Name: rs9503922
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.

rs9503922

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:4121099 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.230908 (61119/264690, TOPMED)
T=0.235607 (33002/140072, GnomAD)
T=0.00591 (167/28258, 14KJPN) (+ 19 more)
T=0.14796 (2824/19086, ALFA)
T=0.00585 (98/16760, 8.3KJPN)
T=0.1772 (1135/6404, 1000G_30x)
T=0.1723 (863/5008, 1000G)
T=0.1855 (831/4480, Estonian)
T=0.2693 (1038/3854, ALSPAC)
T=0.2659 (986/3708, TWINSUK)
T=0.0062 (18/2922, KOREAN)
T=0.0038 (7/1832, Korea1K)
T=0.1824 (324/1776, HapMap)
T=0.290 (289/998, GoNL)
T=0.212 (133/626, Chileans)
T=0.242 (145/600, NorthernSweden)
T=0.222 (48/216, Qatari)
T=0.019 (4/216, Vietnamese)
C=0.420 (47/112, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
C=0.5 (4/8, Siberian)
T=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ECI2 : Intron Variant
C6orf201 : Intron Variant
Publications: 1 citation
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	19086	C=0.85204	A=0.00000, T=0.14796	0.73436	0.030284	0.235356	23
European	Sub	12380	C=0.84426	A=0.00000, T=0.15574	0.721486	0.032956	0.245557	15
African	Sub	2592	C=0.8866	A=0.0000, T=0.1134	0.795525	0.022377	0.182099	7
African Others	Sub	92	C=0.86	A=0.00, T=0.14	0.76087	0.043478	0.195652	1
African American	Sub	2500	C=0.8876	A=0.0000, T=0.1124	0.7968	0.0216	0.1816	6
Asian	Sub	144	C=0.986	A=0.000, T=0.014	0.972222	0.0	0.027778	0
East Asian	Sub	94	C=0.98	A=0.00, T=0.02	0.957447	0.0	0.042553	0
Other Asian	Sub	50	C=1.00	A=0.00, T=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	220	C=0.886	A=0.000, T=0.114	0.790909	0.018182	0.190909	0
Latin American 2	Sub	2546	C=0.8417	A=0.0000, T=0.1583	0.713276	0.029851	0.256874	1
South Asian	Sub	84	C=0.93	A=0.00, T=0.07	0.857143	0.0	0.142857	0
Other	Sub	1120	C=0.8518	A=0.0000, T=0.1482	0.732143	0.028571	0.239286	1

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=0.769092	T=0.230908
gnomAD - Genomes	Global	Study-wide	140072	C=0.764393	T=0.235607
gnomAD - Genomes	European	Sub	75866	C=0.74774	T=0.25226
gnomAD - Genomes	African	Sub	41950	C=0.76596	T=0.23404
gnomAD - Genomes	American	Sub	13646	C=0.79408	T=0.20592
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.7987	T=0.2013
gnomAD - Genomes	East Asian	Sub	3132	C=0.9789	T=0.0211
gnomAD - Genomes	Other	Sub	2154	C=0.7674	T=0.2326
14KJPN	JAPANESE	Study-wide	28258	C=0.99409	T=0.00591
Allele Frequency Aggregator	Total	Global	19086	C=0.85204	A=0.00000, T=0.14796
Allele Frequency Aggregator	European	Sub	12380	C=0.84426	A=0.00000, T=0.15574
Allele Frequency Aggregator	African	Sub	2592	C=0.8866	A=0.0000, T=0.1134
Allele Frequency Aggregator	Latin American 2	Sub	2546	C=0.8417	A=0.0000, T=0.1583
Allele Frequency Aggregator	Other	Sub	1120	C=0.8518	A=0.0000, T=0.1482
Allele Frequency Aggregator	Latin American 1	Sub	220	C=0.886	A=0.000, T=0.114
Allele Frequency Aggregator	Asian	Sub	144	C=0.986	A=0.000, T=0.014
Allele Frequency Aggregator	South Asian	Sub	84	C=0.93	A=0.00, T=0.07
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99415	T=0.00585
1000Genomes_30x	Global	Study-wide	6404	C=0.8228	T=0.1772
1000Genomes_30x	African	Sub	1786	C=0.7520	T=0.2480
1000Genomes_30x	Europe	Sub	1266	C=0.7251	T=0.2749
1000Genomes_30x	South Asian	Sub	1202	C=0.8810	T=0.1190
1000Genomes_30x	East Asian	Sub	1170	C=0.9795	T=0.0205
1000Genomes_30x	American	Sub	980	C=0.819	T=0.181
1000Genomes	Global	Study-wide	5008	C=0.8277	T=0.1723
1000Genomes	African	Sub	1322	C=0.7542	T=0.2458
1000Genomes	East Asian	Sub	1008	C=0.9812	T=0.0188
1000Genomes	Europe	Sub	1006	C=0.7237	T=0.2763
1000Genomes	South Asian	Sub	978	C=0.883	T=0.117
1000Genomes	American	Sub	694	C=0.817	T=0.183
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8145	T=0.1855
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7307	T=0.2693
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7341	T=0.2659
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9938	T=0.0062
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9962	T=0.0038
HapMap	Global	Study-wide	1776	C=0.8176	T=0.1824
HapMap	African	Sub	684	C=0.788	T=0.212
HapMap	American	Sub	668	C=0.828	T=0.172
HapMap	Asian	Sub	250	C=0.988	T=0.012
HapMap	Europe	Sub	174	C=0.649	T=0.351
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.710	T=0.290
Chileans	Chilean	Study-wide	626	C=0.788	T=0.212
Northern Sweden	ACPOP	Study-wide	600	C=0.758	T=0.242
Qatari	Global	Study-wide	216	C=0.778	T=0.222
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.981	T=0.019
SGDP_PRJ	Global	Study-wide	112	C=0.420	T=0.580
The Danish reference pan genome	Danish	Study-wide	40	C=0.82	T=0.17
Siberian	Global	Study-wide	8	C=0.5	T=0.5

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.4121099C>A
GRCh38.p14 chr 6	NC_000006.12:g.4121099C>T
GRCh37.p13 chr 6	NC_000006.11:g.4121333C>A
GRCh37.p13 chr 6	NC_000006.11:g.4121333C>T

Gene: ECI2, enoyl-CoA delta isomerase 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ECI2 transcript variant 3	NM_001166010.2:c.706-1824… NM_001166010.2:c.706-1824G>T	N/A	Intron Variant
ECI2 transcript variant 1	NM_006117.3:c.706-1824G>T	N/A	Intron Variant
ECI2 transcript variant 2	NM_206836.3:c.796-1824G>T	N/A	Intron Variant
ECI2 transcript variant 4	NR_028588.2:n.	N/A	Intron Variant

Gene: C6orf201, chromosome 6 open reading frame 201 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TEX56P transcript variant 2	NR_104463.3:n.	N/A	Intron Variant
TEX56P transcript variant 3	NR_104464.3:n.	N/A	Intron Variant
TEX56P transcript variant 1	NR_172627.1:n.	N/A	Intron Variant
TEX56P transcript variant 4	NR_172628.1: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	C=	A	T
GRCh38.p14 chr 6	NC_000006.12:g.4121099=	NC_000006.12:g.4121099C>A	NC_000006.12:g.4121099C>T
GRCh37.p13 chr 6	NC_000006.11:g.4121333=	NC_000006.11:g.4121333C>A	NC_000006.11:g.4121333C>T
C6orf201 transcript variant 1	NM_001085401.2:c.285-850=	NM_001085401.2:c.285-850C>A	NM_001085401.2:c.285-850C>T
ECI2 transcript variant 3	NM_001166010.1:c.706-1824=	NM_001166010.1:c.706-1824G>T	NM_001166010.1:c.706-1824G>A
ECI2 transcript variant 3	NM_001166010.2:c.706-1824=	NM_001166010.2:c.706-1824G>T	NM_001166010.2:c.706-1824G>A
ECI2 transcript variant 1	NM_006117.2:c.706-1824=	NM_006117.2:c.706-1824G>T	NM_006117.2:c.706-1824G>A
ECI2 transcript variant 1	NM_006117.3:c.706-1824=	NM_006117.3:c.706-1824G>T	NM_006117.3:c.706-1824G>A
ECI2 transcript variant 2	NM_206836.2:c.796-1824=	NM_206836.2:c.796-1824G>T	NM_206836.2:c.796-1824G>A
ECI2 transcript variant 2	NM_206836.3:c.796-1824=	NM_206836.3:c.796-1824G>T	NM_206836.3:c.796-1824G>A

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#.

65 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss13153813	Dec 05, 2003 (119)
2	SSAHASNP	ss22458878	Apr 05, 2004 (121)
3	ABI	ss42672954	Mar 15, 2006 (126)
4	AFFY	ss66413909	Dec 01, 2006 (127)
5	AFFY	ss76174207	Dec 07, 2007 (129)
6	KRIBB_YJKIM	ss82587762	Dec 14, 2007 (130)
7	BCMHGSC_JDW	ss93373325	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss98468874	Feb 05, 2009 (130)
9	1000GENOMES	ss109707369	Jan 24, 2009 (130)
10	1000GENOMES	ss113820142	Jan 25, 2009 (130)
11	ENSEMBL	ss143695782	Dec 01, 2009 (131)
12	ENSEMBL	ss144182364	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss161974679	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss163075839	Jul 04, 2010 (132)
15	BUSHMAN	ss201347481	Jul 04, 2010 (132)
16	1000GENOMES	ss222176978	Jul 14, 2010 (132)
17	1000GENOMES	ss233300376	Jul 14, 2010 (132)
18	BL	ss253997346	May 09, 2011 (134)
19	PJP	ss293587246	May 09, 2011 (134)
20	TISHKOFF	ss558966103	Apr 25, 2013 (138)
21	SSMP	ss652876317	Apr 25, 2013 (138)
22	EVA-GONL	ss982526091	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1073337364	Aug 21, 2014 (142)
24	1000GENOMES	ss1318755539	Aug 21, 2014 (142)
25	DDI	ss1430619318	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1581508375	Apr 01, 2015 (144)
27	EVA_DECODE	ss1592072223	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1614831733	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1657825766	Apr 01, 2015 (144)
30	EVA_SVP	ss1712830833	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1804254195	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1925784124	Feb 12, 2016 (147)
33	GENOMED	ss1970296662	Jul 19, 2016 (147)
34	JJLAB	ss2023506559	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2151668578	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2281347298	Dec 20, 2016 (150)
37	GNOMAD	ss2835190454	Nov 08, 2017 (151)
38	SWEGEN	ss2998427113	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3025536809	Nov 08, 2017 (151)
40	CSHL	ss3346809371	Nov 08, 2017 (151)
41	URBANLAB	ss3648255628	Oct 12, 2018 (152)
42	EGCUT_WGS	ss3666351254	Jul 13, 2019 (153)
43	EVA_DECODE	ss3716473826	Jul 13, 2019 (153)
44	ACPOP	ss3733153689	Jul 13, 2019 (153)
45	EVA	ss3764543959	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3807705154	Jul 13, 2019 (153)
47	EVA	ss3829702064	Apr 26, 2020 (154)
48	EVA	ss3838325269	Apr 26, 2020 (154)
49	EVA	ss3843765157	Apr 26, 2020 (154)
50	SGDP_PRJ	ss3863803587	Apr 26, 2020 (154)
51	KRGDB	ss3910537860	Apr 26, 2020 (154)
52	KOGIC	ss3958394640	Apr 26, 2020 (154)
53	TOPMED	ss4691874636	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5175916810	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5267209099	Oct 13, 2022 (156)
56	EVA	ss5363462984	Oct 13, 2022 (156)
57	HUGCELL_USP	ss5465020765	Oct 13, 2022 (156)
58	EVA	ss5508330563	Oct 13, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5552544781	Oct 13, 2022 (156)
60	SANFORD_IMAGENETICS	ss5639657226	Oct 13, 2022 (156)
61	TOMMO_GENOMICS	ss5713513743	Oct 13, 2022 (156)
62	YY_MCH	ss5807103435	Oct 13, 2022 (156)
63	EVA	ss5841717294	Oct 13, 2022 (156)
64	EVA	ss5882434380	Oct 13, 2022 (156)
65	EVA	ss5968151045	Oct 13, 2022 (156)
66	1000Genomes	NC_000006.11 - 4121333	Oct 12, 2018 (152)
67	1000Genomes_30x	NC_000006.12 - 4121099	Oct 13, 2022 (156)
68	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 4121333	Oct 12, 2018 (152)
69	Chileans	NC_000006.11 - 4121333	Apr 26, 2020 (154)
70	Genetic variation in the Estonian population	NC_000006.11 - 4121333	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000006.11 - 4121333	Apr 26, 2020 (154)
72	gnomAD - Genomes	NC_000006.12 - 4121099	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000006.11 - 4121333	Apr 26, 2020 (154)
74	HapMap	NC_000006.12 - 4121099	Apr 26, 2020 (154)
75	KOREAN population from KRGDB	NC_000006.11 - 4121333	Apr 26, 2020 (154)
76	Korean Genome Project	NC_000006.12 - 4121099	Apr 26, 2020 (154)
77	Northern Sweden	NC_000006.11 - 4121333	Jul 13, 2019 (153)
78	Qatari	NC_000006.11 - 4121333	Apr 26, 2020 (154)
79	SGDP_PRJ	NC_000006.11 - 4121333	Apr 26, 2020 (154)
80	Siberian	NC_000006.11 - 4121333	Apr 26, 2020 (154)
81	8.3KJPN	NC_000006.11 - 4121333	Apr 26, 2021 (155)
82	14KJPN	NC_000006.12 - 4121099	Oct 13, 2022 (156)
83	TopMed	NC_000006.12 - 4121099	Apr 26, 2021 (155)
84	UK 10K study - Twins	NC_000006.11 - 4121333	Oct 12, 2018 (152)
85	A Vietnamese Genetic Variation Database	NC_000006.11 - 4121333	Jul 13, 2019 (153)
86	ALFA	NC_000006.12 - 4121099	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)
rs56826968	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
4040225681	NC_000006.12:4121098:C:A	NC_000006.12:4121098:C:A	(self)
ss66413909, ss76174207, ss93373325, ss109707369, ss113820142, ss161974679, ss163075839, ss201347481, ss253997346, ss293587246, ss1592072223, ss1712830833	NC_000006.10:4066331:C:T	NC_000006.12:4121098:C:T	(self)
30489644, 16971255, 369356, 12089502, 7673314, 7532630, 17715254, 6438554, 7826054, 15820567, 4184932, 33886117, 16971255, 3758480, ss222176978, ss233300376, ss558966103, ss652876317, ss982526091, ss1073337364, ss1318755539, ss1430619318, ss1581508375, ss1614831733, ss1657825766, ss1804254195, ss1925784124, ss1970296662, ss2023506559, ss2151668578, ss2835190454, ss2998427113, ss3346809371, ss3666351254, ss3733153689, ss3764543959, ss3829702064, ss3838325269, ss3863803587, ss3910537860, ss5175916810, ss5363462984, ss5508330563, ss5639657226, ss5841717294, ss5968151045	NC_000006.11:4121332:C:T	NC_000006.12:4121098:C:T	(self)
40070716, 215576209, 3047909, 14772641, 47350847, 529252194, 4040225681, ss2281347298, ss3025536809, ss3648255628, ss3716473826, ss3807705154, ss3843765157, ss3958394640, ss4691874636, ss5267209099, ss5465020765, ss5552544781, ss5713513743, ss5807103435, ss5882434380	NC_000006.12:4121098:C:T	NC_000006.12:4121098:C:T	(self)
ss42672954, ss82587762, ss98468874, ss143695782, ss144182364	NT_007592.15:4061332:C:T	NC_000006.12:4121098:C:T	(self)
ss13153813	NT_034880.2:4061331:C:T	NC_000006.12:4121098:C:T	(self)
ss22458878	NT_034880.3:4061331:C:T	NC_000006.12:4121098:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs9503922

PMID	Title	Author	Year	Journal
20877624	Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.	Hendrickson SL et al.	2010	PloS one

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

rs9503922