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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.

rs7902778

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:62400357 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.02694 (2120/78696, PAGE_STUDY)
T=0.00991 (375/37848, ALFA)
T=0.0240 (154/6404, 1000G_30x) (+ 12 more)
T=0.0242 (121/5008, 1000G)
T=0.0007 (3/4480, Estonian)
T=0.0029 (11/3854, ALSPAC)
T=0.0024 (9/3708, TWINSUK)
T=0.0457 (63/1380, HapMap)
T=0.003 (3/998, GoNL)
T=0.003 (2/626, Chileans)
T=0.012 (7/600, NorthernSweden)
T=0.004 (2/534, MGP)
T=0.028 (6/216, Qatari)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNF365 : 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 37848 C=0.99009 A=0.00000, T=0.00991
European Sub 26146 C=0.99816 A=0.00000, T=0.00184
African Sub 7734 C=0.9633 A=0.0000, T=0.0367
African Others Sub 238 C=0.954 A=0.000, T=0.046
African American Sub 7496 C=0.9636 A=0.0000, T=0.0364
Asian Sub 210 C=1.000 A=0.000, T=0.000
East Asian Sub 150 C=1.000 A=0.000, T=0.000
Other Asian Sub 60 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 226 C=0.996 A=0.000, T=0.004
Latin American 2 Sub 842 C=0.999 A=0.000, T=0.001
South Asian Sub 126 C=1.000 A=0.000, T=0.000
Other Sub 2564 C=0.9840 A=0.0000, T=0.0160


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
The PAGE Study Global Study-wide 78696 C=0.97306 T=0.02694
The PAGE Study AfricanAmerican Sub 32516 C=0.94827 T=0.05173
The PAGE Study Mexican Sub 10810 C=0.99593 T=0.00407
The PAGE Study Asian Sub 8314 C=0.9998 T=0.0002
The PAGE Study PuertoRican Sub 7918 C=0.9799 T=0.0201
The PAGE Study NativeHawaiian Sub 4534 C=0.9982 T=0.0018
The PAGE Study Cuban Sub 4230 C=0.9868 T=0.0132
The PAGE Study Dominican Sub 3828 C=0.9744 T=0.0256
The PAGE Study CentralAmerican Sub 2450 C=0.9873 T=0.0127
The PAGE Study SouthAmerican Sub 1982 C=0.9909 T=0.0091
The PAGE Study NativeAmerican Sub 1260 C=0.9897 T=0.0103
The PAGE Study SouthAsian Sub 854 C=0.989 T=0.011
Allele Frequency Aggregator Total Global 37848 C=0.99009 A=0.00000, T=0.00991
Allele Frequency Aggregator European Sub 26146 C=0.99816 A=0.00000, T=0.00184
Allele Frequency Aggregator African Sub 7734 C=0.9633 A=0.0000, T=0.0367
Allele Frequency Aggregator Other Sub 2564 C=0.9840 A=0.0000, T=0.0160
Allele Frequency Aggregator Latin American 2 Sub 842 C=0.999 A=0.000, T=0.001
Allele Frequency Aggregator Latin American 1 Sub 226 C=0.996 A=0.000, T=0.004
Allele Frequency Aggregator Asian Sub 210 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 126 C=1.000 A=0.000, T=0.000
1000Genomes_30x Global Study-wide 6404 C=0.9760 T=0.0240
1000Genomes_30x African Sub 1786 C=0.9395 T=0.0605
1000Genomes_30x Europe Sub 1266 C=0.9968 T=0.0032
1000Genomes_30x South Asian Sub 1202 C=0.9775 T=0.0225
1000Genomes_30x East Asian Sub 1170 C=0.9983 T=0.0017
1000Genomes_30x American Sub 980 C=0.987 T=0.013
1000Genomes Global Study-wide 5008 C=0.9758 T=0.0242
1000Genomes African Sub 1322 C=0.9380 T=0.0620
1000Genomes East Asian Sub 1008 C=0.9990 T=0.0010
1000Genomes Europe Sub 1006 C=0.9960 T=0.0040
1000Genomes South Asian Sub 978 C=0.974 T=0.026
1000Genomes American Sub 694 C=0.987 T=0.013
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9993 T=0.0007
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9971 T=0.0029
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9976 T=0.0024
HapMap Global Study-wide 1380 C=0.9543 T=0.0457
HapMap African Sub 692 C=0.935 T=0.065
HapMap American Sub 600 C=0.970 T=0.030
HapMap Asian Sub 88 C=1.00 T=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.997 T=0.003
Chileans Chilean Study-wide 626 C=0.997 T=0.003
Northern Sweden ACPOP Study-wide 600 C=0.988 T=0.012
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.996 T=0.004
Qatari Global Study-wide 216 C=0.972 T=0.028
SGDP_PRJ Global Study-wide 4 C=0.5 T=0.5
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 10 NC_000010.11:g.62400357C>A
GRCh38.p14 chr 10 NC_000010.11:g.62400357C>T
GRCh37.p13 chr 10 NC_000010.10:g.64160116C>A
GRCh37.p13 chr 10 NC_000010.10:g.64160116C>T
ZNF365 RefSeqGene NG_021209.2:g.31166C>A
ZNF365 RefSeqGene NG_021209.2:g.31166C>T
Gene: ZNF365, zinc finger protein 365 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF365 transcript variant B NM_199450.3:c.924+11781C>A N/A Intron Variant
ZNF365 transcript variant A NM_014951.3:c.*568= N/A 3 Prime UTR Variant
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= A T
GRCh38.p14 chr 10 NC_000010.11:g.62400357= NC_000010.11:g.62400357C>A NC_000010.11:g.62400357C>T
GRCh37.p13 chr 10 NC_000010.10:g.64160116= NC_000010.10:g.64160116C>A NC_000010.10:g.64160116C>T
ZNF365 RefSeqGene NG_021209.2:g.31166= NG_021209.2:g.31166C>A NG_021209.2:g.31166C>T
ZNF365 transcript variant A NM_014951.3:c.*568= NM_014951.3:c.*568C>A NM_014951.3:c.*568C>T
ZNF365 transcript variant A NM_014951.2:c.*568= NM_014951.2:c.*568C>A NM_014951.2:c.*568C>T
ZNF365 transcript variant B NM_199450.2:c.924+11781= NM_199450.2:c.924+11781C>A NM_199450.2:c.924+11781C>T
ZNF365 transcript variant B NM_199450.3:c.924+11781= NM_199450.3:c.924+11781C>A NM_199450.3:c.924+11781C>T
ZNF365 transcript variant C NM_199451.2:c.924+11781= NM_199451.2:c.924+11781C>A NM_199451.2:c.924+11781C>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#.

53 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss12077113 Jul 11, 2003 (116)
2 ILLUMINA ss75030016 Dec 06, 2007 (129)
3 AFFY ss76568155 Dec 08, 2007 (130)
4 KRIBB_YJKIM ss119574437 Dec 01, 2009 (131)
5 ILLUMINA ss174609819 Jul 04, 2010 (132)
6 BUSHMAN ss201606935 Jul 04, 2010 (132)
7 1000GENOMES ss224764345 Jul 14, 2010 (132)
8 ILLUMINA ss482398651 May 04, 2012 (137)
9 ILLUMINA ss482627507 May 04, 2012 (137)
10 ILLUMINA ss534631991 Sep 08, 2015 (146)
11 TISHKOFF ss561999733 Apr 25, 2013 (138)
12 ILLUMINA ss779364617 Sep 08, 2015 (146)
13 ILLUMINA ss781748345 Sep 08, 2015 (146)
14 ILLUMINA ss834832866 Sep 08, 2015 (146)
15 EVA-GONL ss987562124 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1077041459 Aug 21, 2014 (142)
17 1000GENOMES ss1337713780 Aug 21, 2014 (142)
18 EVA_DECODE ss1597229715 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1624712581 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1667706614 Apr 01, 2015 (144)
21 EVA_MGP ss1711258518 Apr 01, 2015 (144)
22 EVA_SVP ss1713184711 Apr 01, 2015 (144)
23 WEILL_CORNELL_DGM ss1930925195 Feb 12, 2016 (147)
24 ILLUMINA ss1959267699 Feb 12, 2016 (147)
25 HUMAN_LONGEVITY ss2175315005 Dec 20, 2016 (150)
26 ILLUMINA ss2632719231 Nov 08, 2017 (151)
27 GNOMAD ss2889558120 Nov 08, 2017 (151)
28 SWEGEN ss3006591164 Nov 08, 2017 (151)
29 ILLUMINA ss3021245497 Nov 08, 2017 (151)
30 ILLUMINA ss3626460453 Oct 12, 2018 (152)
31 ILLUMINA ss3630744576 Oct 12, 2018 (152)
32 ILLUMINA ss3637853534 Oct 12, 2018 (152)
33 ILLUMINA ss3642856790 Oct 12, 2018 (152)
34 ILLUMINA ss3651600728 Oct 12, 2018 (152)
35 EGCUT_WGS ss3674005160 Jul 13, 2019 (153)
36 EVA_DECODE ss3690014844 Jul 13, 2019 (153)
37 ILLUMINA ss3725162097 Jul 13, 2019 (153)
38 ACPOP ss3737382979 Jul 13, 2019 (153)
39 PAGE_CC ss3771561634 Jul 13, 2019 (153)
40 KHV_HUMAN_GENOMES ss3813560656 Jul 13, 2019 (153)
41 SGDP_PRJ ss3874352175 Apr 26, 2020 (154)
42 FSA-LAB ss3983978513 Apr 26, 2021 (155)
43 TOPMED ss4854810454 Apr 26, 2021 (155)
44 TOPMED ss4854810455 Apr 26, 2021 (155)
45 1000G_HIGH_COVERAGE ss5284288038 Oct 16, 2022 (156)
46 EVA ss5393895968 Oct 16, 2022 (156)
47 HUGCELL_USP ss5479841748 Oct 16, 2022 (156)
48 EVA ss5510044150 Oct 16, 2022 (156)
49 1000G_HIGH_COVERAGE ss5578359152 Oct 16, 2022 (156)
50 SANFORD_IMAGENETICS ss5649424576 Oct 16, 2022 (156)
51 EVA ss5824490648 Oct 16, 2022 (156)
52 EVA ss5879178419 Oct 16, 2022 (156)
53 EVA ss5940697324 Oct 16, 2022 (156)
54 1000Genomes NC_000010.10 - 64160116 Oct 12, 2018 (152)
55 1000Genomes_30x NC_000010.11 - 62400357 Oct 16, 2022 (156)
56 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 64160116 Oct 12, 2018 (152)
57 Chileans NC_000010.10 - 64160116 Apr 26, 2020 (154)
58 Genetic variation in the Estonian population NC_000010.10 - 64160116 Oct 12, 2018 (152)
59 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 354202123 (NC_000010.11:62400356:C:A 7/140226)
Row 354202124 (NC_000010.11:62400356:C:T 2630/140222)

- Apr 26, 2021 (155)
60 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 354202123 (NC_000010.11:62400356:C:A 7/140226)
Row 354202124 (NC_000010.11:62400356:C:T 2630/140222)

- Apr 26, 2021 (155)
61 Genome of the Netherlands Release 5 NC_000010.10 - 64160116 Apr 26, 2020 (154)
62 HapMap NC_000010.11 - 62400357 Apr 26, 2020 (154)
63 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 64160116 Apr 26, 2020 (154)
64 Northern Sweden NC_000010.10 - 64160116 Jul 13, 2019 (153)
65 The PAGE Study NC_000010.11 - 62400357 Jul 13, 2019 (153)
66 Qatari NC_000010.10 - 64160116 Apr 26, 2020 (154)
67 SGDP_PRJ NC_000010.10 - 64160116 Apr 26, 2020 (154)
68 TopMed

Submission ignored due to conflicting rows:
Row 70356109 (NC_000010.11:62400356:C:A 16/264690)
Row 70356110 (NC_000010.11:62400356:C:T 5335/264690)

- Apr 26, 2021 (155)
69 TopMed

Submission ignored due to conflicting rows:
Row 70356109 (NC_000010.11:62400356:C:A 16/264690)
Row 70356110 (NC_000010.11:62400356:C:T 5335/264690)

- Apr 26, 2021 (155)
70 UK 10K study - Twins NC_000010.10 - 64160116 Oct 12, 2018 (152)
71 ALFA NC_000010.11 - 62400357 Apr 26, 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)
rs56594328 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1699048657, ss4854810454 NC_000010.11:62400356:C:A NC_000010.11:62400356:C:A (self)
ss201606935, ss482627507, ss1597229715, ss1713184711, ss3642856790 NC_000010.9:63830121:C:T NC_000010.11:62400356:C:T (self)
50111575, 27814043, 52112, 19743408, 12404239, 374278, 10667844, 12967125, 26369155, 27814043, ss224764345, ss482398651, ss534631991, ss561999733, ss779364617, ss781748345, ss834832866, ss987562124, ss1077041459, ss1337713780, ss1624712581, ss1667706614, ss1711258518, ss1930925195, ss1959267699, ss2632719231, ss2889558120, ss3006591164, ss3021245497, ss3626460453, ss3630744576, ss3637853534, ss3651600728, ss3674005160, ss3737382979, ss3874352175, ss3983978513, ss5393895968, ss5510044150, ss5649424576, ss5824490648, ss5940697324 NC_000010.10:64160115:C:T NC_000010.11:62400356:C:T (self)
65885087, 418266, 783103, 1699048657, ss2175315005, ss3690014844, ss3725162097, ss3771561634, ss3813560656, ss4854810455, ss5284288038, ss5479841748, ss5578359152, ss5879178419 NC_000010.11:62400356:C:T NC_000010.11:62400356:C:T (self)
ss12077113 NT_008583.15:12711263:C:T NC_000010.11:62400356:C:T (self)
ss75030016, ss76568155, ss119574437, ss174609819 NT_030059.13:14964579:C:T NC_000010.11:62400356:C:T (self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
ss2338347611 NC_000010.10:64160115:C:A NC_000010.11:62400356:C:A
Help

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

No publications for rs7902778

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