Name: rs56384016
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.

rs56384016

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:49638805 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.192115 (50851/264690, TOPMED)
A=0.203743 (28544/140098, GnomAD)
A=0.25742 (9588/37246, ALFA) (+ 16 more)
A=0.01741 (492/28258, 14KJPN)
A=0.01766 (296/16760, 8.3KJPN)
A=0.1202 (770/6404, 1000G_30x)
A=0.1190 (596/5008, 1000G)
A=0.2781 (1246/4480, Estonian)
A=0.2929 (1129/3854, ALSPAC)
A=0.2732 (1013/3708, TWINSUK)
A=0.0260 (76/2922, KOREAN)
A=0.0278 (51/1832, Korea1K)
A=0.286 (285/998, GoNL)
A=0.237 (142/600, NorthernSweden)
A=0.227 (49/216, Qatari)
A=0.056 (12/214, Vietnamese)
C=0.450 (54/120, SGDP_PRJ)
A=0.28 (11/40, GENOME_DK)
C=0.39 (7/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RHAG : 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	37340	C=0.74242	A=0.25758
European	Sub	30942	C=0.71760	A=0.28240
African	Sub	3168	C=0.9410	A=0.0590
African Others	Sub	124	C=0.992	A=0.008
African American	Sub	3044	C=0.9389	A=0.0611
Asian	Sub	128	C=0.953	A=0.047
East Asian	Sub	100	C=0.95	A=0.05
Other Asian	Sub	28	C=0.96	A=0.04
Latin American 1	Sub	168	C=0.815	A=0.185
Latin American 2	Sub	700	C=0.829	A=0.171
South Asian	Sub	114	C=0.904	A=0.096
Other	Sub	2120	C=0.7524	A=0.2476

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=0.807885	A=0.192115
gnomAD - Genomes	Global	Study-wide	140098	C=0.796257	A=0.203743
gnomAD - Genomes	European	Sub	75860	C=0.72161	A=0.27839
gnomAD - Genomes	African	Sub	41994	C=0.93578	A=0.06422
gnomAD - Genomes	American	Sub	13648	C=0.77916	A=0.22084
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.6580	A=0.3420
gnomAD - Genomes	East Asian	Sub	3126	C=0.9674	A=0.0326
gnomAD - Genomes	Other	Sub	2148	C=0.7784	A=0.2216
Allele Frequency Aggregator	Total	Global	37246	C=0.74258	A=0.25742
Allele Frequency Aggregator	European	Sub	30866	C=0.71768	A=0.28232
Allele Frequency Aggregator	African	Sub	3168	C=0.9410	A=0.0590
Allele Frequency Aggregator	Other	Sub	2102	C=0.7531	A=0.2469
Allele Frequency Aggregator	Latin American 2	Sub	700	C=0.829	A=0.171
Allele Frequency Aggregator	Latin American 1	Sub	168	C=0.815	A=0.185
Allele Frequency Aggregator	Asian	Sub	128	C=0.953	A=0.047
Allele Frequency Aggregator	South Asian	Sub	114	C=0.904	A=0.096
14KJPN	JAPANESE	Study-wide	28258	C=0.98259	A=0.01741
8.3KJPN	JAPANESE	Study-wide	16760	C=0.98234	A=0.01766
1000Genomes_30x	Global	Study-wide	6404	C=0.8798	A=0.1202
1000Genomes_30x	African	Sub	1786	C=0.9742	A=0.0258
1000Genomes_30x	Europe	Sub	1266	C=0.6919	A=0.3081
1000Genomes_30x	South Asian	Sub	1202	C=0.8927	A=0.1073
1000Genomes_30x	East Asian	Sub	1170	C=0.9598	A=0.0402
1000Genomes_30x	American	Sub	980	C=0.839	A=0.161
1000Genomes	Global	Study-wide	5008	C=0.8810	A=0.1190
1000Genomes	African	Sub	1322	C=0.9705	A=0.0295
1000Genomes	East Asian	Sub	1008	C=0.9593	A=0.0407
1000Genomes	Europe	Sub	1006	C=0.7038	A=0.2962
1000Genomes	South Asian	Sub	978	C=0.891	A=0.109
1000Genomes	American	Sub	694	C=0.840	A=0.160
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7219	A=0.2781
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7071	A=0.2929
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7268	A=0.2732
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9740	A=0.0260
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9722	A=0.0278
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.714	A=0.286
Northern Sweden	ACPOP	Study-wide	600	C=0.763	A=0.237
Qatari	Global	Study-wide	216	C=0.773	A=0.227
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.944	A=0.056
SGDP_PRJ	Global	Study-wide	120	C=0.450	A=0.550
The Danish reference pan genome	Danish	Study-wide	40	C=0.72	A=0.28
Siberian	Global	Study-wide	18	C=0.39	A=0.61

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.49638805C>A
GRCh37.p13 chr 6	NC_000006.11:g.49606518C>A
RHAG RefSeqGene (LRG_822)	NG_011704.1:g.3070G>T

Gene: RHAG, Rh associated glycoprotein (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
RHAG transcript	NM_000324.3:c.	N/A	Upstream Transcript Variant
RHAG transcript variant X1	XM_011514788.2: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=	A
GRCh38.p14 chr 6	NC_000006.12:g.49638805=	NC_000006.12:g.49638805C>A
GRCh37.p13 chr 6	NC_000006.11:g.49606518=	NC_000006.11:g.49606518C>A
RHAG RefSeqGene (LRG_822)	NG_011704.1:g.3070=	NG_011704.1:g.3070G>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#.

77 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss77598594	Dec 07, 2007 (129)
2	BCMHGSC_JDW	ss93457658	Mar 24, 2008 (130)
3	HUMANGENOME_JCVI	ss98391734	Feb 05, 2009 (130)
4	1000GENOMES	ss110093444	Jan 24, 2009 (130)
5	ENSEMBL	ss143816607	Dec 01, 2009 (131)
6	ENSEMBL	ss143899829	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss162333616	Jul 04, 2010 (132)
8	COMPLETE_GENOMICS	ss166648714	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss207422687	Jul 04, 2010 (132)
10	1000GENOMES	ss222387023	Jul 14, 2010 (132)
11	1000GENOMES	ss233467408	Jul 14, 2010 (132)
12	1000GENOMES	ss240525165	Jul 15, 2010 (132)
13	GMI	ss285401911	Apr 25, 2013 (138)
14	PJP	ss293595827	May 09, 2011 (134)
15	ILLUMINA	ss479229275	May 04, 2012 (137)
16	ILLUMINA	ss485255064	May 04, 2012 (137)
17	ILLUMINA	ss532814326	Sep 08, 2015 (146)
18	TISHKOFF	ss559198457	Apr 25, 2013 (138)
19	SSMP	ss653141230	Apr 25, 2013 (138)
20	ILLUMINA	ss779547782	Sep 08, 2015 (146)
21	ILLUMINA	ss780929380	Sep 08, 2015 (146)
22	ILLUMINA	ss835018649	Sep 08, 2015 (146)
23	EVA-GONL	ss982920907	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1073608689	Aug 21, 2014 (142)
25	1000GENOMES	ss1320091419	Aug 21, 2014 (142)
26	DDI	ss1430718596	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1581668665	Apr 01, 2015 (144)
28	EVA_DECODE	ss1592457624	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1615559476	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1658553509	Apr 01, 2015 (144)
31	WEILL_CORNELL_DGM	ss1926178137	Feb 12, 2016 (147)
32	GENOMED	ss1970394152	Jul 19, 2016 (147)
33	JJLAB	ss2023728470	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2151907397	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2284002780	Dec 20, 2016 (150)
36	ILLUMINA	ss2634452232	Nov 08, 2017 (151)
37	GRF	ss2707507548	Nov 08, 2017 (151)
38	GNOMAD	ss2838886067	Nov 08, 2017 (151)
39	AFFY	ss2985369972	Nov 08, 2017 (151)
40	AFFY	ss2986000891	Nov 08, 2017 (151)
41	SWEGEN	ss2999046240	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3025655926	Nov 08, 2017 (151)
43	CSHL	ss3346957292	Nov 08, 2017 (151)
44	ILLUMINA	ss3629547460	Oct 12, 2018 (152)
45	ILLUMINA	ss3632368919	Oct 12, 2018 (152)
46	ILLUMINA	ss3642490065	Oct 12, 2018 (152)
47	URBANLAB	ss3648348790	Oct 12, 2018 (152)
48	ILLUMINA	ss3654135444	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3666942741	Jul 13, 2019 (153)
50	EVA_DECODE	ss3717189895	Jul 13, 2019 (153)
51	ACPOP	ss3733495659	Jul 13, 2019 (153)
52	EVA	ss3765009871	Jul 13, 2019 (153)
53	PACBIO	ss3785471616	Jul 13, 2019 (153)
54	PACBIO	ss3790823017	Jul 13, 2019 (153)
55	PACBIO	ss3795701687	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3808155221	Jul 13, 2019 (153)
57	EVA	ss3829918007	Apr 26, 2020 (154)
58	EVA	ss3838436888	Apr 26, 2020 (154)
59	EVA	ss3843881753	Apr 26, 2020 (154)
60	SGDP_PRJ	ss3864560492	Apr 26, 2020 (154)
61	KRGDB	ss3911373185	Apr 26, 2020 (154)
62	KOGIC	ss3959013856	Apr 26, 2020 (154)
63	TOPMED	ss4702628288	Apr 26, 2021 (155)
64	TOMMO_GENOMICS	ss5177458313	Apr 26, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5268410758	Oct 13, 2022 (156)
66	EVA	ss5315156432	Oct 13, 2022 (156)
67	EVA	ss5365562548	Oct 13, 2022 (156)
68	HUGCELL_USP	ss5466087283	Oct 13, 2022 (156)
69	EVA	ss5508487932	Oct 13, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5554289772	Oct 13, 2022 (156)
71	SANFORD_IMAGENETICS	ss5640380414	Oct 13, 2022 (156)
72	TOMMO_GENOMICS	ss5715491157	Oct 13, 2022 (156)
73	YY_MCH	ss5807458562	Oct 13, 2022 (156)
74	EVA	ss5842228303	Oct 13, 2022 (156)
75	EVA	ss5855353859	Oct 13, 2022 (156)
76	EVA	ss5883777523	Oct 13, 2022 (156)
77	EVA	ss5968881042	Oct 13, 2022 (156)
78	1000Genomes	NC_000006.11 - 49606518	Oct 12, 2018 (152)
79	1000Genomes_30x	NC_000006.12 - 49638805	Oct 13, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 49606518	Oct 12, 2018 (152)
81	Genetic variation in the Estonian population	NC_000006.11 - 49606518	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000006.11 - 49606518	Apr 26, 2020 (154)
83	gnomAD - Genomes	NC_000006.12 - 49638805	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000006.11 - 49606518	Apr 26, 2020 (154)
85	KOREAN population from KRGDB	NC_000006.11 - 49606518	Apr 26, 2020 (154)
86	Korean Genome Project	NC_000006.12 - 49638805	Apr 26, 2020 (154)
87	Northern Sweden	NC_000006.11 - 49606518	Jul 13, 2019 (153)
88	Qatari	NC_000006.11 - 49606518	Apr 26, 2020 (154)
89	SGDP_PRJ	NC_000006.11 - 49606518	Apr 26, 2020 (154)
90	Siberian	NC_000006.11 - 49606518	Apr 26, 2020 (154)
91	8.3KJPN	NC_000006.11 - 49606518	Apr 26, 2021 (155)
92	14KJPN	NC_000006.12 - 49638805	Oct 13, 2022 (156)
93	TopMed	NC_000006.12 - 49638805	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000006.11 - 49606518	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000006.11 - 49606518	Jul 13, 2019 (153)
96	ALFA	NC_000006.12 - 49638805	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)
rs62412440	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77598594	NC_000006.9:49714476:C:A	NC_000006.12:49638804:C:A	(self)
ss93457658, ss110093444, ss162333616, ss166648714, ss207422687, ss285401911, ss293595827, ss485255064, ss1592457624	NC_000006.10:49714476:C:A	NC_000006.12:49638804:C:A	(self)
31878561, 17777838, 12680989, 7833604, 7910713, 18550579, 6780524, 8220067, 16577472, 4423751, 35427620, 17777838, 3945786, ss222387023, ss233467408, ss240525165, ss479229275, ss532814326, ss559198457, ss653141230, ss779547782, ss780929380, ss835018649, ss982920907, ss1073608689, ss1320091419, ss1430718596, ss1581668665, ss1615559476, ss1658553509, ss1926178137, ss1970394152, ss2023728470, ss2151907397, ss2634452232, ss2707507548, ss2838886067, ss2985369972, ss2986000891, ss2999046240, ss3346957292, ss3629547460, ss3632368919, ss3642490065, ss3654135444, ss3666942741, ss3733495659, ss3765009871, ss3785471616, ss3790823017, ss3795701687, ss3829918007, ss3838436888, ss3864560492, ss3911373185, ss5177458313, ss5315156432, ss5365562548, ss5508487932, ss5640380414, ss5842228303, ss5968881042	NC_000006.11:49606517:C:A	NC_000006.12:49638804:C:A	(self)
41815707, 224903210, 15391857, 49328261, 540005846, 4098378124, ss2284002780, ss3025655926, ss3648348790, ss3717189895, ss3808155221, ss3843881753, ss3959013856, ss4702628288, ss5268410758, ss5466087283, ss5554289772, ss5715491157, ss5807458562, ss5855353859, ss5883777523	NC_000006.12:49638804:C:A	NC_000006.12:49638804:C:A	(self)
ss98391734, ss143816607, ss143899829	NT_007592.15:49546517:C:A	NC_000006.12:49638804:C:A	(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 rs56384016

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

rs56384016