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dbSNP Short Genetic Variations

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.

rs939583

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:622531 (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
C=0.141826 (37540/264690, TOPMED)
C=0.144688 (20280/140164, GnomAD)
C=0.11332 (8918/78696, PAGE_STUDY) (+ 20 more)
C=0.15767 (7177/45520, ALFA)
C=0.09282 (2623/28258, 14KJPN)
C=0.09302 (1559/16760, 8.3KJPN)
C=0.1254 (803/6404, 1000G_30x)
C=0.1318 (660/5008, 1000G)
C=0.1638 (734/4480, Estonian)
C=0.1749 (674/3854, ALSPAC)
C=0.1721 (638/3708, TWINSUK)
C=0.0966 (283/2930, KOREAN)
C=0.1105 (209/1892, HapMap)
C=0.1048 (192/1832, Korea1K)
C=0.167 (167/998, GoNL)
C=0.110 (87/790, PRJEB37584)
C=0.197 (118/600, NorthernSweden)
C=0.099 (55/556, SGDP_PRJ)
C=0.181 (39/216, Qatari)
C=0.080 (17/212, Vietnamese)
C=0.22 (14/64, Ancient Sardinia)
C=0.14 (7/50, Siberian)
C=0.15 (6/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 49248 C=0.15822 T=0.84178
European Sub 31780 C=0.17335 T=0.82665
African Sub 4576 C=0.1058 T=0.8942
African Others Sub 136 C=0.088 T=0.912
African American Sub 4440 C=0.1063 T=0.8937
Asian Sub 232 C=0.091 T=0.909
East Asian Sub 168 C=0.113 T=0.887
Other Asian Sub 64 C=0.03 T=0.97
Latin American 1 Sub 390 C=0.159 T=0.841
Latin American 2 Sub 6956 C=0.1162 T=0.8838
South Asian Sub 148 C=0.155 T=0.845
Other Sub 5166 C=0.1713 T=0.8287


Help

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 C=0.141826 T=0.858174
gnomAD - Genomes Global Study-wide 140164 C=0.144688 T=0.855312
gnomAD - Genomes European Sub 75894 C=0.16929 T=0.83071
gnomAD - Genomes African Sub 42014 C=0.10275 T=0.89725
gnomAD - Genomes American Sub 13650 C=0.12645 T=0.87355
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.2565 T=0.7435
gnomAD - Genomes East Asian Sub 3132 C=0.0750 T=0.9250
gnomAD - Genomes Other Sub 2152 C=0.1403 T=0.8597
The PAGE Study Global Study-wide 78696 C=0.11332 T=0.88668
The PAGE Study AfricanAmerican Sub 32512 C=0.10596 T=0.89404
The PAGE Study Mexican Sub 10808 C=0.11121 T=0.88879
The PAGE Study Asian Sub 8318 C=0.0945 T=0.9055
The PAGE Study PuertoRican Sub 7918 C=0.1540 T=0.8460
The PAGE Study NativeHawaiian Sub 4534 C=0.0737 T=0.9263
The PAGE Study Cuban Sub 4230 C=0.1418 T=0.8582
The PAGE Study Dominican Sub 3828 C=0.1277 T=0.8723
The PAGE Study CentralAmerican Sub 2450 C=0.1041 T=0.8959
The PAGE Study SouthAmerican Sub 1982 C=0.1140 T=0.8860
The PAGE Study NativeAmerican Sub 1260 C=0.1532 T=0.8468
The PAGE Study SouthAsian Sub 856 C=0.197 T=0.803
Allele Frequency Aggregator Total Global 45520 C=0.15767 T=0.84233
Allele Frequency Aggregator European Sub 28270 C=0.17439 T=0.82561
Allele Frequency Aggregator Latin American 2 Sub 6956 C=0.1162 T=0.8838
Allele Frequency Aggregator Other Sub 4950 C=0.1715 T=0.8285
Allele Frequency Aggregator African Sub 4574 C=0.1058 T=0.8942
Allele Frequency Aggregator Latin American 1 Sub 390 C=0.159 T=0.841
Allele Frequency Aggregator Asian Sub 232 C=0.091 T=0.909
Allele Frequency Aggregator South Asian Sub 148 C=0.155 T=0.845
14KJPN JAPANESE Study-wide 28258 C=0.09282 T=0.90718
8.3KJPN JAPANESE Study-wide 16760 C=0.09302 T=0.90698
1000Genomes_30x Global Study-wide 6404 C=0.1254 T=0.8746
1000Genomes_30x African Sub 1786 C=0.0873 T=0.9127
1000Genomes_30x Europe Sub 1266 C=0.1603 T=0.8397
1000Genomes_30x South Asian Sub 1202 C=0.1814 T=0.8186
1000Genomes_30x East Asian Sub 1170 C=0.0821 T=0.9179
1000Genomes_30x American Sub 980 C=0.133 T=0.867
1000Genomes Global Study-wide 5008 C=0.1318 T=0.8682
1000Genomes African Sub 1322 C=0.0893 T=0.9107
1000Genomes East Asian Sub 1008 C=0.0853 T=0.9147
1000Genomes Europe Sub 1006 C=0.1700 T=0.8300
1000Genomes South Asian Sub 978 C=0.193 T=0.807
1000Genomes American Sub 694 C=0.138 T=0.862
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.1638 T=0.8362
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.1749 T=0.8251
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.1721 T=0.8279
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.0966 T=0.9034
HapMap Global Study-wide 1892 C=0.1105 T=0.8895
HapMap American Sub 770 C=0.144 T=0.856
HapMap African Sub 692 C=0.058 T=0.942
HapMap Asian Sub 254 C=0.094 T=0.906
HapMap Europe Sub 176 C=0.193 T=0.807
Korean Genome Project KOREAN Study-wide 1832 C=0.1048 T=0.8952
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.167 T=0.833
CNV burdens in cranial meningiomas Global Study-wide 790 C=0.110 T=0.890
CNV burdens in cranial meningiomas CRM Sub 790 C=0.110 T=0.890
Northern Sweden ACPOP Study-wide 600 C=0.197 T=0.803
SGDP_PRJ Global Study-wide 556 C=0.099 T=0.901
Qatari Global Study-wide 216 C=0.181 T=0.819
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.080 T=0.920
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 64 C=0.22 T=0.78
Siberian Global Study-wide 50 C=0.14 T=0.86
The Danish reference pan genome Danish Study-wide 40 C=0.15 T=0.85
Help

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.622531C>T
GRCh37.p13 chr 2 NC_000002.11:g.622531C>T
Help

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
Help

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 2 NC_000002.12:g.622531= NC_000002.12:g.622531C>T
GRCh37.p13 chr 2 NC_000002.11:g.622531= NC_000002.11:g.622531C>T
Help

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#.

103 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1380008 Oct 05, 2000 (86)
2 SSAHASNP ss21726592 Apr 05, 2004 (123)
3 PERLEGEN ss24296899 Sep 20, 2004 (123)
4 ABI ss44194010 Mar 15, 2006 (126)
5 AFFY ss66144364 Nov 30, 2006 (127)
6 AFFY ss76165833 Dec 06, 2007 (129)
7 HGSV ss77520062 Dec 06, 2007 (129)
8 KRIBB_YJKIM ss81446103 Dec 15, 2007 (130)
9 HGSV ss83387807 Dec 15, 2007 (130)
10 BCMHGSC_JDW ss91024695 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss97005518 Feb 04, 2009 (130)
12 BGI ss103449443 Dec 01, 2009 (131)
13 1000GENOMES ss109150165 Jan 23, 2009 (130)
14 1000GENOMES ss112145173 Jan 25, 2009 (130)
15 ILLUMINA-UK ss117556877 Feb 14, 2009 (130)
16 ENSEMBL ss135838300 Dec 01, 2009 (131)
17 ENSEMBL ss138374230 Dec 01, 2009 (131)
18 GMI ss156587452 Dec 01, 2009 (131)
19 ILLUMINA ss161075245 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss162987342 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss163715184 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss165987147 Jul 04, 2010 (132)
23 AFFY ss172689029 Jul 04, 2010 (132)
24 BUSHMAN ss199928658 Jul 04, 2010 (132)
25 BCM-HGSC-SUB ss205702796 Jul 04, 2010 (132)
26 1000GENOMES ss219015961 Jul 14, 2010 (132)
27 1000GENOMES ss231002312 Jul 14, 2010 (132)
28 1000GENOMES ss238595569 Jul 15, 2010 (132)
29 GMI ss276318487 May 04, 2012 (137)
30 GMI ss284274590 Apr 25, 2013 (138)
31 PJP ss292251071 May 09, 2011 (134)
32 ILLUMINA ss479404860 Sep 08, 2015 (146)
33 ILLUMINA ss483403289 May 04, 2012 (137)
34 ILLUMINA ss484113392 May 04, 2012 (137)
35 ILLUMINA ss535615291 Sep 08, 2015 (146)
36 TISHKOFF ss555298558 Apr 25, 2013 (138)
37 SSMP ss648876014 Apr 25, 2013 (138)
38 ILLUMINA ss779414077 Sep 08, 2015 (146)
39 ILLUMINA ss782144822 Sep 08, 2015 (146)
40 ILLUMINA ss834883166 Sep 08, 2015 (146)
41 EVA-GONL ss976401778 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1068794433 Aug 21, 2014 (142)
43 1000GENOMES ss1295593117 Aug 21, 2014 (142)
44 DDI ss1428452149 Apr 01, 2015 (144)
45 EVA_GENOME_DK ss1578703019 Apr 01, 2015 (144)
46 EVA_DECODE ss1585802910 Apr 01, 2015 (144)
47 EVA_UK10K_ALSPAC ss1602636552 Apr 01, 2015 (144)
48 EVA_UK10K_TWINSUK ss1645630585 Apr 01, 2015 (144)
49 EVA_SVP ss1712424764 Apr 01, 2015 (144)
50 HAMMER_LAB ss1796115859 Sep 08, 2015 (146)
51 WEILL_CORNELL_DGM ss1919629133 Feb 12, 2016 (147)
52 ILLUMINA ss1958380733 Feb 12, 2016 (147)
53 GENOMED ss1968673447 Jul 19, 2016 (147)
54 JJLAB ss2020341494 Sep 14, 2016 (149)
55 USC_VALOUEV ss2148381166 Dec 20, 2016 (150)
56 HUMAN_LONGEVITY ss2226871917 Dec 20, 2016 (150)
57 SYSTEMSBIOZJU ss2624685350 Nov 08, 2017 (151)
58 ILLUMINA ss2633560459 Nov 08, 2017 (151)
59 GRF ss2702933441 Nov 08, 2017 (151)
60 GNOMAD ss2768867008 Nov 08, 2017 (151)
61 SWEGEN ss2988848957 Nov 08, 2017 (151)
62 ILLUMINA ss3021931909 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3023934083 Nov 08, 2017 (151)
64 CSHL ss3344032429 Nov 08, 2017 (151)
65 ILLUMINA ss3627972901 Oct 11, 2018 (152)
66 ILLUMINA ss3631530162 Oct 11, 2018 (152)
67 ILLUMINA ss3636432712 Oct 11, 2018 (152)
68 URBANLAB ss3646947073 Oct 11, 2018 (152)
69 ILLUMINA ss3652359942 Oct 11, 2018 (152)
70 EGCUT_WGS ss3656798883 Jul 12, 2019 (153)
71 EVA_DECODE ss3703092656 Jul 12, 2019 (153)
72 ILLUMINA ss3725749640 Jul 12, 2019 (153)
73 ACPOP ss3728080015 Jul 12, 2019 (153)
74 EVA ss3756251497 Jul 12, 2019 (153)
75 PAGE_CC ss3770889840 Jul 12, 2019 (153)
76 PACBIO ss3783756630 Jul 12, 2019 (153)
77 PACBIO ss3789359386 Jul 12, 2019 (153)
78 PACBIO ss3794232069 Jul 12, 2019 (153)
79 KHV_HUMAN_GENOMES ss3800639939 Jul 12, 2019 (153)
80 EVA ss3826774550 Apr 25, 2020 (154)
81 EVA ss3836791929 Apr 25, 2020 (154)
82 EVA ss3842205412 Apr 25, 2020 (154)
83 SGDP_PRJ ss3851414308 Apr 25, 2020 (154)
84 KRGDB ss3896782848 Apr 25, 2020 (154)
85 KOGIC ss3946955746 Apr 25, 2020 (154)
86 EVA ss3984476202 Apr 25, 2021 (155)
87 EVA ss3984867565 Apr 25, 2021 (155)
88 TOPMED ss4491609181 Apr 25, 2021 (155)
89 TOMMO_GENOMICS ss5149518910 Apr 25, 2021 (155)
90 1000G_HIGH_COVERAGE ss5246634500 Oct 12, 2022 (156)
91 EVA ss5314702855 Oct 12, 2022 (156)
92 EVA ss5326290073 Oct 12, 2022 (156)
93 HUGCELL_USP ss5446979181 Oct 12, 2022 (156)
94 EVA ss5506269489 Oct 12, 2022 (156)
95 1000G_HIGH_COVERAGE ss5521133554 Oct 12, 2022 (156)
96 SANFORD_IMAGENETICS ss5624433449 Oct 12, 2022 (156)
97 SANFORD_IMAGENETICS ss5627932927 Oct 12, 2022 (156)
98 TOMMO_GENOMICS ss5677596596 Oct 12, 2022 (156)
99 YY_MCH ss5801857513 Oct 12, 2022 (156)
100 EVA ss5819547981 Oct 12, 2022 (156)
101 EVA ss5852353897 Oct 12, 2022 (156)
102 EVA ss5928707017 Oct 12, 2022 (156)
103 EVA ss5954117329 Oct 12, 2022 (156)
104 1000Genomes NC_000002.11 - 622531 Oct 11, 2018 (152)
105 1000Genomes_30x NC_000002.12 - 622531 Oct 12, 2022 (156)
106 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 622531 Oct 11, 2018 (152)
107 Genetic variation in the Estonian population NC_000002.11 - 622531 Oct 11, 2018 (152)
108 The Danish reference pan genome NC_000002.11 - 622531 Apr 25, 2020 (154)
109 gnomAD - Genomes NC_000002.12 - 622531 Apr 25, 2021 (155)
110 Genome of the Netherlands Release 5 NC_000002.11 - 622531 Apr 25, 2020 (154)
111 HapMap NC_000002.12 - 622531 Apr 25, 2020 (154)
112 KOREAN population from KRGDB NC_000002.11 - 622531 Apr 25, 2020 (154)
113 Korean Genome Project NC_000002.12 - 622531 Apr 25, 2020 (154)
114 Northern Sweden NC_000002.11 - 622531 Jul 12, 2019 (153)
115 The PAGE Study NC_000002.12 - 622531 Jul 12, 2019 (153)
116 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000002.11 - 622531 Apr 25, 2021 (155)
117 CNV burdens in cranial meningiomas NC_000002.11 - 622531 Apr 25, 2021 (155)
118 Qatari NC_000002.11 - 622531 Apr 25, 2020 (154)
119 SGDP_PRJ NC_000002.11 - 622531 Apr 25, 2020 (154)
120 Siberian NC_000002.11 - 622531 Apr 25, 2020 (154)
121 8.3KJPN NC_000002.11 - 622531 Apr 25, 2021 (155)
122 14KJPN NC_000002.12 - 622531 Oct 12, 2022 (156)
123 TopMed NC_000002.12 - 622531 Apr 25, 2021 (155)
124 UK 10K study - Twins NC_000002.11 - 622531 Oct 11, 2018 (152)
125 A Vietnamese Genetic Variation Database NC_000002.11 - 622531 Jul 12, 2019 (153)
126 ALFA NC_000002.12 - 622531 Apr 25, 2021 (155)
Help

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)
rs13028878 Sep 24, 2004 (123)
rs17785356 Oct 08, 2004 (123)
rs58185439 May 24, 2008 (130)
rs60877665 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77520062, ss83387807 NC_000002.9:612530:C:T NC_000002.12:622530:C:T (self)
ss66144364, ss76165833, ss91024695, ss109150165, ss112145173, ss117556877, ss162987342, ss163715184, ss165987147, ss172689029, ss199928658, ss205702796, ss276318487, ss284274590, ss292251071, ss484113392, ss1585802910, ss1712424764 NC_000002.10:612530:C:T NC_000002.12:622530:C:T (self)
6483600, 3587498, 2537131, 4882846, 1576936, 3960242, 1364880, 93492, 25526, 1671063, 3431288, 897520, 7488217, 3587498, 782973, ss219015961, ss231002312, ss238595569, ss479404860, ss483403289, ss535615291, ss555298558, ss648876014, ss779414077, ss782144822, ss834883166, ss976401778, ss1068794433, ss1295593117, ss1428452149, ss1578703019, ss1602636552, ss1645630585, ss1796115859, ss1919629133, ss1958380733, ss1968673447, ss2020341494, ss2148381166, ss2624685350, ss2633560459, ss2702933441, ss2768867008, ss2988848957, ss3021931909, ss3344032429, ss3627972901, ss3631530162, ss3636432712, ss3652359942, ss3656798883, ss3728080015, ss3756251497, ss3783756630, ss3789359386, ss3794232069, ss3826774550, ss3836791929, ss3851414308, ss3896782848, ss3984476202, ss3984867565, ss5149518910, ss5314702855, ss5326290073, ss5506269489, ss5624433449, ss5627932927, ss5819547981, ss5954117329 NC_000002.11:622530:C:T NC_000002.12:622530:C:T (self)
8659489, 46281662, 1719139, 3333747, 111309, 11433700, 295432060, 519956968, ss2226871917, ss3023934083, ss3646947073, ss3703092656, ss3725749640, ss3770889840, ss3800639939, ss3842205412, ss3946955746, ss4491609181, ss5246634500, ss5446979181, ss5521133554, ss5677596596, ss5801857513, ss5852353897, ss5928707017 NC_000002.12:622530:C:T NC_000002.12:622530:C:T (self)
ss1380008, ss24296899, ss44194010, ss81446103, ss97005518, ss103449443, ss135838300, ss138374230, ss156587452, ss161075245 NT_022221.13:612530:C:T NC_000002.12:622530:C:T (self)
ss21726592 NT_022327.13:612530:C:T NC_000002.12:622530:C:T (self)
Help

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

1 citation for rs939583
PMID Title Author Year Journal
24064335 Meta-analysis of genome-wide association data identifies novel susceptibility loci for obesity. Pei YF et al. 2014 Human molecular genetics
Help

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.

Software version is: 2.0.1.post761+d5e8e07