Name: rs66709408
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.

rs66709408

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:32702637 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.181968 (48165/264690, TOPMED)
T=0.190612 (26672/139928, GnomAD)
T=0.21220 (16700/78698, PAGE_STUDY) (+ 17 more)
T=0.21258 (6007/28258, 14KJPN)
T=0.16987 (3341/19668, ALFA)
T=0.21229 (3558/16760, 8.3KJPN)
T=0.1785 (1143/6404, 1000G_30x)
T=0.1813 (908/5008, 1000G)
T=0.1859 (833/4480, Estonian)
T=0.1297 (500/3854, ALSPAC)
T=0.1330 (493/3708, TWINSUK)
T=0.1988 (581/2922, KOREAN)
T=0.130 (130/998, GoNL)
T=0.182 (109/600, NorthernSweden)
T=0.102 (22/216, Qatari)
T=0.099 (21/212, Vietnamese)
C=0.446 (74/166, SGDP_PRJ)
T=0.07 (3/40, GENOME_DK)
C=0.50 (10/20, Siberian)
T=0.50 (10/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	19668	C=0.83013	T=0.16987
European	Sub	14286	C=0.84670	T=0.15330
African	Sub	3396	C=0.7644	T=0.2356
African Others	Sub	114	C=0.675	T=0.325
African American	Sub	3282	C=0.7675	T=0.2325
Asian	Sub	116	C=0.871	T=0.129
East Asian	Sub	88	C=0.88	T=0.12
Other Asian	Sub	28	C=0.86	T=0.14
Latin American 1	Sub	154	C=0.812	T=0.188
Latin American 2	Sub	616	C=0.778	T=0.222
South Asian	Sub	98	C=0.91	T=0.09
Other	Sub	1002	C=0.8393	T=0.1607

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=0.818032	T=0.181968
gnomAD - Genomes	Global	Study-wide	139928	C=0.809388	T=0.190612
gnomAD - Genomes	European	Sub	75802	C=0.82917	T=0.17083
gnomAD - Genomes	African	Sub	41894	C=0.77214	T=0.22786
gnomAD - Genomes	American	Sub	13634	C=0.78678	T=0.21322
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.8454	T=0.1546
gnomAD - Genomes	East Asian	Sub	3128	C=0.8827	T=0.1173
gnomAD - Genomes	Other	Sub	2146	C=0.8187	T=0.1813
The PAGE Study	Global	Study-wide	78698	C=0.78780	T=0.21220
The PAGE Study	AfricanAmerican	Sub	32516	C=0.77580	T=0.22420
The PAGE Study	Mexican	Sub	10810	C=0.76586	T=0.23414
The PAGE Study	Asian	Sub	8318	C=0.7622	T=0.2378
The PAGE Study	PuertoRican	Sub	7916	C=0.7863	T=0.2137
The PAGE Study	NativeHawaiian	Sub	4534	C=0.8979	T=0.1021
The PAGE Study	Cuban	Sub	4228	C=0.8165	T=0.1835
The PAGE Study	Dominican	Sub	3828	C=0.7918	T=0.2082
The PAGE Study	CentralAmerican	Sub	2450	C=0.7927	T=0.2073
The PAGE Study	SouthAmerican	Sub	1982	C=0.8184	T=0.1816
The PAGE Study	NativeAmerican	Sub	1260	C=0.8294	T=0.1706
The PAGE Study	SouthAsian	Sub	856	C=0.895	T=0.105
14KJPN	JAPANESE	Study-wide	28258	C=0.78742	T=0.21258
Allele Frequency Aggregator	Total	Global	19668	C=0.83013	T=0.16987
Allele Frequency Aggregator	European	Sub	14286	C=0.84670	T=0.15330
Allele Frequency Aggregator	African	Sub	3396	C=0.7644	T=0.2356
Allele Frequency Aggregator	Other	Sub	1002	C=0.8393	T=0.1607
Allele Frequency Aggregator	Latin American 2	Sub	616	C=0.778	T=0.222
Allele Frequency Aggregator	Latin American 1	Sub	154	C=0.812	T=0.188
Allele Frequency Aggregator	Asian	Sub	116	C=0.871	T=0.129
Allele Frequency Aggregator	South Asian	Sub	98	C=0.91	T=0.09
8.3KJPN	JAPANESE	Study-wide	16760	C=0.78771	T=0.21229
1000Genomes_30x	Global	Study-wide	6404	C=0.8215	T=0.1785
1000Genomes_30x	African	Sub	1786	C=0.7542	T=0.2458
1000Genomes_30x	Europe	Sub	1266	C=0.8175	T=0.1825
1000Genomes_30x	South Asian	Sub	1202	C=0.8993	T=0.1007
1000Genomes_30x	East Asian	Sub	1170	C=0.8838	T=0.1162
1000Genomes_30x	American	Sub	980	C=0.780	T=0.220
1000Genomes	Global	Study-wide	5008	C=0.8187	T=0.1813
1000Genomes	African	Sub	1322	C=0.7481	T=0.2519
1000Genomes	East Asian	Sub	1008	C=0.8780	T=0.1220
1000Genomes	Europe	Sub	1006	C=0.8052	T=0.1948
1000Genomes	South Asian	Sub	978	C=0.900	T=0.100
1000Genomes	American	Sub	694	C=0.772	T=0.228
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8141	T=0.1859
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8703	T=0.1297
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8670	T=0.1330
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.8012	T=0.1988
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.870	T=0.130
Northern Sweden	ACPOP	Study-wide	600	C=0.818	T=0.182
Qatari	Global	Study-wide	216	C=0.898	T=0.102
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.901	T=0.099
SGDP_PRJ	Global	Study-wide	166	C=0.446	T=0.554
The Danish reference pan genome	Danish	Study-wide	40	C=0.93	T=0.07
Siberian	Global	Study-wide	20	C=0.50	T=0.50

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.32702637C>T
GRCh37.p13 chr 6	NC_000006.11:g.32670414C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.4115949C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.4116055C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.3896913C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.3902509C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.3947244C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.3952829C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.4103275C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.4102573C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.4122457C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.4128077C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.4001879C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.4007464C>T

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=	T
GRCh38.p14 chr 6	NC_000006.12:g.32702637=	NC_000006.12:g.32702637C>T
GRCh37.p13 chr 6	NC_000006.11:g.32670414=	NC_000006.11:g.32670414C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.4115949=	NT_113891.3:g.4115949C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.4116055=	NT_113891.2:g.4116055C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.3896913=	NT_167248.2:g.3896913C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.3902509=	NT_167248.1:g.3902509C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.3947244=	NT_167245.2:g.3947244C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.3952829=	NT_167245.1:g.3952829C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.4103275=	NT_167249.2:g.4103275C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.4102573=	NT_167249.1:g.4102573C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.4122457=	NT_167246.2:g.4122457C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.4128077=	NT_167246.1:g.4128077C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.4001879=	NT_167247.2:g.4001879C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.4007464=	NT_167247.1:g.4007464C>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#.

66 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HUMANGENOME_JCVI	ss98488017	Feb 04, 2009 (130)
2	1000GENOMES	ss109920101	Feb 04, 2009 (137)
3	ENSEMBL	ss133422661	Dec 01, 2009 (131)
4	BUSHMAN	ss201648940	Jul 04, 2010 (135)
5	BCM-HGSC-SUB	ss207372148	Jul 04, 2010 (135)
6	1000GENOMES	ss211818590	Jul 14, 2010 (137)
7	1000GENOMES	ss222318237	Jul 14, 2010 (137)
8	1000GENOMES	ss233415623	Jul 14, 2010 (137)
9	1000GENOMES	ss240482575	Jul 15, 2010 (137)
10	GMI	ss278741273	May 04, 2012 (137)
11	ILLUMINA	ss533160810	Sep 08, 2015 (146)
12	TISHKOFF	ss559120646	Apr 25, 2013 (138)
13	SSMP	ss653052009	Apr 25, 2013 (138)
14	EVA-GONL	ss982785979	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1073512591	Aug 21, 2014 (142)
16	1000GENOMES	ss1319597649	Aug 21, 2014 (142)
17	EVA_GENOME_DK	ss1581614719	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1615292021	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1658286054	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1804367222	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1926043708	Feb 12, 2016 (147)
22	ILLUMINA	ss1958894899	Feb 12, 2016 (147)
23	GENOMED	ss1970364048	Jul 19, 2016 (147)
24	JJLAB	ss2023656586	Sep 14, 2016 (149)
25	USC_VALOUEV	ss2151832282	Dec 20, 2016 (150)
26	HUMAN_LONGEVITY	ss2282992715	Dec 20, 2016 (150)
27	GRF	ss2707427016	Nov 08, 2017 (151)
28	GNOMAD	ss2837517639	Nov 08, 2017 (151)
29	SWEGEN	ss2998840755	Nov 08, 2017 (151)
30	ILLUMINA	ss3022605703	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3025619296	Nov 08, 2017 (151)
32	ILLUMINA	ss3629511304	Oct 12, 2018 (152)
33	URBANLAB	ss3648321617	Oct 12, 2018 (152)
34	ILLUMINA	ss3653119525	Oct 12, 2018 (152)
35	EGCUT_WGS	ss3666728496	Jul 13, 2019 (153)
36	EVA_DECODE	ss3716938921	Jul 13, 2019 (153)
37	ILLUMINA	ss3726333612	Jul 13, 2019 (153)
38	ACPOP	ss3733381384	Jul 13, 2019 (153)
39	EVA	ss3764846252	Jul 13, 2019 (153)
40	PAGE_CC	ss3771282246	Jul 13, 2019 (153)
41	PACBIO	ss3785437192	Jul 13, 2019 (153)
42	PACBIO	ss3790794344	Jul 13, 2019 (153)
43	PACBIO	ss3795672918	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3808002440	Jul 13, 2019 (153)
45	EVA	ss3829850275	Apr 26, 2020 (154)
46	EVA	ss3838402598	Apr 26, 2020 (154)
47	EVA	ss3843846520	Apr 26, 2020 (154)
48	SGDP_PRJ	ss3864301950	Apr 26, 2020 (154)
49	KRGDB	ss3911079926	Apr 26, 2020 (154)
50	VINODS	ss4025214725	Apr 26, 2021 (155)
51	VINODS	ss4025235842	Apr 26, 2021 (155)
52	VINODS	ss4025252132	Apr 26, 2021 (155)
53	VINODS	ss4025294377	Apr 26, 2021 (155)
54	TOPMED	ss4698584884	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5176910797	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5267972810	Oct 13, 2022 (156)
57	HUGCELL_USP	ss5465694317	Oct 13, 2022 (156)
58	EVA	ss5508437547	Oct 13, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5553648040	Oct 13, 2022 (156)
60	SANFORD_IMAGENETICS	ss5640130596	Oct 13, 2022 (156)
61	TOMMO_GENOMICS	ss5714780959	Oct 13, 2022 (156)
62	YY_MCH	ss5807343782	Oct 13, 2022 (156)
63	EVA	ss5842050046	Oct 13, 2022 (156)
64	EVA	ss5855295680	Oct 13, 2022 (156)
65	EVA	ss5883277770	Oct 13, 2022 (156)
66	EVA	ss5968619860	Oct 13, 2022 (156)
67	1000Genomes	NC_000006.11 - 32670414	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000006.12 - 32702637	Oct 13, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 32670414	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000006.11 - 32670414	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000006.11 - 32670414	Apr 26, 2020 (154)
72	gnomAD - Genomes	NC_000006.12 - 32702637	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000006.11 - 32670414	Apr 26, 2020 (154)
74	KOREAN population from KRGDB	NC_000006.11 - 32670414	Apr 26, 2020 (154)
75	Northern Sweden	NC_000006.11 - 32670414	Jul 13, 2019 (153)
76	The PAGE Study	NC_000006.12 - 32702637	Jul 13, 2019 (153)
77	Qatari	NC_000006.11 - 32670414	Apr 26, 2020 (154)
78	SGDP_PRJ	NC_000006.11 - 32670414	Apr 26, 2020 (154)
79	Siberian	NC_000006.11 - 32670414	Apr 26, 2020 (154)
80	8.3KJPN	NC_000006.11 - 32670414	Apr 26, 2021 (155)
81	14KJPN	NC_000006.12 - 32702637	Oct 13, 2022 (156)
82	TopMed	NC_000006.12 - 32702637	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000006.11 - 32670414	Oct 12, 2018 (152)
84	A Vietnamese Genetic Variation Database	NC_000006.11 - 32670414	Jul 13, 2019 (153)
85	ALFA	NC_000006.12 - 32702637	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)
rs66709409	Feb 26, 2009 (130)
rs113297627	Sep 17, 2011 (135)
rs114482127	May 04, 2012 (137)
rs117484577	Aug 16, 2010 (132)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss109920101, ss201648940, ss207372148, ss211818590, ss278741273	NC_000006.10:32778391:C:T	NC_000006.12:32702636:C:T	(self)
31366435, 17483548, 12466744, 7779658, 7780429, 18257320, 6666249, 8085638, 16318930, 4348636, 34880104, 17483548, 3880142, ss222318237, ss233415623, ss240482575, ss533160810, ss559120646, ss653052009, ss982785979, ss1073512591, ss1319597649, ss1581614719, ss1615292021, ss1658286054, ss1804367222, ss1926043708, ss1958894899, ss1970364048, ss2023656586, ss2151832282, ss2707427016, ss2837517639, ss2998840755, ss3022605703, ss3629511304, ss3653119525, ss3666728496, ss3733381384, ss3764846252, ss3785437192, ss3790794344, ss3795672918, ss3829850275, ss3838402598, ss3864301950, ss3911079926, ss5176910797, ss5508437547, ss5640130596, ss5842050046, ss5968619860	NC_000006.11:32670413:C:T	NC_000006.12:32702636:C:T	(self)
41173975, 221431886, 503715, 48618063, 535962442, 14699410101, ss2282992715, ss3025619296, ss3648321617, ss3716938921, ss3726333612, ss3771282246, ss3808002440, ss3843846520, ss4698584884, ss5267972810, ss5465694317, ss5553648040, ss5714780959, ss5807343782, ss5855295680, ss5883277770	NC_000006.12:32702636:C:T	NC_000006.12:32702636:C:T	(self)
ss98488017, ss133422661	NT_007592.15:32610413:C:T	NC_000006.12:32702636:C:T	(self)
ss4025214725	NT_167245.2:3947243:C:T	NC_000006.12:32702636:C:T	(self)
ss4025235842	NT_167246.2:4122456:C:T	NC_000006.12:32702636:C:T	(self)
ss4025252132	NT_167247.2:4001878:C:T	NC_000006.12:32702636:C:T	(self)
ss4025294377	NT_167249.2:4103274:C:T	NC_000006.12:32702636:C:T	(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 rs66709408

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

rs66709408