Name: rs884409
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.

rs884409

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:171522147 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.218070 (57721/264690, TOPMED)
G=0.224835 (31485/140036, GnomAD)
G=0.11222 (3171/28256, 14KJPN) (+ 20 more)
G=0.20605 (5780/28052, ALFA)
G=0.11229 (1882/16760, 8.3KJPN)
G=0.2317 (1484/6404, 1000G_30x)
G=0.2272 (1138/5008, 1000G)
G=0.2062 (924/4480, Estonian)
G=0.1515 (584/3854, ALSPAC)
G=0.1510 (560/3708, TWINSUK)
G=0.1328 (389/2930, KOREAN)
G=0.1294 (237/1832, Korea1K)
G=0.2011 (224/1114, Daghestan)
G=0.157 (157/998, GoNL)
G=0.155 (93/600, NorthernSweden)
G=0.155 (83/534, MGP)
G=0.261 (84/322, HapMap)
G=0.139 (30/216, Qatari)
G=0.178 (38/214, Vietnamese)
T=0.408 (71/174, SGDP_PRJ)
G=0.17 (7/40, GENOME_DK)
T=0.5 (5/10, Siberian)
G=0.5 (5/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CYBRD1 : 2KB Upstream Variant
Publications: 8 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	28146	T=0.79429	G=0.20571	0.639594	0.05102	0.309387	22
European	Sub	20574	T=0.83275	G=0.16725	0.694372	0.028871	0.276757	0
African	Sub	5580	T=0.6315	G=0.3685	0.403584	0.140502	0.455914	1
African Others	Sub	198	T=0.646	G=0.354	0.414141	0.121212	0.464646	0
African American	Sub	5382	T=0.6310	G=0.3690	0.403196	0.141211	0.455593	1
Asian	Sub	114	T=0.868	G=0.132	0.754386	0.017544	0.22807	0
East Asian	Sub	88	T=0.88	G=0.12	0.772727	0.022727	0.204545	0
Other Asian	Sub	26	T=0.85	G=0.15	0.692308	0.0	0.307692	0
Latin American 1	Sub	146	T=0.856	G=0.144	0.753425	0.041096	0.205479	1
Latin American 2	Sub	610	T=0.933	G=0.067	0.872131	0.006557	0.121311	0
South Asian	Sub	100	T=0.81	G=0.19	0.66	0.04	0.3	0
Other	Sub	1022	T=0.8072	G=0.1928	0.655577	0.041096	0.303327	0

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=0.781930	G=0.218070
gnomAD - Genomes	Global	Study-wide	140036	T=0.775165	G=0.224835
gnomAD - Genomes	European	Sub	75866	T=0.82542	G=0.17458
gnomAD - Genomes	African	Sub	41918	T=0.64547	G=0.35453
gnomAD - Genomes	American	Sub	13646	T=0.84787	G=0.15213
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.8760	G=0.1240
gnomAD - Genomes	East Asian	Sub	3130	T=0.8514	G=0.1486
gnomAD - Genomes	Other	Sub	2154	T=0.8022	G=0.1978
14KJPN	JAPANESE	Study-wide	28256	T=0.88778	G=0.11222
Allele Frequency Aggregator	Total	Global	28052	T=0.79395	G=0.20605
Allele Frequency Aggregator	European	Sub	20498	T=0.83257	G=0.16743
Allele Frequency Aggregator	African	Sub	5580	T=0.6315	G=0.3685
Allele Frequency Aggregator	Other	Sub	1004	T=0.8048	G=0.1952
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.933	G=0.067
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.856	G=0.144
Allele Frequency Aggregator	Asian	Sub	114	T=0.868	G=0.132
Allele Frequency Aggregator	South Asian	Sub	100	T=0.81	G=0.19
8.3KJPN	JAPANESE	Study-wide	16760	T=0.88771	G=0.11229
1000Genomes_30x	Global	Study-wide	6404	T=0.7683	G=0.2317
1000Genomes_30x	African	Sub	1786	T=0.5851	G=0.4149
1000Genomes_30x	Europe	Sub	1266	T=0.8357	G=0.1643
1000Genomes_30x	South Asian	Sub	1202	T=0.8253	G=0.1747
1000Genomes_30x	East Asian	Sub	1170	T=0.8453	G=0.1547
1000Genomes_30x	American	Sub	980	T=0.853	G=0.147
1000Genomes	Global	Study-wide	5008	T=0.7728	G=0.2272
1000Genomes	African	Sub	1322	T=0.5877	G=0.4123
1000Genomes	East Asian	Sub	1008	T=0.8512	G=0.1488
1000Genomes	Europe	Sub	1006	T=0.8320	G=0.1680
1000Genomes	South Asian	Sub	978	T=0.822	G=0.178
1000Genomes	American	Sub	694	T=0.856	G=0.144
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.7937	G=0.2062
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8485	G=0.1515
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8490	G=0.1510
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8672	G=0.1328
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8706	G=0.1294
Genome-wide autozygosity in Daghestan	Global	Study-wide	1114	T=0.7989	G=0.2011
Genome-wide autozygosity in Daghestan	Daghestan	Sub	622	T=0.775	G=0.225
Genome-wide autozygosity in Daghestan	Near_East	Sub	140	T=0.893	G=0.107
Genome-wide autozygosity in Daghestan	Central Asia	Sub	120	T=0.850	G=0.150
Genome-wide autozygosity in Daghestan	Europe	Sub	108	T=0.759	G=0.241
Genome-wide autozygosity in Daghestan	South Asian	Sub	88	T=0.80	G=0.20
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	T=0.81	G=0.19
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.843	G=0.157
Northern Sweden	ACPOP	Study-wide	600	T=0.845	G=0.155
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.845	G=0.155
HapMap	Global	Study-wide	322	T=0.739	G=0.261
HapMap	African	Sub	118	T=0.576	G=0.424
HapMap	American	Sub	116	T=0.828	G=0.172
HapMap	Asian	Sub	88	T=0.84	G=0.16
Qatari	Global	Study-wide	216	T=0.861	G=0.139
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.822	G=0.178
SGDP_PRJ	Global	Study-wide	174	T=0.408	G=0.592
The Danish reference pan genome	Danish	Study-wide	40	T=0.82	G=0.17
Siberian	Global	Study-wide	10	T=0.5	G=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 2	NC_000002.12:g.171522147T>G
GRCh37.p13 chr 2	NC_000002.11:g.172378657T>G

Gene: CYBRD1, cytochrome b reductase 1 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
CYBRD1 transcript variant 2	NM_001127383.2:c.	N/A	Upstream Transcript Variant
CYBRD1 transcript variant 3	NM_001256909.2:c.	N/A	Upstream Transcript Variant
CYBRD1 transcript variant 1	NM_024843.4: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	T=	G
GRCh38.p14 chr 2	NC_000002.12:g.171522147=	NC_000002.12:g.171522147T>G
GRCh37.p13 chr 2	NC_000002.11:g.172378657=	NC_000002.11:g.172378657T>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#.

81 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1311738	Oct 05, 2000 (86)
2	YUSUKE	ss4992960	Aug 28, 2002 (108)
3	WUGSC_SSAHASNP	ss14508283	Dec 05, 2003 (119)
4	CSHL-HAPMAP	ss17676385	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss20110537	Feb 27, 2004 (120)
6	SSAHASNP	ss21684329	Apr 05, 2004 (121)
7	KYUGEN	ss28477373	Sep 20, 2004 (126)
8	ABI	ss44350326	Mar 10, 2006 (126)
9	ILLUMINA	ss65753950	Oct 15, 2006 (127)
10	HUMANGENOME_JCVI	ss97099189	Feb 06, 2009 (130)
11	1000GENOMES	ss110267451	Jan 24, 2009 (130)
12	1000GENOMES	ss111273001	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss117974974	Feb 14, 2009 (130)
14	ENSEMBL	ss136065107	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss164848549	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss165611483	Jul 04, 2010 (132)
17	BUSHMAN	ss201373781	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss205898851	Jul 04, 2010 (132)
19	1000GENOMES	ss219654894	Jul 14, 2010 (132)
20	1000GENOMES	ss231469502	Jul 14, 2010 (132)
21	1000GENOMES	ss238958204	Jul 15, 2010 (132)
22	BL	ss253680817	May 09, 2011 (134)
23	GMI	ss276788476	May 04, 2012 (137)
24	PJP	ss292425098	May 09, 2011 (134)
25	TISHKOFF	ss556036918	Apr 25, 2013 (138)
26	SSMP	ss649689701	Apr 25, 2013 (138)
27	EVA-GONL	ss977645627	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1069705801	Aug 21, 2014 (142)
29	1000GENOMES	ss1300429788	Aug 21, 2014 (142)
30	HAMMER_LAB	ss1397312125	Sep 08, 2015 (146)
31	DDI	ss1428821619	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1579198557	Apr 01, 2015 (144)
33	EVA_DECODE	ss1587083375	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1605148317	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1648142350	Apr 01, 2015 (144)
36	EVA_MGP	ss1710987104	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1797916135	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1920897596	Feb 12, 2016 (147)
39	JJLAB	ss2020983960	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2149049693	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2236582676	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2624996197	Nov 08, 2017 (151)
43	GRF	ss2703687803	Nov 08, 2017 (151)
44	GNOMAD	ss2782825164	Nov 08, 2017 (151)
45	AFFY	ss2985191701	Nov 08, 2017 (151)
46	AFFY	ss2985812896	Nov 08, 2017 (151)
47	SWEGEN	ss2990865965	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3024252382	Nov 08, 2017 (151)
49	CSHL	ss3344606136	Nov 08, 2017 (151)
50	URBANLAB	ss3647206522	Oct 11, 2018 (152)
51	ILLUMINA	ss3653958696	Oct 11, 2018 (152)
52	EGCUT_WGS	ss3658738032	Jul 13, 2019 (153)
53	EVA_DECODE	ss3705426916	Jul 13, 2019 (153)
54	ACPOP	ss3729107916	Jul 13, 2019 (153)
55	EVA	ss3757721341	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3802080028	Jul 13, 2019 (153)
57	EVA	ss3825612780	Apr 25, 2020 (154)
58	EVA	ss3827354698	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3853976979	Apr 25, 2020 (154)
60	KRGDB	ss3899612303	Apr 25, 2020 (154)
61	KOGIC	ss3949501657	Apr 25, 2020 (154)
62	FSA-LAB	ss3984194008	Apr 26, 2021 (155)
63	FSA-LAB	ss3984194009	Apr 26, 2021 (155)
64	EVA	ss3986204133	Apr 26, 2021 (155)
65	TOPMED	ss4533758376	Apr 26, 2021 (155)
66	TOMMO_GENOMICS	ss5155122867	Apr 26, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5250971755	Oct 12, 2022 (156)
68	EVA	ss5334101894	Oct 12, 2022 (156)
69	HUGCELL_USP	ss5450691153	Oct 12, 2022 (156)
70	EVA	ss5506689611	Oct 12, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5527757528	Oct 12, 2022 (156)
72	EVA	ss5624105487	Oct 12, 2022 (156)
73	SANFORD_IMAGENETICS	ss5630357241	Oct 12, 2022 (156)
74	TOMMO_GENOMICS	ss5685607857	Oct 12, 2022 (156)
75	YY_MCH	ss5802966410	Oct 12, 2022 (156)
76	EVA	ss5821178854	Oct 12, 2022 (156)
77	EVA	ss5848527957	Oct 12, 2022 (156)
78	EVA	ss5852831958	Oct 12, 2022 (156)
79	EVA	ss5933482151	Oct 12, 2022 (156)
80	EVA	ss5956582270	Oct 12, 2022 (156)
81	EVA	ss5980095970	Oct 12, 2022 (156)
82	1000Genomes	NC_000002.11 - 172378657	Oct 11, 2018 (152)
83	1000Genomes_30x	NC_000002.12 - 171522147	Oct 12, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 172378657	Oct 11, 2018 (152)
85	Genome-wide autozygosity in Daghestan	NC_000002.10 - 172086903	Apr 25, 2020 (154)
86	Genetic variation in the Estonian population	NC_000002.11 - 172378657	Oct 11, 2018 (152)
87	The Danish reference pan genome	NC_000002.11 - 172378657	Apr 25, 2020 (154)
88	gnomAD - Genomes	NC_000002.12 - 171522147	Apr 26, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000002.11 - 172378657	Apr 25, 2020 (154)
90	HapMap	NC_000002.12 - 171522147	Apr 25, 2020 (154)
91	KOREAN population from KRGDB	NC_000002.11 - 172378657	Apr 25, 2020 (154)
92	Korean Genome Project	NC_000002.12 - 171522147	Apr 25, 2020 (154)
93	Medical Genome Project healthy controls from Spanish population	NC_000002.11 - 172378657	Apr 25, 2020 (154)
94	Northern Sweden	NC_000002.11 - 172378657	Jul 13, 2019 (153)
95	Qatari	NC_000002.11 - 172378657	Apr 25, 2020 (154)
96	SGDP_PRJ	NC_000002.11 - 172378657	Apr 25, 2020 (154)
97	Siberian	NC_000002.11 - 172378657	Apr 25, 2020 (154)
98	8.3KJPN	NC_000002.11 - 172378657	Apr 26, 2021 (155)
99	14KJPN	NC_000002.12 - 171522147	Oct 12, 2022 (156)
100	TopMed	NC_000002.12 - 171522147	Apr 26, 2021 (155)
101	UK 10K study - Twins	NC_000002.11 - 172378657	Oct 11, 2018 (152)
102	A Vietnamese Genetic Variation Database	NC_000002.11 - 172378657	Jul 13, 2019 (153)
103	ALFA	NC_000002.12 - 171522147	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)
rs3806567	Oct 08, 2002 (108)
rs17524150	Mar 10, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
261996, ss110267451, ss111273001, ss117974974, ss164848549, ss165611483, ss201373781, ss205898851, ss253680817, ss276788476, ss292425098, ss1397312125, ss1587083375	NC_000002.10:172086902:T:G	NC_000002.12:171522146:T:G	(self)
11487404, 6339760, 4476280, 5363496, 2785876, 6789697, 103643, 2392781, 2939526, 5993959, 1566047, 13092174, 6339760, 1378509, ss219654894, ss231469502, ss238958204, ss556036918, ss649689701, ss977645627, ss1069705801, ss1300429788, ss1428821619, ss1579198557, ss1605148317, ss1648142350, ss1710987104, ss1797916135, ss1920897596, ss2020983960, ss2149049693, ss2624996197, ss2703687803, ss2782825164, ss2985191701, ss2985812896, ss2990865965, ss3344606136, ss3653958696, ss3658738032, ss3729107916, ss3757721341, ss3825612780, ss3827354698, ss3853976979, ss3899612303, ss3984194008, ss3984194009, ss3986204133, ss5155122867, ss5334101894, ss5506689611, ss5624105487, ss5630357241, ss5821178854, ss5848527957, ss5956582270, ss5980095970	NC_000002.11:172378656:T:G	NC_000002.12:171522146:T:G	(self)
15283463, 81891830, 1949090, 5879658, 19444961, 337581255, 5844569531, ss2236582676, ss3024252382, ss3647206522, ss3705426916, ss3802080028, ss3949501657, ss4533758376, ss5250971755, ss5450691153, ss5527757528, ss5685607857, ss5802966410, ss5852831958, ss5933482151	NC_000002.12:171522146:T:G	NC_000002.12:171522146:T:G	(self)
ss14508283, ss17676385, ss20110537, ss21684329	NT_005403.14:22588073:T:G	NC_000002.12:171522146:T:G	(self)
ss1311738, ss4992960, ss28477373, ss44350326, ss65753950, ss97099189, ss136065107	NT_005403.17:22588074:T:G	NC_000002.12:171522146:T:G	(self)

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

8 citations for rs884409

PMID	Title	Author	Year	Journal
19673882	A novel association between a SNP in CYBRD1 and serum ferritin levels in a cohort study of HFE hereditary haemochromatosis.	Constantine CC et al.	2009	British journal of haematology
21483845	Genome-wide association study identifies genetic loci associated with iron deficiency.	McLaren CE et al.	2011	PloS one
22773607	CYBRD1 as a modifier gene that modulates iron phenotype in HFE p.C282Y homozygous patients.	Pelucchi S et al.	2012	Haematologica
23236349	A novel test for gene-ancestry interactions in genome-wide association data.	Davies JL et al.	2012	PloS one
23820649	Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease.	Cooper DN et al.	2013	Human genetics
26582562	Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver.	Engelken J et al.	2016	Molecular biology and evolution
27439017	Analysis of polymorphism and hepatic expression of duodenal cytochrome b in chronic hepatitis C.	Rudnicka A et al.	2017	Journal of gastroenterology and hepatology
31483113	GutSelf: Interindividual Variability in the Processing of Dietary Compounds by the Human Gastrointestinal Tract.	Walther B et al.	2019	Molecular nutrition & food research

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

rs884409