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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.

rs17838304

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:109132472 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.259783 (68762/264690, TOPMED)
A=0.252404 (35327/139962, GnomAD)
A=0.20494 (6322/30848, ALFA) (+ 17 more)
A=0.06721 (1899/28256, 14KJPN)
A=0.06909 (1158/16760, 8.3KJPN)
A=0.2469 (1581/6404, 1000G_30x)
A=0.2430 (1217/5008, 1000G)
A=0.1473 (660/4480, Estonian)
A=0.1790 (690/3854, ALSPAC)
A=0.1861 (690/3708, TWINSUK)
A=0.0770 (225/2922, KOREAN)
A=0.0770 (141/1832, Korea1K)
A=0.172 (172/998, GoNL)
A=0.152 (91/600, NorthernSweden)
G=0.438 (98/224, SGDP_PRJ)
A=0.153 (33/216, Qatari)
A=0.088 (19/216, Vietnamese)
A=0.17 (7/40, GENOME_DK)
G=0.50 (8/16, Siberian)
A=0.50 (8/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ELAPOR1 : 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 30848 G=0.79506 A=0.20494
European Sub 24722 G=0.82129 A=0.17871
African Sub 3166 G=0.5985 A=0.4015
African Others Sub 124 G=0.548 A=0.452
African American Sub 3042 G=0.6006 A=0.3994
Asian Sub 128 G=0.945 A=0.055
East Asian Sub 100 G=0.93 A=0.07
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 168 G=0.738 A=0.262
Latin American 2 Sub 700 G=0.773 A=0.227
South Asian Sub 114 G=0.781 A=0.219
Other Sub 1850 G=0.7849 A=0.2151


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=0.740217 A=0.259783
gnomAD - Genomes Global Study-wide 139962 G=0.747596 A=0.252404
gnomAD - Genomes European Sub 75852 G=0.82161 A=0.17839
gnomAD - Genomes African Sub 41876 G=0.59330 A=0.40670
gnomAD - Genomes American Sub 13632 G=0.75169 A=0.24831
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.8168 A=0.1832
gnomAD - Genomes East Asian Sub 3134 G=0.9183 A=0.0817
gnomAD - Genomes Other Sub 2150 G=0.7600 A=0.2400
Allele Frequency Aggregator Total Global 30848 G=0.79506 A=0.20494
Allele Frequency Aggregator European Sub 24722 G=0.82129 A=0.17871
Allele Frequency Aggregator African Sub 3166 G=0.5985 A=0.4015
Allele Frequency Aggregator Other Sub 1850 G=0.7849 A=0.2151
Allele Frequency Aggregator Latin American 2 Sub 700 G=0.773 A=0.227
Allele Frequency Aggregator Latin American 1 Sub 168 G=0.738 A=0.262
Allele Frequency Aggregator Asian Sub 128 G=0.945 A=0.055
Allele Frequency Aggregator South Asian Sub 114 G=0.781 A=0.219
14KJPN JAPANESE Study-wide 28256 G=0.93279 A=0.06721
8.3KJPN JAPANESE Study-wide 16760 G=0.93091 A=0.06909
1000Genomes_30x Global Study-wide 6404 G=0.7531 A=0.2469
1000Genomes_30x African Sub 1786 G=0.5890 A=0.4110
1000Genomes_30x Europe Sub 1266 G=0.8144 A=0.1856
1000Genomes_30x South Asian Sub 1202 G=0.7829 A=0.2171
1000Genomes_30x East Asian Sub 1170 G=0.9188 A=0.0812
1000Genomes_30x American Sub 980 G=0.739 A=0.261
1000Genomes Global Study-wide 5008 G=0.7570 A=0.2430
1000Genomes African Sub 1322 G=0.5893 A=0.4107
1000Genomes East Asian Sub 1008 G=0.9187 A=0.0813
1000Genomes Europe Sub 1006 G=0.8161 A=0.1839
1000Genomes South Asian Sub 978 G=0.775 A=0.225
1000Genomes American Sub 694 G=0.731 A=0.269
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8527 A=0.1473
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8210 A=0.1790
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8139 A=0.1861
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9230 A=0.0770
Korean Genome Project KOREAN Study-wide 1832 G=0.9230 A=0.0770
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.828 A=0.172
Northern Sweden ACPOP Study-wide 600 G=0.848 A=0.152
SGDP_PRJ Global Study-wide 224 G=0.438 A=0.562
Qatari Global Study-wide 216 G=0.847 A=0.153
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.912 A=0.088
The Danish reference pan genome Danish Study-wide 40 G=0.82 A=0.17
Siberian Global Study-wide 16 G=0.50 A=0.50
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 1 NC_000001.11:g.109132472G>A
GRCh37.p13 chr 1 NC_000001.10:g.109675094G>A
ELAPOR1 RefSeqGene NG_032763.1:g.23510G>A
Gene: ELAPOR1, endosome-lysosome associated apoptosis and autophagy regulator 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ELAPOR1 transcript variant 2 NM_001267048.2:c.153+1813…

NM_001267048.2:c.153+18136G>A

N/A Intron Variant
ELAPOR1 transcript variant 4 NM_001284352.2:c.-33+1813…

NM_001284352.2:c.-33+18136G>A

N/A Intron Variant
ELAPOR1 transcript variant 1 NM_020775.5:c.153+18136G>A N/A Intron Variant
ELAPOR1 transcript variant 5 NM_001284353.2:c. N/A Genic Upstream Transcript Variant
ELAPOR1 transcript variant X1 XM_011541825.3:c.153+1813…

XM_011541825.3:c.153+18136G>A

N/A Intron Variant
ELAPOR1 transcript variant X2 XM_011541826.4:c.153+1813…

XM_011541826.4:c.153+18136G>A

N/A Intron Variant
ELAPOR1 transcript variant X3 XM_011541827.3:c.153+1813…

XM_011541827.3:c.153+18136G>A

N/A Intron Variant
ELAPOR1 transcript variant X4 XM_047426133.1:c. N/A Genic Upstream Transcript 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= A
GRCh38.p14 chr 1 NC_000001.11:g.109132472= NC_000001.11:g.109132472G>A
GRCh37.p13 chr 1 NC_000001.10:g.109675094= NC_000001.10:g.109675094G>A
ELAPOR1 RefSeqGene NG_032763.1:g.23510= NG_032763.1:g.23510G>A
KIAA1324 transcript variant 2 NM_001267048.1:c.153+18136= NM_001267048.1:c.153+18136G>A
ELAPOR1 transcript variant 2 NM_001267048.2:c.153+18136= NM_001267048.2:c.153+18136G>A
ELAPOR1 transcript variant 4 NM_001284352.2:c.-33+18136= NM_001284352.2:c.-33+18136G>A
KIAA1324 transcript variant 1 NM_020775.4:c.153+18136= NM_020775.4:c.153+18136G>A
ELAPOR1 transcript variant 1 NM_020775.5:c.153+18136= NM_020775.5:c.153+18136G>A
ELAPOR1 transcript variant X1 XM_011541825.3:c.153+18136= XM_011541825.3:c.153+18136G>A
ELAPOR1 transcript variant X2 XM_011541826.4:c.153+18136= XM_011541826.4:c.153+18136G>A
ELAPOR1 transcript variant X3 XM_011541827.3:c.153+18136= XM_011541827.3:c.153+18136G>A
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#.

69 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23198560 Sep 21, 2004 (123)
2 ABI ss41257320 Mar 14, 2006 (126)
3 COMPLETE_GENOMICS ss163875053 Jul 04, 2010 (132)
4 BUSHMAN ss198917393 Jul 04, 2010 (132)
5 BL ss253371268 May 09, 2011 (134)
6 PJP ss290595475 May 09, 2011 (134)
7 1000GENOMES ss328848073 May 09, 2011 (134)
8 ILLUMINA ss410764777 Sep 17, 2011 (135)
9 ILLUMINA ss482064564 May 04, 2012 (137)
10 ILLUMINA ss483462259 May 04, 2012 (137)
11 ILLUMINA ss535671841 Sep 08, 2015 (146)
12 TISHKOFF ss554556577 Apr 25, 2013 (138)
13 SSMP ss648303497 Apr 25, 2013 (138)
14 ILLUMINA ss780286460 Sep 08, 2015 (146)
15 ILLUMINA ss782174492 Sep 08, 2015 (146)
16 ILLUMINA ss835772863 Sep 08, 2015 (146)
17 EVA-GONL ss975555835 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1068182080 Aug 21, 2014 (142)
19 1000GENOMES ss1292374667 Aug 21, 2014 (142)
20 DDI ss1425932970 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1574313929 Apr 01, 2015 (144)
22 EVA_DECODE ss1584934987 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1600958320 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1643952353 Apr 01, 2015 (144)
25 HAMMER_LAB ss1794909703 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1918755800 Feb 12, 2016 (147)
27 GENOMED ss1966838362 Jul 19, 2016 (147)
28 JJLAB ss2019902339 Sep 14, 2016 (149)
29 USC_VALOUEV ss2147919824 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2165593291 Dec 20, 2016 (150)
31 SYSTEMSBIOZJU ss2624460492 Nov 08, 2017 (151)
32 ILLUMINA ss2632560902 Nov 08, 2017 (151)
33 GRF ss2697849638 Nov 08, 2017 (151)
34 GNOMAD ss2759396083 Nov 08, 2017 (151)
35 SWEGEN ss2987415027 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3023714972 Nov 08, 2017 (151)
37 CSHL ss3343628659 Nov 08, 2017 (151)
38 ILLUMINA ss3626178643 Oct 11, 2018 (152)
39 ILLUMINA ss3630594764 Oct 11, 2018 (152)
40 ILLUMINA ss3641610009 Oct 11, 2018 (152)
41 EGCUT_WGS ss3655503519 Jul 12, 2019 (153)
42 EVA_DECODE ss3687501947 Jul 12, 2019 (153)
43 ACPOP ss3727376749 Jul 12, 2019 (153)
44 EVA ss3746654483 Jul 12, 2019 (153)
45 PACBIO ss3783515314 Jul 12, 2019 (153)
46 PACBIO ss3789157785 Jul 12, 2019 (153)
47 PACBIO ss3794030690 Jul 12, 2019 (153)
48 KHV_HUMAN_GENOMES ss3799659007 Jul 12, 2019 (153)
49 EVA ss3826361839 Apr 25, 2020 (154)
50 EVA ss3836572377 Apr 25, 2020 (154)
51 EVA ss3841980691 Apr 25, 2020 (154)
52 SGDP_PRJ ss3849620842 Apr 25, 2020 (154)
53 KRGDB ss3894710280 Apr 25, 2020 (154)
54 KOGIC ss3945217082 Apr 25, 2020 (154)
55 TOPMED ss4463097046 Apr 25, 2021 (155)
56 TOMMO_GENOMICS ss5145616695 Apr 25, 2021 (155)
57 1000G_HIGH_COVERAGE ss5243560921 Oct 12, 2022 (156)
58 EVA ss5314642468 Oct 12, 2022 (156)
59 EVA ss5321093844 Oct 12, 2022 (156)
60 HUGCELL_USP ss5444489103 Oct 12, 2022 (156)
61 1000G_HIGH_COVERAGE ss5516529144 Oct 12, 2022 (156)
62 SANFORD_IMAGENETICS ss5626271098 Oct 12, 2022 (156)
63 TOMMO_GENOMICS ss5670865431 Oct 12, 2022 (156)
64 YY_MCH ss5800919960 Oct 12, 2022 (156)
65 EVA ss5832464360 Oct 12, 2022 (156)
66 EVA ss5849062108 Oct 12, 2022 (156)
67 EVA ss5909742456 Oct 12, 2022 (156)
68 EVA ss5938135116 Oct 12, 2022 (156)
69 EVA ss5979977034 Oct 12, 2022 (156)
70 1000Genomes NC_000001.10 - 109675094 Oct 11, 2018 (152)
71 1000Genomes_30x NC_000001.11 - 109132472 Oct 12, 2022 (156)
72 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 109675094 Oct 11, 2018 (152)
73 Genetic variation in the Estonian population NC_000001.10 - 109675094 Oct 11, 2018 (152)
74 The Danish reference pan genome NC_000001.10 - 109675094 Apr 25, 2020 (154)
75 gnomAD - Genomes NC_000001.11 - 109132472 Apr 25, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000001.10 - 109675094 Apr 25, 2020 (154)
77 KOREAN population from KRGDB NC_000001.10 - 109675094 Apr 25, 2020 (154)
78 Korean Genome Project NC_000001.11 - 109132472 Apr 25, 2020 (154)
79 Northern Sweden NC_000001.10 - 109675094 Jul 12, 2019 (153)
80 Qatari NC_000001.10 - 109675094 Apr 25, 2020 (154)
81 SGDP_PRJ NC_000001.10 - 109675094 Apr 25, 2020 (154)
82 Siberian NC_000001.10 - 109675094 Apr 25, 2020 (154)
83 8.3KJPN NC_000001.10 - 109675094 Apr 25, 2021 (155)
84 14KJPN NC_000001.11 - 109132472 Oct 12, 2022 (156)
85 TopMed NC_000001.11 - 109132472 Apr 25, 2021 (155)
86 UK 10K study - Twins NC_000001.10 - 109675094 Oct 11, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000001.10 - 109675094 Jul 12, 2019 (153)
88 ALFA NC_000001.11 - 109132472 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss163875053, ss198917393, ss253371268, ss290595475, ss482064564, ss1584934987 NC_000001.9:109476616:G:A NC_000001.11:109132471:G:A (self)
3148627, 1739241, 1241767, 1658976, 757774, 1887674, 661614, 797730, 1637822, 436178, 3586002, 1739241, 377448, ss328848073, ss483462259, ss535671841, ss554556577, ss648303497, ss780286460, ss782174492, ss835772863, ss975555835, ss1068182080, ss1292374667, ss1425932970, ss1574313929, ss1600958320, ss1643952353, ss1794909703, ss1918755800, ss1966838362, ss2019902339, ss2147919824, ss2624460492, ss2632560902, ss2697849638, ss2759396083, ss2987415027, ss3343628659, ss3626178643, ss3630594764, ss3641610009, ss3655503519, ss3727376749, ss3746654483, ss3783515314, ss3789157785, ss3794030690, ss3826361839, ss3836572377, ss3849620842, ss3894710280, ss5145616695, ss5314642468, ss5321093844, ss5626271098, ss5832464360, ss5938135116, ss5979977034 NC_000001.10:109675093:G:A NC_000001.11:109132471:G:A (self)
4055079, 22276890, 1595083, 4702535, 26703381, 5850710073, ss2165593291, ss3023714972, ss3687501947, ss3799659007, ss3841980691, ss3945217082, ss4463097046, ss5243560921, ss5444489103, ss5516529144, ss5670865431, ss5800919960, ss5849062108, ss5909742456 NC_000001.11:109132471:G:A NC_000001.11:109132471:G:A (self)
ss23198560, ss41257320, ss410764777 NT_032977.9:79647011:G:A NC_000001.11:109132471:G:A (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 rs17838304

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