Name: rs3738880
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.

rs3738880

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:120989380 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.405973 (107457/264690, TOPMED)
G=0.368200 (90952/247018, GnomAD_exome)
G=0.289894 (69651/240264, ALFA) (+ 23 more)
G=0.389748 (54606/140106, GnomAD)
G=0.370405 (43350/117034, ExAC)
T=0.49901 (39226/78608, PAGE_STUDY)
T=0.47494 (13420/28256, 14KJPN)
T=0.47041 (7884/16760, 8.3KJPN)
G=0.37659 (4852/12884, GO-ESP)
G=0.4894 (3134/6404, 1000G_30x)
G=0.4910 (2459/5008, 1000G)
G=0.2975 (1333/4480, Estonian)
G=0.2769 (1067/3854, ALSPAC)
G=0.2824 (1047/3708, TWINSUK)
T=0.4887 (1431/2928, KOREAN)
G=0.4661 (881/1890, HapMap)
T=0.4951 (907/1832, Korea1K)
G=0.271 (270/998, GoNL)
T=0.453 (278/614, Vietnamese)
G=0.265 (159/600, NorthernSweden)
G=0.403 (215/534, MGP)
G=0.293 (116/396, SGDP_PRJ)
G=0.361 (107/296, FINRISK)
G=0.421 (91/216, Qatari)
G=0.33 (15/46, Siberian)
G=0.33 (13/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: GLI2 : Missense Variant
Publications: 5 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	256584	G=0.295412	A=0.000000, T=0.704588
European	Sub	217612	G=0.271809	A=0.000000, T=0.728191
African	Sub	11208	G=0.61652	A=0.00000, T=0.38348
African Others	Sub	394	G=0.655	A=0.000, T=0.345
African American	Sub	10814	G=0.61513	A=0.00000, T=0.38487
Asian	Sub	710	G=0.568	A=0.000, T=0.432
East Asian	Sub	536	G=0.567	A=0.000, T=0.433
Other Asian	Sub	174	G=0.569	A=0.000, T=0.431
Latin American 1	Sub	986	G=0.428	A=0.000, T=0.572
Latin American 2	Sub	5796	G=0.4244	A=0.0000, T=0.5756
South Asian	Sub	118	G=0.559	A=0.000, T=0.441
Other	Sub	20154	G=0.31696	A=0.00000, T=0.68304

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	G=0.405973	T=0.594027
gnomAD - Exomes	Global	Study-wide	247018	G=0.368200	T=0.631800
gnomAD - Exomes	European	Sub	132272	G=0.280044	T=0.719956
gnomAD - Exomes	Asian	Sub	48820	G=0.50125	T=0.49875
gnomAD - Exomes	American	Sub	34468	G=0.42796	T=0.57204
gnomAD - Exomes	African	Sub	15414	G=0.60575	T=0.39425
gnomAD - Exomes	Ashkenazi Jewish	Sub	9970	G=0.3334	T=0.6666
gnomAD - Exomes	Other	Sub	6074	G=0.3337	T=0.6663
Allele Frequency Aggregator	Total	Global	240264	G=0.289894	A=0.000000, T=0.710106
Allele Frequency Aggregator	European	Sub	207550	G=0.271747	A=0.000000, T=0.728253
Allele Frequency Aggregator	Other	Sub	18726	G=0.31673	A=0.00000, T=0.68327
Allele Frequency Aggregator	African	Sub	6378	G=0.6221	A=0.0000, T=0.3779
Allele Frequency Aggregator	Latin American 2	Sub	5796	G=0.4244	A=0.0000, T=0.5756
Allele Frequency Aggregator	Latin American 1	Sub	986	G=0.428	A=0.000, T=0.572
Allele Frequency Aggregator	Asian	Sub	710	G=0.568	A=0.000, T=0.432
Allele Frequency Aggregator	South Asian	Sub	118	G=0.559	A=0.000, T=0.441
gnomAD - Genomes	Global	Study-wide	140106	G=0.389748	T=0.610252
gnomAD - Genomes	European	Sub	75864	G=0.27870	T=0.72130
gnomAD - Genomes	African	Sub	41982	G=0.59375	T=0.40625
gnomAD - Genomes	American	Sub	13660	G=0.36713	T=0.63287
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.3271	T=0.6729
gnomAD - Genomes	East Asian	Sub	3128	G=0.5179	T=0.4821
gnomAD - Genomes	Other	Sub	2152	G=0.3787	T=0.6213
ExAC	Global	Study-wide	117034	G=0.370405	T=0.629595
ExAC	Europe	Sub	70310	G=0.28280	T=0.71720
ExAC	Asian	Sub	24966	G=0.49884	T=0.50116
ExAC	American	Sub	11456	G=0.44422	T=0.55578
ExAC	African	Sub	9434	G=0.5954	T=0.4046
ExAC	Other	Sub	868	G=0.353	T=0.647
The PAGE Study	Global	Study-wide	78608	G=0.50099	T=0.49901
The PAGE Study	AfricanAmerican	Sub	32460	G=0.58672	T=0.41328
The PAGE Study	Mexican	Sub	10802	G=0.42501	T=0.57499
The PAGE Study	Asian	Sub	8314	G=0.5428	T=0.4572
The PAGE Study	PuertoRican	Sub	7914	G=0.4206	T=0.5794
The PAGE Study	NativeHawaiian	Sub	4530	G=0.4700	T=0.5300
The PAGE Study	Cuban	Sub	4230	G=0.3128	T=0.6872
The PAGE Study	Dominican	Sub	3828	G=0.4556	T=0.5444
The PAGE Study	CentralAmerican	Sub	2446	G=0.4154	T=0.5846
The PAGE Study	SouthAmerican	Sub	1982	G=0.4178	T=0.5822
The PAGE Study	NativeAmerican	Sub	1258	G=0.3641	T=0.6359
The PAGE Study	SouthAsian	Sub	844	G=0.481	T=0.519
14KJPN	JAPANESE	Study-wide	28256	G=0.52506	T=0.47494
8.3KJPN	JAPANESE	Study-wide	16760	G=0.52959	T=0.47041
GO Exome Sequencing Project	Global	Study-wide	12884	G=0.37659	T=0.62341
GO Exome Sequencing Project	European American	Sub	8528	G=0.2693	T=0.7307
GO Exome Sequencing Project	African American	Sub	4356	G=0.5865	T=0.4135
1000Genomes_30x	Global	Study-wide	6404	G=0.4894	T=0.5106
1000Genomes_30x	African	Sub	1786	G=0.6411	T=0.3589
1000Genomes_30x	Europe	Sub	1266	G=0.2725	T=0.7275
1000Genomes_30x	South Asian	Sub	1202	G=0.5183	T=0.4817
1000Genomes_30x	East Asian	Sub	1170	G=0.5256	T=0.4744
1000Genomes_30x	American	Sub	980	G=0.414	T=0.586
1000Genomes	Global	Study-wide	5008	G=0.4910	T=0.5090
1000Genomes	African	Sub	1322	G=0.6422	T=0.3578
1000Genomes	East Asian	Sub	1008	G=0.5278	T=0.4722
1000Genomes	Europe	Sub	1006	G=0.2753	T=0.7247
1000Genomes	South Asian	Sub	978	G=0.524	T=0.476
1000Genomes	American	Sub	694	G=0.416	T=0.584
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.2975	T=0.7025
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.2769	T=0.7231
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.2824	T=0.7176
KOREAN population from KRGDB	KOREAN	Study-wide	2928	G=0.5113	T=0.4887
HapMap	Global	Study-wide	1890	G=0.4661	T=0.5339
HapMap	American	Sub	770	G=0.427	T=0.573
HapMap	African	Sub	692	G=0.561	T=0.439
HapMap	Asian	Sub	252	G=0.500	T=0.500
HapMap	Europe	Sub	176	G=0.216	T=0.784
Korean Genome Project	KOREAN	Study-wide	1832	G=0.5049	T=0.4951
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.271	T=0.729
A Vietnamese Genetic Variation Database	Global	Study-wide	614	G=0.547	T=0.453
Northern Sweden	ACPOP	Study-wide	600	G=0.265	T=0.735
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.403	T=0.597
SGDP_PRJ	Global	Study-wide	396	G=0.293	T=0.707
FINRISK	Finnish from FINRISK project	Study-wide	296	G=0.361	T=0.639
Qatari	Global	Study-wide	216	G=0.421	T=0.579
Siberian	Global	Study-wide	46	G=0.33	T=0.67
The Danish reference pan genome	Danish	Study-wide	40	G=0.33	T=0.68

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.120989380G>A
GRCh38.p14 chr 2	NC_000002.12:g.120989380G>T
GRCh37.p13 chr 2	NC_000002.11:g.121746956G>A
GRCh37.p13 chr 2	NC_000002.11:g.121746956G>T
GLI2 RefSeqGene	NG_009030.1:g.197090G>A
GLI2 RefSeqGene	NG_009030.1:g.197090G>T

Gene: GLI2, GLI family zinc finger 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GLI2 transcript variant 2	NM_005270.5:c.3466G>A	A [GCC] > T [ACC]	Coding Sequence Variant
zinc finger protein GLI2 isoform 1	NP_005261.2:p.Ala1156Thr	A (Ala) > T (Thr)	Missense Variant
GLI2 transcript variant 2	NM_005270.5:c.3466G>T	A [GCC] > S [TCC]	Coding Sequence Variant
zinc finger protein GLI2 isoform 1	NP_005261.2:p.Ala1156Ser	A (Ala) > S (Ser)	Missense Variant
GLI2 transcript variant 1	NM_001371271.1:c.3466G>A	A [GCC] > T [ACC]	Coding Sequence Variant
zinc finger protein GLI2 isoform 1	NP_001358200.1:p.Ala1156T… NP_001358200.1:p.Ala1156Thr	A (Ala) > T (Thr)	Missense Variant
GLI2 transcript variant 1	NM_001371271.1:c.3466G>T	A [GCC] > S [TCC]	Coding Sequence Variant
zinc finger protein GLI2 isoform 1	NP_001358200.1:p.Ala1156S… NP_001358200.1:p.Ala1156Ser	A (Ala) > S (Ser)	Missense Variant
GLI2 transcript variant 3	NM_001374353.1:c.3415G>A	A [GCC] > T [ACC]	Coding Sequence Variant
zinc finger protein GLI2 isoform 2	NP_001361282.1:p.Ala1139T… NP_001361282.1:p.Ala1139Thr	A (Ala) > T (Thr)	Missense Variant
GLI2 transcript variant 3	NM_001374353.1:c.3415G>T	A [GCC] > S [TCC]	Coding Sequence Variant
zinc finger protein GLI2 isoform 2	NP_001361282.1:p.Ala1139S… NP_001361282.1:p.Ala1139Ser	A (Ala) > S (Ser)	Missense Variant
GLI2 transcript variant 4	NM_001374354.1:c.3040G>A	A [GCC] > T [ACC]	Coding Sequence Variant
zinc finger protein GLI2 isoform 3	NP_001361283.1:p.Ala1014T… NP_001361283.1:p.Ala1014Thr	A (Ala) > T (Thr)	Missense Variant
GLI2 transcript variant 4	NM_001374354.1:c.3040G>T	A [GCC] > S [TCC]	Coding Sequence Variant
zinc finger protein GLI2 isoform 3	NP_001361283.1:p.Ala1014S… NP_001361283.1:p.Ala1014Ser	A (Ala) > S (Ser)	Missense Variant
GLI2 transcript variant X1	XM_011510969.3:c.3448G>A	A [GCC] > T [ACC]	Coding Sequence Variant
zinc finger protein GLI2 isoform X1	XP_011509271.3:p.Ala1150T… XP_011509271.3:p.Ala1150Thr	A (Ala) > T (Thr)	Missense Variant
GLI2 transcript variant X1	XM_011510969.3:c.3448G>T	A [GCC] > S [TCC]	Coding Sequence Variant
zinc finger protein GLI2 isoform X1	XP_011509271.3:p.Ala1150S… XP_011509271.3:p.Ala1150Ser	A (Ala) > S (Ser)	Missense Variant
GLI2 transcript variant X2	XM_017003818.2:c.3397G>A	A [GCC] > T [ACC]	Coding Sequence Variant
zinc finger protein GLI2 isoform X2	XP_016859307.2:p.Ala1133T… XP_016859307.2:p.Ala1133Thr	A (Ala) > T (Thr)	Missense Variant
GLI2 transcript variant X2	XM_017003818.2:c.3397G>T	A [GCC] > S [TCC]	Coding Sequence Variant
zinc finger protein GLI2 isoform X2	XP_016859307.2:p.Ala1133S… XP_016859307.2:p.Ala1133Ser	A (Ala) > S (Ser)	Missense Variant
GLI2 transcript variant X3	XM_047443947.1:c.3415G>A	A [GCC] > T [ACC]	Coding Sequence Variant
zinc finger protein GLI2 isoform X3	XP_047299903.1:p.Ala1139T… XP_047299903.1:p.Ala1139Thr	A (Ala) > T (Thr)	Missense Variant
GLI2 transcript variant X3	XM_047443947.1:c.3415G>T	A [GCC] > S [TCC]	Coding Sequence Variant
zinc finger protein GLI2 isoform X3	XP_047299903.1:p.Ala1139S… XP_047299903.1:p.Ala1139Ser	A (Ala) > S (Ser)	Missense Variant
GLI2 transcript variant X4	XM_011510971.3:c.3271G>A	A [GCC] > T [ACC]	Coding Sequence Variant
zinc finger protein GLI2 isoform X4	XP_011509273.1:p.Ala1091T… XP_011509273.1:p.Ala1091Thr	A (Ala) > T (Thr)	Missense Variant
GLI2 transcript variant X4	XM_011510971.3:c.3271G>T	A [GCC] > S [TCC]	Coding Sequence Variant
zinc finger protein GLI2 isoform X4	XP_011509273.1:p.Ala1091S… XP_011509273.1:p.Ala1091Ser	A (Ala) > S (Ser)	Missense 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.

Allele: T (allele ID: 101170 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000081284.13	not specified	Benign
RCV000273393.6	Holoprosencephaly 9	Benign
RCV001650921.3	not provided	Benign
RCV001701658.3	Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome	Benign
RCV002055195.4	Holoprosencephaly 9,Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome	Benign

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	G=	A	T
GRCh38.p14 chr 2	NC_000002.12:g.120989380=	NC_000002.12:g.120989380G>A	NC_000002.12:g.120989380G>T
GRCh37.p13 chr 2	NC_000002.11:g.121746956=	NC_000002.11:g.121746956G>A	NC_000002.11:g.121746956G>T
GLI2 RefSeqGene	NG_009030.1:g.197090=	NG_009030.1:g.197090G>A	NG_009030.1:g.197090G>T
GLI2 transcript variant 2	NM_005270.5:c.3466=	NM_005270.5:c.3466G>A	NM_005270.5:c.3466G>T
GLI2 transcript	NM_005270.4:c.3466=	NM_005270.4:c.3466G>A	NM_005270.4:c.3466G>T
GLI2 transcript variant 1	NM_001371271.1:c.3466=	NM_001371271.1:c.3466G>A	NM_001371271.1:c.3466G>T
GLI2 transcript variant 3	NM_001374353.1:c.3415=	NM_001374353.1:c.3415G>A	NM_001374353.1:c.3415G>T
GLI2 transcript variant 4	NM_001374354.1:c.3040=	NM_001374354.1:c.3040G>A	NM_001374354.1:c.3040G>T
GLI2 transcript variant X1	XM_011510969.3:c.3448=	XM_011510969.3:c.3448G>A	XM_011510969.3:c.3448G>T
GLI2 transcript variant X1	XM_011510969.2:c.3718=	XM_011510969.2:c.3718G>A	XM_011510969.2:c.3718G>T
GLI2 transcript variant X1	XM_011510969.1:c.3448=	XM_011510969.1:c.3448G>A	XM_011510969.1:c.3448G>T
GLI2 transcript variant X4	XM_011510971.3:c.3271=	XM_011510971.3:c.3271G>A	XM_011510971.3:c.3271G>T
GLI2 transcript variant X8	XM_011510971.2:c.3271=	XM_011510971.2:c.3271G>A	XM_011510971.2:c.3271G>T
GLI2 transcript variant X4	XM_011510971.1:c.3271=	XM_011510971.1:c.3271G>A	XM_011510971.1:c.3271G>T
GLI2 transcript variant X2	XM_017003818.2:c.3397=	XM_017003818.2:c.3397G>A	XM_017003818.2:c.3397G>T
GLI2 transcript variant X2	XM_017003818.1:c.3667=	XM_017003818.1:c.3667G>A	XM_017003818.1:c.3667G>T
GLI2 transcript variant X3	XM_047443947.1:c.3415=	XM_047443947.1:c.3415G>A	XM_047443947.1:c.3415G>T
GLI2 transcript variant 1	NM_030379.1:c.2482T>G	NM_030379.1:c.2482T>A	NM_030379.1:c.2482=
GLI2 transcript variant 2	NM_030380.1:c.2431T>G	NM_030380.1:c.2431T>A	NM_030380.1:c.2431=
zinc finger protein GLI2 isoform 1	NP_005261.2:p.Ala1156=	NP_005261.2:p.Ala1156Thr	NP_005261.2:p.Ala1156Ser
zinc finger protein GLI2 isoform 1	NP_001358200.1:p.Ala1156=	NP_001358200.1:p.Ala1156Thr	NP_001358200.1:p.Ala1156Ser
zinc finger protein GLI2 isoform 2	NP_001361282.1:p.Ala1139=	NP_001361282.1:p.Ala1139Thr	NP_001361282.1:p.Ala1139Ser
zinc finger protein GLI2 isoform 3	NP_001361283.1:p.Ala1014=	NP_001361283.1:p.Ala1014Thr	NP_001361283.1:p.Ala1014Ser
zinc finger protein GLI2 isoform X1	XP_011509271.3:p.Ala1150=	XP_011509271.3:p.Ala1150Thr	XP_011509271.3:p.Ala1150Ser
zinc finger protein GLI2 isoform X4	XP_011509273.1:p.Ala1091=	XP_011509273.1:p.Ala1091Thr	XP_011509273.1:p.Ala1091Ser
zinc finger protein GLI2 isoform X2	XP_016859307.2:p.Ala1133=	XP_016859307.2:p.Ala1133Thr	XP_016859307.2:p.Ala1133Ser
zinc finger protein GLI2 isoform X3	XP_047299903.1:p.Ala1139=	XP_047299903.1:p.Ala1139Thr	XP_047299903.1:p.Ala1139Ser

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#.

162 SubSNP, 26 Frequency, 5 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1342346	Oct 08, 2002 (108)
2	YUSUKE	ss4924880	Aug 28, 2002 (107)
3	TSC-CSHL	ss5445581	Oct 08, 2002 (108)
4	SC_JCM	ss5659735	Feb 20, 2003 (111)
5	CSHL-HAPMAP	ss17658513	Feb 27, 2004 (120)
6	SSAHASNP	ss21565415	Apr 05, 2004 (121)
7	ABI	ss44201243	Mar 14, 2006 (126)
8	ILLUMINA	ss74890905	Dec 06, 2007 (129)
9	HUMANGENOME_JCVI	ss96422566	Feb 04, 2009 (130)
10	BGI	ss103572458	Dec 01, 2009 (131)
11	1000GENOMES	ss109832485	Jan 24, 2009 (130)
12	ENSEMBL	ss136174189	Dec 01, 2009 (131)
13	GMI	ss157579927	Dec 01, 2009 (131)
14	SEATTLESEQ	ss159702703	Dec 01, 2009 (131)
15	ILLUMINA	ss160633565	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss165105652	Jul 04, 2010 (132)
17	ILLUMINA	ss173616547	Jul 04, 2010 (132)
18	BUSHMAN	ss200962491	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss205907074	Jul 04, 2010 (132)
20	1000GENOMES	ss210986326	Jul 14, 2010 (132)
21	1000GENOMES	ss219470608	Jul 14, 2010 (132)
22	1000GENOMES	ss231333418	Jul 14, 2010 (132)
23	1000GENOMES	ss238848191	Jul 15, 2010 (132)
24	GMI	ss276645310	May 04, 2012 (137)
25	PJP	ss292353124	May 09, 2011 (134)
26	NHLBI-ESP	ss342076895	May 09, 2011 (134)
27	ILLUMINA	ss480806435	May 04, 2012 (137)
28	ILLUMINA	ss480822130	May 04, 2012 (137)
29	ILLUMINA	ss481749135	Sep 08, 2015 (146)
30	ILLUMINA	ss485198012	May 04, 2012 (137)
31	1000GENOMES	ss489830828	May 04, 2012 (137)
32	EXOME_CHIP	ss491323794	May 04, 2012 (137)
33	CLINSEQ_SNP	ss491790489	May 04, 2012 (137)
34	ILLUMINA	ss537185879	Sep 08, 2015 (146)
35	TISHKOFF	ss555829038	Apr 25, 2013 (138)
36	SSMP	ss649450518	Apr 25, 2013 (138)
37	ILLUMINA	ss778893711	Sep 08, 2015 (146)
38	ILLUMINA	ss780790162	Sep 08, 2015 (146)
39	ILLUMINA	ss783045026	Aug 21, 2014 (142)
40	ILLUMINA	ss783470970	Sep 08, 2015 (146)
41	ILLUMINA	ss784004035	Sep 08, 2015 (146)
42	ILLUMINA	ss832302801	Apr 01, 2015 (144)
43	ILLUMINA	ss834354864	Sep 08, 2015 (146)
44	JMKIDD_LAB	ss974443558	Aug 21, 2014 (142)
45	EVA-GONL	ss977284252	Aug 21, 2014 (142)
46	JMKIDD_LAB	ss1067440562	Aug 21, 2014 (142)
47	JMKIDD_LAB	ss1069439776	Aug 21, 2014 (142)
48	1000GENOMES	ss1299028850	Aug 21, 2014 (142)
49	DDI	ss1428713390	Apr 01, 2015 (144)
50	EVA_GENOME_DK	ss1579056440	Apr 01, 2015 (144)
51	EVA_FINRISK	ss1584020666	Apr 01, 2015 (144)
52	EVA_DECODE	ss1586709834	Apr 01, 2015 (144)
53	EVA_UK10K_ALSPAC	ss1604422944	Apr 01, 2015 (144)
54	EVA_UK10K_TWINSUK	ss1647416977	Apr 01, 2015 (144)
55	EVA_EXAC	ss1686490049	Apr 01, 2015 (144)
56	EVA_MGP	ss1710978035	Apr 01, 2015 (144)
57	EVA_SVP	ss1712485485	Apr 01, 2015 (144)
58	ILLUMINA	ss1752308125	Sep 08, 2015 (146)
59	ILLUMINA	ss1752308126	Sep 08, 2015 (146)
60	ILLUMINA	ss1917753274	Feb 12, 2016 (147)
61	WEILL_CORNELL_DGM	ss1920535906	Feb 12, 2016 (147)
62	ILLUMINA	ss1946050628	Feb 12, 2016 (147)
63	ILLUMINA	ss1946050629	Feb 12, 2016 (147)
64	ILLUMINA	ss1958453269	Feb 12, 2016 (147)
65	ILLUMINA	ss1958453270	Feb 12, 2016 (147)
66	GENOMED	ss1968870029	Jul 19, 2016 (147)
67	JJLAB	ss2020795084	Sep 14, 2016 (149)
68	USC_VALOUEV	ss2148851297	Dec 20, 2016 (150)
69	HUMAN_LONGEVITY	ss2233764055	Dec 20, 2016 (150)
70	ILLUMINA	ss2633665187	Nov 08, 2017 (151)
71	GRF	ss2703463854	Nov 08, 2017 (151)
72	ILLUMINA	ss2710910595	Nov 08, 2017 (151)
73	GNOMAD	ss2732948301	Nov 08, 2017 (151)
74	GNOMAD	ss2746767510	Nov 08, 2017 (151)
75	GNOMAD	ss2778806337	Nov 08, 2017 (151)
76	AFFY	ss2985183627	Nov 08, 2017 (151)
77	AFFY	ss2985805064	Nov 08, 2017 (151)
78	SWEGEN	ss2990294105	Nov 08, 2017 (151)
79	ILLUMINA	ss3022010159	Nov 08, 2017 (151)
80	ILLUMINA	ss3022010160	Nov 08, 2017 (151)
81	EVA_SAMSUNG_MC	ss3023058525	Nov 08, 2017 (151)
82	BIOINF_KMB_FNS_UNIBA	ss3024159497	Nov 08, 2017 (151)
83	CSHL	ss3344439399	Nov 08, 2017 (151)
84	ILLUMINA	ss3625764182	Oct 11, 2018 (152)
85	ILLUMINA	ss3628152694	Oct 11, 2018 (152)
86	ILLUMINA	ss3628152695	Oct 11, 2018 (152)
87	ILLUMINA	ss3631629189	Oct 11, 2018 (152)
88	ILLUMINA	ss3633214241	Oct 11, 2018 (152)
89	ILLUMINA	ss3633926567	Oct 11, 2018 (152)
90	ILLUMINA	ss3634784877	Oct 11, 2018 (152)
91	ILLUMINA	ss3634784878	Oct 11, 2018 (152)
92	ILLUMINA	ss3635612502	Oct 11, 2018 (152)
93	ILLUMINA	ss3636473277	Oct 11, 2018 (152)
94	ILLUMINA	ss3637364433	Oct 11, 2018 (152)
95	ILLUMINA	ss3638284183	Oct 11, 2018 (152)
96	ILLUMINA	ss3640492178	Oct 11, 2018 (152)
97	ILLUMINA	ss3640492179	Oct 11, 2018 (152)
98	ILLUMINA	ss3643251542	Oct 11, 2018 (152)
99	ILLUMINA	ss3644753340	Oct 11, 2018 (152)
100	ILLUMINA	ss3644753341	Oct 11, 2018 (152)
101	OMUKHERJEE_ADBS	ss3646270199	Oct 11, 2018 (152)
102	URBANLAB	ss3647126948	Oct 11, 2018 (152)
103	ILLUMINA	ss3652450292	Oct 11, 2018 (152)
104	ILLUMINA	ss3652450293	Oct 11, 2018 (152)
105	ILLUMINA	ss3653950275	Oct 11, 2018 (152)
106	EGCUT_WGS	ss3658168775	Jul 13, 2019 (153)
107	EVA_DECODE	ss3704754331	Jul 13, 2019 (153)
108	ILLUMINA	ss3725818827	Jul 13, 2019 (153)
109	ACPOP	ss3728805881	Jul 13, 2019 (153)
110	ILLUMINA	ss3744181628	Jul 13, 2019 (153)
111	ILLUMINA	ss3744479477	Jul 13, 2019 (153)
112	ILLUMINA	ss3745084758	Jul 13, 2019 (153)
113	ILLUMINA	ss3745084759	Jul 13, 2019 (153)
114	EVA	ss3757293011	Jul 13, 2019 (153)
115	PAGE_CC	ss3770945146	Jul 13, 2019 (153)
116	ILLUMINA	ss3772581447	Jul 13, 2019 (153)
117	ILLUMINA	ss3772581448	Jul 13, 2019 (153)
118	KHV_HUMAN_GENOMES	ss3801658894	Jul 13, 2019 (153)
119	EVA	ss3823805024	Apr 25, 2020 (154)
120	EVA	ss3825519848	Apr 25, 2020 (154)
121	EVA	ss3825536567	Apr 25, 2020 (154)
122	EVA	ss3825608184	Apr 25, 2020 (154)
123	EVA	ss3827184600	Apr 25, 2020 (154)
124	EVA	ss3837007014	Apr 25, 2020 (154)
125	EVA	ss3842425730	Apr 25, 2020 (154)
126	SGDP_PRJ	ss3853246850	Apr 25, 2020 (154)
127	KRGDB	ss3898766051	Apr 25, 2020 (154)
128	KOGIC	ss3948814606	Apr 25, 2020 (154)
129	FSA-LAB	ss3984187335	Apr 26, 2021 (155)
130	FSA-LAB	ss3984187336	Apr 26, 2021 (155)
131	EVA	ss3986019173	Apr 26, 2021 (155)
132	EVA	ss3986195399	Apr 26, 2021 (155)
133	EVA	ss4017017634	Apr 26, 2021 (155)
134	TOPMED	ss4521452312	Apr 26, 2021 (155)
135	TOMMO_GENOMICS	ss5153521300	Apr 26, 2021 (155)
136	EVA	ss5236973632	Apr 26, 2021 (155)
137	EVA	ss5237171386	Apr 26, 2021 (155)
138	EVA	ss5237636376	Oct 12, 2022 (156)
139	1000G_HIGH_COVERAGE	ss5249745224	Oct 12, 2022 (156)
140	TRAN_CS_UWATERLOO	ss5314402298	Oct 12, 2022 (156)
141	EVA	ss5314764617	Oct 12, 2022 (156)
142	EVA	ss5331858251	Oct 12, 2022 (156)
143	HUGCELL_USP	ss5449610374	Oct 12, 2022 (156)
144	EVA	ss5506558386	Oct 12, 2022 (156)
145	1000G_HIGH_COVERAGE	ss5525876171	Oct 12, 2022 (156)
146	EVA	ss5623921797	Oct 12, 2022 (156)
147	EVA	ss5624103241	Oct 12, 2022 (156)
148	SANFORD_IMAGENETICS	ss5629650551	Oct 12, 2022 (156)
149	TOMMO_GENOMICS	ss5683541915	Oct 12, 2022 (156)
150	EVA	ss5799543578	Oct 12, 2022 (156)
151	EVA	ss5800049127	Oct 12, 2022 (156)
152	EVA	ss5800097743	Oct 12, 2022 (156)
153	YY_MCH	ss5802657009	Oct 12, 2022 (156)
154	EVA	ss5820700924	Oct 12, 2022 (156)
155	EVA	ss5847881111	Oct 12, 2022 (156)
156	EVA	ss5848522591	Oct 12, 2022 (156)
157	EVA	ss5852686889	Oct 12, 2022 (156)
158	EVA	ss5932089974	Oct 12, 2022 (156)
159	EVA	ss5936517597	Oct 12, 2022 (156)
160	EVA	ss5955862539	Oct 12, 2022 (156)
161	EVA	ss5980079235	Oct 12, 2022 (156)
162	EVA	ss5981207229	Oct 12, 2022 (156)
163	1000Genomes	NC_000002.11 - 121746956	Oct 11, 2018 (152)
164	1000Genomes_30x	NC_000002.12 - 120989380	Oct 12, 2022 (156)
165	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 121746956	Oct 11, 2018 (152)
166	Genetic variation in the Estonian population	NC_000002.11 - 121746956	Oct 11, 2018 (152)
167	ExAC	NC_000002.11 - 121746956	Oct 11, 2018 (152)
168	FINRISK	NC_000002.11 - 121746956	Apr 25, 2020 (154)
169	The Danish reference pan genome	NC_000002.11 - 121746956	Apr 25, 2020 (154)
170	gnomAD - Genomes	NC_000002.12 - 120989380	Apr 26, 2021 (155)
171	gnomAD - Exomes	NC_000002.11 - 121746956	Jul 13, 2019 (153)
172	GO Exome Sequencing Project	NC_000002.11 - 121746956	Oct 11, 2018 (152)
173	Genome of the Netherlands Release 5	NC_000002.11 - 121746956	Apr 25, 2020 (154)
174	HapMap	NC_000002.12 - 120989380	Apr 25, 2020 (154)
175	KOREAN population from KRGDB	NC_000002.11 - 121746956	Apr 25, 2020 (154)
176	Korean Genome Project	NC_000002.12 - 120989380	Apr 25, 2020 (154)
177	Medical Genome Project healthy controls from Spanish population	NC_000002.11 - 121746956	Apr 25, 2020 (154)
178	Northern Sweden	NC_000002.11 - 121746956	Jul 13, 2019 (153)
179	The PAGE Study	NC_000002.12 - 120989380	Jul 13, 2019 (153)
180	Qatari	NC_000002.11 - 121746956	Apr 25, 2020 (154)
181	SGDP_PRJ	NC_000002.11 - 121746956	Apr 25, 2020 (154)
182	Siberian	NC_000002.11 - 121746956	Apr 25, 2020 (154)
183	8.3KJPN	NC_000002.11 - 121746956	Apr 26, 2021 (155)
184	14KJPN	NC_000002.12 - 120989380	Oct 12, 2022 (156)
185	TopMed	NC_000002.12 - 120989380	Apr 26, 2021 (155)
186	UK 10K study - Twins	NC_000002.11 - 121746956	Oct 11, 2018 (152)
187	A Vietnamese Genetic Variation Database	NC_000002.11 - 121746956	Jul 13, 2019 (153)
188	ALFA	NC_000002.12 - 120989380	Apr 26, 2021 (155)
189	ClinVar	RCV000081284.13	Oct 12, 2022 (156)
190	ClinVar	RCV000273393.6	Oct 12, 2022 (156)
191	ClinVar	RCV001650921.3	Oct 12, 2022 (156)
192	ClinVar	RCV001701658.3	Oct 12, 2022 (156)
193	ClinVar	RCV002055195.4	Oct 12, 2022 (156)

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
3140235492	NC_000002.12:120989379:G:A	NC_000002.12:120989379:G:A	(self)
ss109832485, ss165105652, ss200962491, ss205907074, ss210986326, ss276645310, ss292353124, ss480806435, ss491790489, ss1586709834, ss1712485485, ss3643251542	NC_000002.10:121463425:G:T	NC_000002.12:120989379:G:T	(self)
10034664, 5541149, 3907023, 6375241, 17127, 5222106, 2004890, 263458, 2433799, 5943445, 94652, 2090746, 2577836, 5263830, 1367651, 11490607, 5541149, 1199138, ss219470608, ss231333418, ss238848191, ss342076895, ss480822130, ss481749135, ss485198012, ss489830828, ss491323794, ss537185879, ss555829038, ss649450518, ss778893711, ss780790162, ss783045026, ss783470970, ss784004035, ss832302801, ss834354864, ss974443558, ss977284252, ss1067440562, ss1069439776, ss1299028850, ss1428713390, ss1579056440, ss1584020666, ss1604422944, ss1647416977, ss1686490049, ss1710978035, ss1752308125, ss1752308126, ss1917753274, ss1920535906, ss1946050628, ss1946050629, ss1958453269, ss1958453270, ss1968870029, ss2020795084, ss2148851297, ss2633665187, ss2703463854, ss2710910595, ss2732948301, ss2746767510, ss2778806337, ss2985183627, ss2985805064, ss2990294105, ss3022010159, ss3022010160, ss3023058525, ss3344439399, ss3625764182, ss3628152694, ss3628152695, ss3631629189, ss3633214241, ss3633926567, ss3634784877, ss3634784878, ss3635612502, ss3636473277, ss3637364433, ss3638284183, ss3640492178, ss3640492179, ss3644753340, ss3644753341, ss3646270199, ss3652450292, ss3652450293, ss3653950275, ss3658168775, ss3728805881, ss3744181628, ss3744479477, ss3745084758, ss3745084759, ss3757293011, ss3772581447, ss3772581448, ss3823805024, ss3825519848, ss3825536567, ss3825608184, ss3827184600, ss3837007014, ss3853246850, ss3898766051, ss3984187335, ss3984187336, ss3986019173, ss3986195399, ss4017017634, ss5153521300, ss5314764617, ss5331858251, ss5506558386, ss5623921797, ss5624103241, ss5629650551, ss5799543578, ss5800049127, ss5800097743, ss5820700924, ss5847881111, ss5848522591, ss5936517597, ss5955862539, ss5980079235, ss5981207229	NC_000002.11:121746955:G:T	NC_000002.12:120989379:G:T	(self)
RCV000081284.13, RCV000273393.6, RCV001650921.3, RCV001701658.3, RCV002055195.4, 13402106, 71656898, 1879989, 5192607, 166615, 17379019, 325275191, 3140235492, ss2233764055, ss3024159497, ss3647126948, ss3704754331, ss3725818827, ss3770945146, ss3801658894, ss3842425730, ss3948814606, ss4521452312, ss5236973632, ss5237171386, ss5237636376, ss5249745224, ss5314402298, ss5449610374, ss5525876171, ss5683541915, ss5802657009, ss5852686889, ss5932089974	NC_000002.12:120989379:G:T	NC_000002.12:120989379:G:T	(self)
ss17658513, ss21565415	NT_022135.13:10454697:G:T	NC_000002.12:120989379:G:T	(self)
ss1342346, ss4924880, ss5445581, ss5659735, ss44201243, ss74890905, ss96422566, ss103572458, ss136174189, ss157579927, ss159702703, ss160633565, ss173616547	NT_022135.16:11495618:G:T	NC_000002.12:120989379:G:T	(self)

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

5 citations for rs3738880

PMID	Title	Author	Year	Journal
19223936	Characterization of two ectrodactyly-associated translocation breakpoints separated by 2.5 Mb on chromosome 2q14.1-q14.2.	David D et al.	2009	European journal of human genetics
23757202	Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.	Bean LJ et al.	2013	Human mutation
25741868	Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.	Richards S et al.	2015	Genetics in medicine
28057877	Previous miscarriages and GLI2 are associated with anorectal malformations in offspring.	van de Putte R et al.	2017	Human reproduction (Oxford, England)
31112935	Tooth agenesis-related GLI2 and GLI3 genes may contribute to craniofacial skeletal morphology in humans.	Marañón-Vásquez GA et al.	2019	Archives of oral biology

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
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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

rs3738880