Name: rs9366890
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.

rs9366890

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:35595197 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.176112 (46615/264690, TOPMED)
T=0.171677 (24055/140118, GnomAD)
T=0.18151 (5129/28258, 14KJPN) (+ 17 more)
T=0.17099 (3230/18890, ALFA)
T=0.18383 (3081/16760, 8.3KJPN)
T=0.1854 (1187/6404, 1000G_30x)
T=0.1895 (949/5008, 1000G)
T=0.1578 (707/4480, Estonian)
T=0.1692 (652/3854, ALSPAC)
T=0.1799 (667/3708, TWINSUK)
T=0.1679 (492/2930, KOREAN)
T=0.1709 (313/1832, Korea1K)
T=0.164 (164/998, GoNL)
T=0.187 (112/600, NorthernSweden)
T=0.139 (72/518, SGDP_PRJ)
T=0.174 (57/328, HapMap)
T=0.241 (52/216, Qatari)
T=0.262 (56/214, Vietnamese)
T=0.22 (12/54, Siberian)
T=0.17 (7/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FKBP5 : Intron Variant
Publications: 1 citation
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	18890	T=0.17099	A=0.82901
European	Sub	14286	T=0.17122	A=0.82878
African	Sub	2946	T=0.1684	A=0.8316
African Others	Sub	114	T=0.123	A=0.877
African American	Sub	2832	T=0.1702	A=0.8298
Asian	Sub	112	T=0.170	A=0.830
East Asian	Sub	86	T=0.15	A=0.85
Other Asian	Sub	26	T=0.23	A=0.77
Latin American 1	Sub	146	T=0.199	A=0.801
Latin American 2	Sub	610	T=0.123	A=0.877
South Asian	Sub	98	T=0.30	A=0.70
Other	Sub	692	T=0.197	A=0.803

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.176112	A=0.823888
gnomAD - Genomes	Global	Study-wide	140118	T=0.171677	A=0.828323
gnomAD - Genomes	European	Sub	75918	T=0.17494	A=0.82506
gnomAD - Genomes	African	Sub	41940	T=0.16187	A=0.83813
gnomAD - Genomes	American	Sub	13654	T=0.16654	A=0.83346
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.1907	A=0.8093
gnomAD - Genomes	East Asian	Sub	3130	T=0.2067	A=0.7933
gnomAD - Genomes	Other	Sub	2152	T=0.1998	A=0.8002
14KJPN	JAPANESE	Study-wide	28258	T=0.18151	A=0.81849
Allele Frequency Aggregator	Total	Global	18890	T=0.17099	A=0.82901
Allele Frequency Aggregator	European	Sub	14286	T=0.17122	A=0.82878
Allele Frequency Aggregator	African	Sub	2946	T=0.1684	A=0.8316
Allele Frequency Aggregator	Other	Sub	692	T=0.197	A=0.803
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.123	A=0.877
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.199	A=0.801
Allele Frequency Aggregator	Asian	Sub	112	T=0.170	A=0.830
Allele Frequency Aggregator	South Asian	Sub	98	T=0.30	A=0.70
8.3KJPN	JAPANESE	Study-wide	16760	T=0.18383	A=0.81617
1000Genomes_30x	Global	Study-wide	6404	T=0.1854	A=0.8146
1000Genomes_30x	African	Sub	1786	T=0.1517	A=0.8483
1000Genomes_30x	Europe	Sub	1266	T=0.2038	A=0.7962
1000Genomes_30x	South Asian	Sub	1202	T=0.2629	A=0.7371
1000Genomes_30x	East Asian	Sub	1170	T=0.1821	A=0.8179
1000Genomes_30x	American	Sub	980	T=0.132	A=0.868
1000Genomes	Global	Study-wide	5008	T=0.1895	A=0.8105
1000Genomes	African	Sub	1322	T=0.1520	A=0.8480
1000Genomes	East Asian	Sub	1008	T=0.1746	A=0.8254
1000Genomes	Europe	Sub	1006	T=0.2048	A=0.7952
1000Genomes	South Asian	Sub	978	T=0.271	A=0.729
1000Genomes	American	Sub	694	T=0.146	A=0.854
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1578	A=0.8422
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1692	A=0.8308
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1799	A=0.8201
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.1679	A=0.8321
Korean Genome Project	KOREAN	Study-wide	1832	T=0.1709	A=0.8291
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.164	A=0.836
Northern Sweden	ACPOP	Study-wide	600	T=0.187	A=0.813
SGDP_PRJ	Global	Study-wide	518	T=0.139	A=0.861
HapMap	Global	Study-wide	328	T=0.174	A=0.826
HapMap	African	Sub	120	T=0.183	A=0.817
HapMap	American	Sub	120	T=0.175	A=0.825
HapMap	Asian	Sub	88	T=0.16	A=0.84
Qatari	Global	Study-wide	216	T=0.241	A=0.759
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.262	A=0.738
Siberian	Global	Study-wide	54	T=0.22	A=0.78
The Danish reference pan genome	Danish	Study-wide	40	T=0.17	A=0.82

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.35595197T>A
GRCh37.p13 chr 6	NC_000006.11:g.35562974T>A
FKBP5 RefSeqGene	NG_012645.2:g.138387A>T

Gene: FKBP5, FKBP prolyl isomerase 5 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FKBP5 transcript variant 2	NM_001145775.3:c.665+2051… NM_001145775.3:c.665+2051A>T	N/A	Intron Variant
FKBP5 transcript variant 3	NM_001145776.2:c.665+2051… NM_001145776.2:c.665+2051A>T	N/A	Intron Variant
FKBP5 transcript variant 4	NM_001145777.2:c.665+2051… NM_001145777.2:c.665+2051A>T	N/A	Intron Variant
FKBP5 transcript variant 1	NM_004117.4:c.665+2051A>T	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	T=	A
GRCh38.p14 chr 6	NC_000006.12:g.35595197=	NC_000006.12:g.35595197T>A
GRCh37.p13 chr 6	NC_000006.11:g.35562974=	NC_000006.11:g.35562974T>A
FKBP5 RefSeqGene	NG_012645.2:g.138387=	NG_012645.2:g.138387A>T
FKBP5 transcript variant 2	NM_001145775.1:c.665+2051=	NM_001145775.1:c.665+2051A>T
FKBP5 transcript variant 2	NM_001145775.3:c.665+2051=	NM_001145775.3:c.665+2051A>T
FKBP5 transcript variant 3	NM_001145776.1:c.665+2051=	NM_001145776.1:c.665+2051A>T
FKBP5 transcript variant 3	NM_001145776.2:c.665+2051=	NM_001145776.2:c.665+2051A>T
FKBP5 transcript variant 4	NM_001145777.1:c.665+2051=	NM_001145777.1:c.665+2051A>T
FKBP5 transcript variant 4	NM_001145777.2:c.665+2051=	NM_001145777.2:c.665+2051A>T
FKBP5 transcript variant 1	NM_004117.3:c.665+2051=	NM_004117.3:c.665+2051A>T
FKBP5 transcript variant 1	NM_004117.4:c.665+2051=	NM_004117.4:c.665+2051A>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#.

80 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss12834058	Dec 05, 2003 (119)
2	SSAHASNP	ss22461397	Apr 05, 2004 (121)
3	ABI	ss42726171	Mar 15, 2006 (126)
4	KRIBB_YJKIM	ss65847868	Nov 29, 2006 (127)
5	HGSV	ss82780488	Dec 15, 2007 (130)
6	BCMHGSC_JDW	ss93442670	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss98385558	Feb 05, 2009 (130)
8	BGI	ss105993522	Feb 05, 2009 (130)
9	1000GENOMES	ss109947593	Jan 24, 2009 (130)
10	1000GENOMES	ss114206067	Jan 25, 2009 (130)
11	ILLUMINA-UK	ss116417730	Feb 14, 2009 (130)
12	ENSEMBL	ss143676594	Dec 01, 2009 (131)
13	ENSEMBL	ss143837746	Dec 01, 2009 (131)
14	GMI	ss156801265	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss162243019	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss163398811	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss166502065	Jul 04, 2010 (132)
18	BUSHMAN	ss201683855	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss207670587	Jul 04, 2010 (132)
20	1000GENOMES	ss222332551	Jul 14, 2010 (132)
21	1000GENOMES	ss233427978	Jul 14, 2010 (132)
22	1000GENOMES	ss240493521	Jul 15, 2010 (132)
23	GMI	ss278753081	May 04, 2012 (137)
24	GMI	ss285386040	Apr 25, 2013 (138)
25	PJP	ss293836781	May 09, 2011 (134)
26	TISHKOFF	ss559136665	Apr 25, 2013 (138)
27	SSMP	ss653072861	Apr 25, 2013 (138)
28	EVA-GONL	ss982814099	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1073529992	Aug 21, 2014 (142)
30	1000GENOMES	ss1319683681	Aug 21, 2014 (142)
31	DDI	ss1430687744	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1581626912	Apr 01, 2015 (144)
33	EVA_DECODE	ss1592347594	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1615338792	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1658332825	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1804379434	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1926070744	Feb 12, 2016 (147)
38	GENOMED	ss1970370801	Jul 19, 2016 (147)
39	JJLAB	ss2023672808	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2151849913	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2283159223	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2626324785	Nov 08, 2017 (151)
43	GRF	ss2707446188	Nov 08, 2017 (151)
44	GNOMAD	ss2837750347	Nov 08, 2017 (151)
45	SWEGEN	ss2998884638	Nov 08, 2017 (151)
46	ILLUMINA	ss3022610880	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3025628176	Nov 08, 2017 (151)
48	CSHL	ss3346910963	Nov 08, 2017 (151)
49	URBANLAB	ss3648328129	Oct 12, 2018 (152)
50	ILLUMINA	ss3653127064	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3666771839	Jul 13, 2019 (153)
52	EVA_DECODE	ss3716989503	Jul 13, 2019 (153)
53	ILLUMINA	ss3726337814	Jul 13, 2019 (153)
54	ACPOP	ss3733406393	Jul 13, 2019 (153)
55	EVA	ss3764881250	Jul 13, 2019 (153)
56	PACBIO	ss3785444475	Jul 13, 2019 (153)
57	PACBIO	ss3790800482	Jul 13, 2019 (153)
58	PACBIO	ss3795679099	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3808033590	Jul 13, 2019 (153)
60	EVA	ss3829866122	Apr 26, 2020 (154)
61	EVA	ss3838410360	Apr 26, 2020 (154)
62	EVA	ss3843854479	Apr 26, 2020 (154)
63	SGDP_PRJ	ss3864351811	Apr 26, 2020 (154)
64	KRGDB	ss3911137195	Apr 26, 2020 (154)
65	KOGIC	ss3958799443	Apr 26, 2020 (154)
66	TOPMED	ss4699231812	Apr 26, 2021 (155)
67	TOMMO_GENOMICS	ss5177009102	Apr 26, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5268052982	Oct 17, 2022 (156)
69	EVA	ss5364911556	Oct 17, 2022 (156)
70	HUGCELL_USP	ss5465764154	Oct 17, 2022 (156)
71	EVA	ss5508451583	Oct 17, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5553759098	Oct 17, 2022 (156)
73	SANFORD_IMAGENETICS	ss5640178319	Oct 17, 2022 (156)
74	TOMMO_GENOMICS	ss5714909985	Oct 17, 2022 (156)
75	YY_MCH	ss5807370637	Oct 17, 2022 (156)
76	EVA	ss5842086943	Oct 17, 2022 (156)
77	EVA	ss5848093564	Oct 17, 2022 (156)
78	EVA	ss5855310434	Oct 17, 2022 (156)
79	EVA	ss5883364693	Oct 17, 2022 (156)
80	EVA	ss5968667806	Oct 17, 2022 (156)
81	1000Genomes	NC_000006.11 - 35562974	Oct 12, 2018 (152)
82	1000Genomes_30x	NC_000006.12 - 35595197	Oct 17, 2022 (156)
83	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 35562974	Oct 12, 2018 (152)
84	Genetic variation in the Estonian population	NC_000006.11 - 35562974	Oct 12, 2018 (152)
85	The Danish reference pan genome	NC_000006.11 - 35562974	Apr 26, 2020 (154)
86	gnomAD - Genomes	NC_000006.12 - 35595197	Apr 26, 2021 (155)
87	Genome of the Netherlands Release 5	NC_000006.11 - 35562974	Apr 26, 2020 (154)
88	HapMap	NC_000006.12 - 35595197	Apr 26, 2020 (154)
89	KOREAN population from KRGDB	NC_000006.11 - 35562974	Apr 26, 2020 (154)
90	Korean Genome Project	NC_000006.12 - 35595197	Apr 26, 2020 (154)
91	Northern Sweden	NC_000006.11 - 35562974	Jul 13, 2019 (153)
92	Qatari	NC_000006.11 - 35562974	Apr 26, 2020 (154)
93	SGDP_PRJ	NC_000006.11 - 35562974	Apr 26, 2020 (154)
94	Siberian	NC_000006.11 - 35562974	Apr 26, 2020 (154)
95	8.3KJPN	NC_000006.11 - 35562974	Apr 26, 2021 (155)
96	14KJPN	NC_000006.12 - 35595197	Oct 17, 2022 (156)
97	TopMed	NC_000006.12 - 35595197	Apr 26, 2021 (155)
98	UK 10K study - Twins	NC_000006.11 - 35562974	Oct 12, 2018 (152)
99	A Vietnamese Genetic Variation Database	NC_000006.11 - 35562974	Jul 13, 2019 (153)
100	ALFA	NC_000006.12 - 35595197	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)
rs59568403	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82780488	NC_000006.9:35670951:T:A	NC_000006.12:35595196:T:A	(self)
ss93442670, ss109947593, ss114206067, ss116417730, ss162243019, ss163398811, ss166502065, ss201683855, ss207670587, ss278753081, ss285386040, ss293836781, ss1592347594	NC_000006.10:35670951:T:A	NC_000006.12:35595196:T:A	(self)
31456035, 17535489, 12510087, 7791851, 7807156, 18314589, 6691258, 8112674, 16368791, 4366267, 34978409, 17535489, 3894011, ss222332551, ss233427978, ss240493521, ss559136665, ss653072861, ss982814099, ss1073529992, ss1319683681, ss1430687744, ss1581626912, ss1615338792, ss1658332825, ss1804379434, ss1926070744, ss1970370801, ss2023672808, ss2151849913, ss2626324785, ss2707446188, ss2837750347, ss2998884638, ss3022610880, ss3346910963, ss3653127064, ss3666771839, ss3733406393, ss3764881250, ss3785444475, ss3790800482, ss3795679099, ss3829866122, ss3838410360, ss3864351811, ss3911137195, ss5177009102, ss5364911556, ss5508451583, ss5640178319, ss5842086943, ss5848093564, ss5968667806	NC_000006.11:35562973:T:A	NC_000006.12:35595196:T:A	(self)
41285033, 222007927, 3108335, 15177444, 48747089, 536609370, 6593650594, ss2283159223, ss3025628176, ss3648328129, ss3716989503, ss3726337814, ss3808033590, ss3843854479, ss3958799443, ss4699231812, ss5268052982, ss5465764154, ss5553759098, ss5714909985, ss5807370637, ss5855310434, ss5883364693	NC_000006.12:35595196:T:A	NC_000006.12:35595196:T:A	(self)
ss12834058, ss22461397	NT_007592.13:26360100:T:A	NC_000006.12:35595196:T:A	(self)
ss42726171, ss65847868, ss98385558, ss105993522, ss143676594, ss143837746, ss156801265	NT_007592.15:35502973:T:A	NC_000006.12:35595196:T:A	(self)

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

1 citation for rs9366890

PMID	Title	Author	Year	Journal
20376328	Assessment of SNPs associated with the human glucocorticoid receptor in primary open-angle glaucoma and steroid responders.	Fingert JH et al.	2010	Molecular vision

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

rs9366890