct 11, 2018 (152)
91	1000Genomes_30x	NC_000001.11 - 155130671	Oct 12, 2022 (156)
92	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 155103147	Oct 11, 2018 (152)
93	Genetic variation in the Estonian population	NC_000001.10 - 155103147	Oct 11, 2018 (152)
94	The Danish reference pan genome	NC_000001.10 - 155103147	Apr 25, 2020 (154)
95	gnomAD - Genomes Submission ignored due to conflicting rows: Row 27160119 (NC_000001.11:155130670:C:A 75147/139682) Row 27160120 (NC_000001.11:155130670:C:T 2/139770)	-	Apr 25, 2021 (155)
96	gnomAD - Genomes Submission ignored due to conflicting rows: Row 27160119 (NC_000001.11:155130670:C:A 75147/139682) Row 27160120 (NC_000001.11:155130670:C:T 2/139770)	-	Apr 25, 2021 (155)
97	Genome of the Netherlands Release 5	NC_000001.10 - 155103147	Apr 25, 2020 (154)
98	HapMap	NC_000001.11 - 155130671	Apr 25, 2020 (154)
99	KOREAN population from KRGDB	NC_000001.10 - 155103147	Apr 25, 2020 (154)
100	Northern Sweden	NC_000001.10 - 155103147	Jul 12, 2019 (153)
101	Qatari	NC_000001.10 - 155103147	Apr 25, 2020 (154)
102	SGDP_PRJ	NC_000001.10 - 155103147	Apr 25, 2020 (154)
103	Siberian	NC_000001.10 - 155103147	Apr 25, 2020 (154)
104	8.3KJPN	NC_000001.10 - 155103147	Apr 25, 2021 (155)
105	14KJPN	NC_000001.11 - 155130671	Oct 12, 2022 (156)
106	TopMed	NC_000001.11 - 155130671	Apr 25, 2021 (155)
107	UK 10K study - Twins	NC_000001.10 - 155103147	Oct 11, 2018 (152)
108	A Vietnamese Genetic Variation Database	NC_000001.10 - 155103147	Jul 12, 2019 (153)
109	ALFA	NC_000001.11 - 155130671	Apr 25, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss87825815, ss108602163, ss111159362, ss119034268, ss164127277, ss165226341, ss167138148, ss199090714, ss276052338, ss284153275, ss290637767, ss482107784, ss1585067673, ss1712371242, ss2094848755, ss3642796872	NC_000001.9:153369770:C:A	NC_000001.11:155130670:C:A	(self)
3732251, 2029618, 1436507, 1709893, 881440, 2398998, 773343, 961861, 2030429, 516597, 4469765, 2029618, 435954, ss218652944, ss230733204, ss238380748, ss484266993, ss536451998, ss554699787, ss648416106, ss780589488, ss782579537, ss836082351, ss975686017, ss1068271913, ss1292939744, ss1425979935, ss1574394153, ss1601221617, ss1644215650, ss1795097205, ss1918919931, ss1966868218, ss2019975437, ss2094976661, ss2148000243, ss2624495674, ss2632576652, ss2697973066, ss2761358091, ss2984879621, ss2985525260, ss2987757691, ss3343712084, ss3626209530, ss3630609516, ss3641616917, ss3651471344, ss3653648830, ss3655698259, ss3727488478, ss3746812512, ss3783567274, ss3789198625, ss3794070632, ss3826425853, ss3850013449, ss3895221604, ss5146500458, ss5314651331, ss5322073377, ss5626598085, ss5832670140, ss5938392334	NC_000001.10:155103146:C:A	NC_000001.11:155130670:C:A	(self)
5165687, 177181, 7538830, 32041337, 4123254355, ss2166572228, ss3023744926, ss3646791992, ss3687789708, ss3799813598, ss4468435002, ss5244305147, ss5444897457, ss5517639752, ss5673701726, ss5801263052, ss5849110097, ss5910260006	NC_000001.11:155130670:C:A	NC_000001.11:155130670:C:A	(self)
ss75034430, ss99251426, ss102785949, ss119519821, ss139415865, ss155757244	NT_004487.19:6591788:C:A	NC_000001.11:155130670:C:A	(self)
ss9827330	NT_004668.15:1552978:C:A	NC_000001.11:155130670:C:A	(self)
ss19834163, ss20506554	NT_079484.1:1552978:C:A	NC_000001.11:155130670:C:A	(self)
2398998, ss2761358091, ss3895221604	NC_000001.10:155103146:C:G	NC_000001.11:155130670:C:G	(self)
4123254355	NC_000001.11:155130670:C:G	NC_000001.11:155130670:C:G	(self)
4123254355	NC_000001.11:155130670:C:T	NC_000001.11:155130670:C:T	(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 rs6665822

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

rs6665822