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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.

rs766

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:93347426 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.039544 (10467/264690, TOPMED)
C=0.047544 (6401/134632, GnomAD)
C=0.05232 (988/18882, ALFA) (+ 13 more)
C=0.0292 (187/6404, 1000G_30x)
C=0.0278 (139/5008, 1000G)
C=0.0789 (353/4474, Estonian)
C=0.0405 (156/3854, ALSPAC)
C=0.0418 (155/3708, TWINSUK)
C=0.037 (37/998, GoNL)
C=0.050 (30/600, NorthernSweden)
C=0.042 (9/216, Qatari)
C=0.03 (1/40, GENOME_DK)
G=0.50 (8/16, SGDP_PRJ)
C=0.50 (8/16, SGDP_PRJ)
G=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EPHA7 : 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 18882 G=0.94768 C=0.05232
European Sub 14278 G=0.94467 C=0.05533
African Sub 2946 G=0.9467 C=0.0533
African Others Sub 114 G=0.947 C=0.053
African American Sub 2832 G=0.9467 C=0.0533
Asian Sub 112 G=1.000 C=0.000
East Asian Sub 86 G=1.00 C=0.00
Other Asian Sub 26 G=1.00 C=0.00
Latin American 1 Sub 146 G=0.979 C=0.021
Latin American 2 Sub 610 G=0.992 C=0.008
South Asian Sub 98 G=0.99 C=0.01
Other Sub 692 G=0.954 C=0.046


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 G=0.960456 C=0.039544
gnomAD - Genomes Global Study-wide 134632 G=0.952456 C=0.047544
gnomAD - Genomes European Sub 72848 G=0.94970 C=0.05030
gnomAD - Genomes African Sub 41078 G=0.94347 C=0.05653
gnomAD - Genomes American Sub 12636 G=0.97523 C=0.02477
gnomAD - Genomes Ashkenazi Jewish Sub 3276 G=0.9921 C=0.0079
gnomAD - Genomes East Asian Sub 2744 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2050 G=0.9629 C=0.0371
Allele Frequency Aggregator Total Global 18882 G=0.94768 C=0.05232
Allele Frequency Aggregator European Sub 14278 G=0.94467 C=0.05533
Allele Frequency Aggregator African Sub 2946 G=0.9467 C=0.0533
Allele Frequency Aggregator Other Sub 692 G=0.954 C=0.046
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.992 C=0.008
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.979 C=0.021
Allele Frequency Aggregator Asian Sub 112 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.99 C=0.01
1000Genomes_30x Global Study-wide 6404 G=0.9708 C=0.0292
1000Genomes_30x African Sub 1786 G=0.9446 C=0.0554
1000Genomes_30x Europe Sub 1266 G=0.9613 C=0.0387
1000Genomes_30x South Asian Sub 1202 G=0.9908 C=0.0092
1000Genomes_30x East Asian Sub 1170 G=1.0000 C=0.0000
1000Genomes_30x American Sub 980 G=0.971 C=0.029
1000Genomes Global Study-wide 5008 G=0.9722 C=0.0278
1000Genomes African Sub 1322 G=0.9433 C=0.0567
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=0.9592 C=0.0408
1000Genomes South Asian Sub 978 G=0.993 C=0.007
1000Genomes American Sub 694 G=0.977 C=0.023
Genetic variation in the Estonian population Estonian Study-wide 4474 G=0.9211 C=0.0789
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9595 C=0.0405
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9582 C=0.0418
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.963 C=0.037
Northern Sweden ACPOP Study-wide 600 G=0.950 C=0.050
Qatari Global Study-wide 216 G=0.958 C=0.042
The Danish reference pan genome Danish Study-wide 40 G=0.97 C=0.03
SGDP_PRJ Global Study-wide 16 G=0.50 C=0.50
Siberian Global Study-wide 4 G=0.5 C=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 6 NC_000006.12:g.93347426G>C
GRCh37.p13 chr 6 NC_000006.11:g.94057144G>C
EPHA7 RefSeqGene NG_033944.1:g.77157C>G
Gene: EPHA7, EPH receptor A7 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EPHA7 transcript variant 2 NM_001288629.2:c.1324+929…

NM_001288629.2:c.1324+9291C>G

N/A Intron Variant
EPHA7 transcript variant 4 NM_001376465.1:c.1324+929…

NM_001376465.1:c.1324+9291C>G

N/A Intron Variant
EPHA7 transcript variant 5 NM_001376466.1:c.1324+929…

NM_001376466.1:c.1324+9291C>G

N/A Intron Variant
EPHA7 transcript variant 6 NM_001376467.1:c.1324+929…

NM_001376467.1:c.1324+9291C>G

N/A Intron Variant
EPHA7 transcript variant 7 NM_001376468.1:c.1324+929…

NM_001376468.1:c.1324+9291C>G

N/A Intron Variant
EPHA7 transcript variant 8 NM_001376469.1:c.1325-361…

NM_001376469.1:c.1325-3618C>G

N/A Intron Variant
EPHA7 transcript variant 9 NM_001376470.1:c.1096+929…

NM_001376470.1:c.1096+9291C>G

N/A Intron Variant
EPHA7 transcript variant 10 NM_001376471.1:c.1096+929…

NM_001376471.1:c.1096+9291C>G

N/A Intron Variant
EPHA7 transcript variant 1 NM_004440.4:c.1324+9291C>G N/A Intron Variant
EPHA7 transcript variant 3 NM_001288630.2:c. N/A Genic Downstream Transcript Variant
EPHA7 transcript variant 11 NR_164810.1:n. N/A Intron Variant
EPHA7 transcript variant X2 XM_017010366.3:c.1325-367…

XM_017010366.3:c.1325-3679C>G

N/A Intron Variant
EPHA7 transcript variant X1 XM_047418274.1:c.1324+929…

XM_047418274.1:c.1324+9291C>G

N/A Intron 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 G= C
GRCh38.p14 chr 6 NC_000006.12:g.93347426= NC_000006.12:g.93347426G>C
GRCh37.p13 chr 6 NC_000006.11:g.94057144= NC_000006.11:g.94057144G>C
EPHA7 RefSeqGene NG_033944.1:g.77157= NG_033944.1:g.77157C>G
EPHA7 transcript variant 2 NM_001288629.2:c.1324+9291= NM_001288629.2:c.1324+9291C>G
EPHA7 transcript variant 4 NM_001376465.1:c.1324+9291= NM_001376465.1:c.1324+9291C>G
EPHA7 transcript variant 5 NM_001376466.1:c.1324+9291= NM_001376466.1:c.1324+9291C>G
EPHA7 transcript variant 6 NM_001376467.1:c.1324+9291= NM_001376467.1:c.1324+9291C>G
EPHA7 transcript variant 7 NM_001376468.1:c.1324+9291= NM_001376468.1:c.1324+9291C>G
EPHA7 transcript variant 8 NM_001376469.1:c.1325-3618= NM_001376469.1:c.1325-3618C>G
EPHA7 transcript variant 9 NM_001376470.1:c.1096+9291= NM_001376470.1:c.1096+9291C>G
EPHA7 transcript variant 10 NM_001376471.1:c.1096+9291= NM_001376471.1:c.1096+9291C>G
EPHA7 transcript variant 1 NM_004440.3:c.1324+9291= NM_004440.3:c.1324+9291C>G
EPHA7 transcript variant 1 NM_004440.4:c.1324+9291= NM_004440.4:c.1324+9291C>G
EPHA7 transcript variant X1 XM_005248669.1:c.1324+9291= XM_005248669.1:c.1324+9291C>G
EPHA7 transcript variant X2 XM_005248670.1:c.1324+9291= XM_005248670.1:c.1324+9291C>G
EPHA7 transcript variant X2 XM_005248671.1:c.1324+9291= XM_005248671.1:c.1324+9291C>G
EPHA7 transcript variant X2 XM_017010366.3:c.1325-3679= XM_017010366.3:c.1325-3679C>G
EPHA7 transcript variant X1 XM_047418274.1:c.1324+9291= XM_047418274.1:c.1324+9291C>G
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#.

40 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss779 Sep 19, 2000 (36)
2 PERLEGEN ss23362506 Sep 20, 2004 (123)
3 KRIBB_YJKIM ss104796518 Feb 03, 2009 (130)
4 COMPLETE_GENOMICS ss162619221 Jul 04, 2010 (132)
5 1000GENOMES ss222546301 Jul 14, 2010 (132)
6 1000GENOMES ss233590324 Jul 15, 2010 (132)
7 TISHKOFF ss559379269 Apr 25, 2013 (138)
8 EVA-GONL ss983246028 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1073842413 Aug 21, 2014 (142)
10 1000GENOMES ss1321313545 Aug 21, 2014 (142)
11 EVA_GENOME_DK ss1581797822 Apr 01, 2015 (144)
12 EVA_DECODE ss1592800950 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1616184089 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1659178122 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1926500823 Feb 12, 2016 (147)
16 JJLAB ss2023895672 Sep 14, 2016 (149)
17 USC_VALOUEV ss2152087999 Dec 20, 2016 (150)
18 HUMAN_LONGEVITY ss2286324914 Dec 20, 2016 (150)
19 GNOMAD ss2842338905 Nov 08, 2017 (151)
20 SWEGEN ss2999562744 Nov 08, 2017 (151)
21 BIOINF_KMB_FNS_UNIBA ss3025742207 Nov 08, 2017 (151)
22 CSHL ss3347118340 Nov 08, 2017 (151)
23 EGCUT_WGS ss3667448444 Jul 13, 2019 (153)
24 EVA_DECODE ss3717795199 Jul 13, 2019 (153)
25 ACPOP ss3733769660 Jul 13, 2019 (153)
26 KHV_HUMAN_GENOMES ss3808527279 Jul 13, 2019 (153)
27 EVA ss3830076727 Apr 26, 2020 (154)
28 EVA ss3838520311 Apr 26, 2020 (154)
29 EVA ss3843968444 Apr 26, 2020 (154)
30 SGDP_PRJ ss3865203469 Apr 26, 2020 (154)
31 TOPMED ss4713289194 Apr 26, 2021 (155)
32 1000G_HIGH_COVERAGE ss5269494364 Oct 14, 2022 (156)
33 EVA ss5367476816 Oct 14, 2022 (156)
34 HUGCELL_USP ss5467021506 Oct 14, 2022 (156)
35 EVA ss5508619029 Oct 14, 2022 (156)
36 1000G_HIGH_COVERAGE ss5555977140 Oct 14, 2022 (156)
37 SANFORD_IMAGENETICS ss5641006866 Oct 14, 2022 (156)
38 EVA ss5842662431 Oct 14, 2022 (156)
39 EVA ss5884979464 Oct 14, 2022 (156)
40 EVA ss5969514384 Oct 14, 2022 (156)
41 1000Genomes NC_000006.11 - 94057144 Oct 12, 2018 (152)
42 1000Genomes_30x NC_000006.12 - 93347426 Oct 14, 2022 (156)
43 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 94057144 Oct 12, 2018 (152)
44 Genetic variation in the Estonian population NC_000006.11 - 94057144 Oct 12, 2018 (152)
45 The Danish reference pan genome NC_000006.11 - 94057144 Apr 26, 2020 (154)
46 gnomAD - Genomes NC_000006.12 - 93347426 Apr 26, 2021 (155)
47 Genome of the Netherlands Release 5 NC_000006.11 - 94057144 Apr 26, 2020 (154)
48 Northern Sweden NC_000006.11 - 94057144 Jul 13, 2019 (153)
49 Qatari NC_000006.11 - 94057144 Apr 26, 2020 (154)
50 SGDP_PRJ NC_000006.11 - 94057144 Apr 26, 2020 (154)
51 Siberian NC_000006.11 - 94057144 Apr 26, 2020 (154)
52 TopMed NC_000006.12 - 93347426 Apr 26, 2021 (155)
53 UK 10K study - Twins NC_000006.11 - 94057144 Oct 12, 2018 (152)
54 ALFA NC_000006.12 - 93347426 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss162619221, ss1592800950 NC_000006.10:94113864:G:C NC_000006.12:93347425:G:C (self)
33145516, 18463891, 13186692, 7962761, 8226973, 7054525, 8542753, 17220449, 4604353, 18463891, ss222546301, ss233590324, ss559379269, ss983246028, ss1073842413, ss1321313545, ss1581797822, ss1616184089, ss1659178122, ss1926500823, ss2023895672, ss2152087999, ss2842338905, ss2999562744, ss3347118340, ss3667448444, ss3733769660, ss3830076727, ss3838520311, ss3865203469, ss5367476816, ss5508619029, ss5641006866, ss5842662431, ss5969514384 NC_000006.11:94057143:G:C NC_000006.12:93347425:G:C (self)
43503075, 233899397, 550666752, 11198270848, ss2286324914, ss3025742207, ss3717795199, ss3808527279, ss3843968444, ss4713289194, ss5269494364, ss5467021506, ss5555977140, ss5884979464 NC_000006.12:93347425:G:C NC_000006.12:93347425:G:C (self)
ss779, ss23362506, ss104796518 NT_007299.13:32176977:G:C NC_000006.12:93347425:G:C (self)
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 rs766

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