Name: rs3940549
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.

rs3940549

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:135381057 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.349730 (92570/264690, TOPMED)
A=0.400080 (55988/139942, GnomAD)
A=0.49530 (20431/41250, ALFA) (+ 16 more)
A=0.00000 (0/28256, 14KJPN)
A=0.00000 (0/16760, 8.3KJPN)
A=0.1633 (1046/6404, 1000G_30x)
A=0.1567 (785/5008, 1000G)
A=0.4842 (2169/4480, Estonian)
G=0.2870 (1106/3854, ALSPAC)
G=0.3026 (1122/3708, TWINSUK)
A=0.0003 (1/2930, KOREAN)
A=0.0000 (0/1832, Korea1K)
G=0.293 (292/998, GoNL)
G=0.253 (152/600, NorthernSweden)
A=0.056 (30/536, SGDP_PRJ)
A=0.032 (7/216, Qatari)
A=0.000 (0/216, Vietnamese)
A=0.10 (5/48, Siberian)
G=0.30 (12/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZRANB3 : 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	41250	A=0.49530	G=0.50470
European	Sub	33580	A=0.53788	G=0.46212
African	Sub	2898	A=0.1270	G=0.8730
African Others	Sub	114	A=0.018	G=0.982
African American	Sub	2784	A=0.1315	G=0.8685
Asian	Sub	112	A=0.018	G=0.982
East Asian	Sub	86	A=0.02	G=0.98
Other Asian	Sub	26	A=0.00	G=1.00
Latin American 1	Sub	146	A=0.192	G=0.808
Latin American 2	Sub	610	A=0.205	G=0.795
South Asian	Sub	98	A=0.13	G=0.87
Other	Sub	3806	A=0.4816	G=0.5184

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	A=0.349730	G=0.650270
gnomAD - Genomes	Global	Study-wide	139942	A=0.400080	G=0.599920
gnomAD - Genomes	European	Sub	75740	A=0.61767	G=0.38233
gnomAD - Genomes	African	Sub	41968	A=0.12219	G=0.87781
gnomAD - Genomes	American	Sub	13638	A=0.22137	G=0.77863
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.1229	G=0.8771
gnomAD - Genomes	East Asian	Sub	3128	A=0.0010	G=0.9990
gnomAD - Genomes	Other	Sub	2148	A=0.3017	G=0.6983
Allele Frequency Aggregator	Total	Global	41250	A=0.49530	G=0.50470
Allele Frequency Aggregator	European	Sub	33580	A=0.53788	G=0.46212
Allele Frequency Aggregator	Other	Sub	3806	A=0.4816	G=0.5184
Allele Frequency Aggregator	African	Sub	2898	A=0.1270	G=0.8730
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.205	G=0.795
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.192	G=0.808
Allele Frequency Aggregator	Asian	Sub	112	A=0.018	G=0.982
Allele Frequency Aggregator	South Asian	Sub	98	A=0.13	G=0.87
14KJPN	JAPANESE	Study-wide	28256	A=0.00000	G=1.00000
8.3KJPN	JAPANESE	Study-wide	16760	A=0.00000	G=1.00000
1000Genomes_30x	Global	Study-wide	6404	A=0.1633	G=0.8367
1000Genomes_30x	African	Sub	1786	A=0.0235	G=0.9765
1000Genomes_30x	Europe	Sub	1266	A=0.5166	G=0.4834
1000Genomes_30x	South Asian	Sub	1202	A=0.1090	G=0.8910
1000Genomes_30x	East Asian	Sub	1170	A=0.0000	G=1.0000
1000Genomes_30x	American	Sub	980	A=0.223	G=0.777
1000Genomes	Global	Study-wide	5008	A=0.1567	G=0.8433
1000Genomes	African	Sub	1322	A=0.0257	G=0.9743
1000Genomes	East Asian	Sub	1008	A=0.0000	G=1.0000
1000Genomes	Europe	Sub	1006	A=0.4891	G=0.5109
1000Genomes	South Asian	Sub	978	A=0.111	G=0.889
1000Genomes	American	Sub	694	A=0.216	G=0.784
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.4842	G=0.5158
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7130	G=0.2870
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.6974	G=0.3026
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.0003	G=0.9997
Korean Genome Project	KOREAN	Study-wide	1832	A=0.0000	G=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.707	G=0.293
Northern Sweden	ACPOP	Study-wide	600	A=0.747	G=0.253
SGDP_PRJ	Global	Study-wide	536	A=0.056	G=0.944
Qatari	Global	Study-wide	216	A=0.032	G=0.968
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.000	G=1.000
Siberian	Global	Study-wide	48	A=0.10	G=0.90
The Danish reference pan genome	Danish	Study-wide	40	A=0.70	G=0.30

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.135381057A>G
GRCh37.p13 chr 2	NC_000002.11:g.136138627A>G

Gene: ZRANB3, zinc finger RANBP2-type containing 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZRANB3 transcript variant 2	NM_001286568.2:c.180+9745… NM_001286568.2:c.180+9745T>C	N/A	Intron Variant
ZRANB3 transcript variant 3	NM_001286569.1:c.-1278+97… NM_001286569.1:c.-1278+9745T>C	N/A	Intron Variant
ZRANB3 transcript variant 1	NM_032143.4:c.180+9745T>C	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	A=	G
GRCh38.p14 chr 2	NC_000002.12:g.135381057=	NC_000002.12:g.135381057A>G
GRCh37.p13 chr 2	NC_000002.11:g.136138627=	NC_000002.11:g.136138627A>G
ZRANB3 transcript variant 2	NM_001286568.2:c.180+9745=	NM_001286568.2:c.180+9745T>C
ZRANB3 transcript variant 3	NM_001286569.1:c.-1278+9745=	NM_001286569.1:c.-1278+9745T>C
ZRANB3 transcript	NM_032143.2:c.180+9745=	NM_032143.2:c.180+9745T>C
ZRANB3 transcript variant 1	NM_032143.4:c.180+9745=	NM_032143.4:c.180+9745T>C
ZRANB3 transcript variant X10	XM_005263809.1:c.180+9745=	XM_005263809.1:c.180+9745T>C
ZRANB3 transcript variant X2	XM_005263810.1:c.180+9745=	XM_005263810.1:c.180+9745T>C

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#.

70 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss5204836	Oct 10, 2002 (108)
2	SC_JCM	ss5665303	Feb 20, 2003 (113)
3	WI_SSAHASNP	ss6854870	Feb 20, 2003 (113)
4	BCM_SSAHASNP	ss9962167	Jul 11, 2003 (116)
5	HGSV	ss78689863	Dec 07, 2007 (129)
6	BCMHGSC_JDW	ss91357926	Mar 24, 2008 (129)
7	BGI	ss106121076	Feb 04, 2009 (130)
8	1000GENOMES	ss110963847	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss117887468	Dec 01, 2009 (131)
10	ENSEMBL	ss138537144	Dec 01, 2009 (131)
11	GMI	ss157717946	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss164292123	Jul 04, 2010 (132)
13	BUSHMAN	ss201095709	Jul 04, 2010 (132)
14	1000GENOMES	ss219527332	Jul 14, 2010 (132)
15	1000GENOMES	ss231373270	Jul 14, 2010 (132)
16	1000GENOMES	ss238879724	Jul 15, 2010 (132)
17	GMI	ss276692852	May 04, 2012 (137)
18	PJP	ss292373593	May 09, 2011 (134)
19	TISHKOFF	ss555894942	Apr 25, 2013 (138)
20	SSMP	ss649522923	Apr 25, 2013 (138)
21	EVA-GONL	ss977388614	Aug 21, 2014 (142)
22	JMKIDD_LAB	ss1069518269	Aug 21, 2014 (142)
23	1000GENOMES	ss1299448827	Aug 21, 2014 (142)
24	DDI	ss1428749538	Apr 01, 2015 (144)
25	EVA_GENOME_DK	ss1579098534	Apr 01, 2015 (144)
26	EVA_DECODE	ss1586817217	Apr 01, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1604626859	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1647620892	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1797575767	Sep 08, 2015 (146)
30	WEILL_CORNELL_DGM	ss1920647525	Feb 12, 2016 (147)
31	GENOMED	ss1968895624	Jul 19, 2016 (147)
32	JJLAB	ss2020847221	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2148913672	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2234522524	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2624930132	Nov 08, 2017 (151)
36	GRF	ss2703538449	Nov 08, 2017 (151)
37	GNOMAD	ss2780006709	Nov 08, 2017 (151)
38	AFFY	ss2985807262	Nov 08, 2017 (151)
39	SWEGEN	ss2990477520	Nov 08, 2017 (151)
40	BIOINF_KMB_FNS_UNIBA	ss3024187035	Nov 08, 2017 (151)
41	CSHL	ss3344494847	Nov 08, 2017 (151)
42	EGCUT_WGS	ss3658320025	Jul 13, 2019 (153)
43	EVA_DECODE	ss3704950069	Jul 13, 2019 (153)
44	ACPOP	ss3728893032	Jul 13, 2019 (153)
45	ILLUMINA	ss3744480556	Jul 13, 2019 (153)
46	EVA	ss3757418779	Jul 13, 2019 (153)
47	PACBIO	ss3784001995	Jul 13, 2019 (153)
48	PACBIO	ss3789564331	Jul 13, 2019 (153)
49	PACBIO	ss3794437254	Jul 13, 2019 (153)
50	KHV_HUMAN_GENOMES	ss3801785968	Jul 13, 2019 (153)
51	EVA	ss3827235643	Apr 25, 2020 (154)
52	EVA	ss3837032619	Apr 25, 2020 (154)
53	EVA	ss3842451235	Apr 25, 2020 (154)
54	SGDP_PRJ	ss3853478086	Apr 25, 2020 (154)
55	KRGDB	ss3899040315	Apr 25, 2020 (154)
56	KOGIC	ss3949029632	Apr 25, 2020 (154)
57	TOPMED	ss4524979552	Apr 26, 2021 (155)
58	TOMMO_GENOMICS	ss5154005761	Apr 26, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5250121941	Oct 12, 2022 (156)
60	EVA	ss5332533339	Oct 12, 2022 (156)
61	HUGCELL_USP	ss5449923371	Oct 12, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5526444770	Oct 12, 2022 (156)
63	SANFORD_IMAGENETICS	ss5629869435	Oct 12, 2022 (156)
64	TOMMO_GENOMICS	ss5684172464	Oct 12, 2022 (156)
65	YY_MCH	ss5802750150	Oct 12, 2022 (156)
66	EVA	ss5820847106	Oct 12, 2022 (156)
67	EVA	ss5852726580	Oct 12, 2022 (156)
68	EVA	ss5932492305	Oct 12, 2022 (156)
69	EVA	ss5956070797	Oct 12, 2022 (156)
70	EVA	ss5980084899	Oct 12, 2022 (156)
71	1000Genomes	NC_000002.11 - 136138627	Oct 11, 2018 (152)
72	1000Genomes_30x	NC_000002.12 - 135381057	Oct 12, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 136138627	Oct 11, 2018 (152)
74	Genetic variation in the Estonian population	NC_000002.11 - 136138627	Oct 11, 2018 (152)
75	The Danish reference pan genome	NC_000002.11 - 136138627	Apr 25, 2020 (154)
76	gnomAD - Genomes	NC_000002.12 - 135381057	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000002.11 - 136138627	Apr 25, 2020 (154)
78	KOREAN population from KRGDB	NC_000002.11 - 136138627	Apr 25, 2020 (154)
79	Korean Genome Project	NC_000002.12 - 135381057	Apr 25, 2020 (154)
80	Northern Sweden	NC_000002.11 - 136138627	Jul 13, 2019 (153)
81	Qatari	NC_000002.11 - 136138627	Apr 25, 2020 (154)
82	SGDP_PRJ	NC_000002.11 - 136138627	Apr 25, 2020 (154)
83	Siberian	NC_000002.11 - 136138627	Apr 25, 2020 (154)
84	8.3KJPN	NC_000002.11 - 136138627	Apr 26, 2021 (155)
85	14KJPN	NC_000002.12 - 135381057	Oct 12, 2022 (156)
86	TopMed	NC_000002.12 - 135381057	Apr 26, 2021 (155)
87	UK 10K study - Twins	NC_000002.11 - 136138627	Oct 11, 2018 (152)
88	A Vietnamese Genetic Variation Database	NC_000002.11 - 136138627	Jul 13, 2019 (153)
89	ALFA	NC_000002.12 - 135381057	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)
rs4283470	Mar 31, 2003 (113)
rs4953950	Mar 31, 2003 (113)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78689863	NC_000002.9:135972358:A:G	NC_000002.12:135381056:A:G	(self)
ss91357926, ss110963847, ss117887468, ss164292123, ss201095709, ss276692852, ss292373593, ss1586817217	NC_000002.10:135855096:A:G	NC_000002.12:135381056:A:G	(self)
10468969, 5765088, 4058273, 5263473, 2534532, 6217709, 2177897, 2689455, 5495066, 1430026, 11975068, 5765088, 1247591, ss219527332, ss231373270, ss238879724, ss555894942, ss649522923, ss977388614, ss1069518269, ss1299448827, ss1428749538, ss1579098534, ss1604626859, ss1647620892, ss1797575767, ss1920647525, ss1968895624, ss2020847221, ss2148913672, ss2624930132, ss2703538449, ss2780006709, ss2985807262, ss2990477520, ss3344494847, ss3658320025, ss3728893032, ss3744480556, ss3757418779, ss3784001995, ss3789564331, ss3794437254, ss3827235643, ss3837032619, ss3853478086, ss3899040315, ss5154005761, ss5332533339, ss5629869435, ss5820847106, ss5956070797, ss5980084899	NC_000002.11:136138626:A:G	NC_000002.12:135381056:A:G	(self)
13970705, 74637925, 5407633, 18009568, 328802431, 12976064066, ss2234522524, ss3024187035, ss3704950069, ss3801785968, ss3842451235, ss3949029632, ss4524979552, ss5250121941, ss5449923371, ss5526444770, ss5684172464, ss5802750150, ss5852726580, ss5932492305	NC_000002.12:135381056:A:G	NC_000002.12:135381056:A:G	(self)
ss9962167	NT_005058.13:4747525:A:G	NC_000002.12:135381056:A:G	(self)
ss5204836, ss5665303, ss6854870, ss106121076, ss138537144, ss157717946	NT_022135.16:25887289:A:G	NC_000002.12:135381056:A: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 rs3940549

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

rs3940549