Name: rs635900
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.

rs635900

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:79068471 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.142200 (37639/264690, TOPMED)
G=0.139200 (19500/140086, GnomAD)
G=0.01072 (303/28258, 14KJPN) (+ 16 more)
G=0.11462 (2300/20066, ALFA)
G=0.01056 (177/16760, 8.3KJPN)
G=0.1230 (788/6404, 1000G_30x)
G=0.1164 (583/5008, 1000G)
G=0.0866 (388/4480, Estonian)
G=0.0944 (364/3854, ALSPAC)
G=0.0941 (349/3708, TWINSUK)
G=0.0140 (41/2922, KOREAN)
G=0.096 (96/998, GoNL)
G=0.152 (91/600, NorthernSweden)
G=0.074 (16/216, Qatari)
G=0.042 (9/214, Vietnamese)
C=0.49 (35/72, SGDP_PRJ)
G=0.10 (4/40, GENOME_DK)
C=0.5 (3/6, Siberian)
G=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP9B : 2KB Upstream 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	20066	C=0.88538	G=0.11462
European	Sub	15434	C=0.91091	G=0.08909
African	Sub	2946	C=0.7400	G=0.2600
African Others	Sub	114	C=0.632	G=0.368
African American	Sub	2832	C=0.7444	G=0.2556
Asian	Sub	112	C=0.964	G=0.036
East Asian	Sub	86	C=0.97	G=0.03
Other Asian	Sub	26	C=0.96	G=0.04
Latin American 1	Sub	146	C=0.897	G=0.103
Latin American 2	Sub	610	C=0.939	G=0.061
South Asian	Sub	98	C=0.97	G=0.03
Other	Sub	720	C=0.861	G=0.139

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.857800	G=0.142200
gnomAD - Genomes	Global	Study-wide	140086	C=0.860800	G=0.139200
gnomAD - Genomes	European	Sub	75906	C=0.91092	G=0.08908
gnomAD - Genomes	African	Sub	41932	C=0.73416	G=0.26584
gnomAD - Genomes	American	Sub	13644	C=0.91769	G=0.08231
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9621	G=0.0379
gnomAD - Genomes	East Asian	Sub	3126	C=0.9789	G=0.0211
gnomAD - Genomes	Other	Sub	2154	C=0.8719	G=0.1281
14KJPN	JAPANESE	Study-wide	28258	C=0.98928	G=0.01072
Allele Frequency Aggregator	Total	Global	20066	C=0.88538	G=0.11462
Allele Frequency Aggregator	European	Sub	15434	C=0.91091	G=0.08909
Allele Frequency Aggregator	African	Sub	2946	C=0.7400	G=0.2600
Allele Frequency Aggregator	Other	Sub	720	C=0.861	G=0.139
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.939	G=0.061
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.897	G=0.103
Allele Frequency Aggregator	Asian	Sub	112	C=0.964	G=0.036
Allele Frequency Aggregator	South Asian	Sub	98	C=0.97	G=0.03
8.3KJPN	JAPANESE	Study-wide	16760	C=0.98944	G=0.01056
1000Genomes_30x	Global	Study-wide	6404	C=0.8770	G=0.1230
1000Genomes_30x	African	Sub	1786	C=0.7004	G=0.2996
1000Genomes_30x	Europe	Sub	1266	C=0.8965	G=0.1035
1000Genomes_30x	South Asian	Sub	1202	C=0.9800	G=0.0200
1000Genomes_30x	East Asian	Sub	1170	C=0.9735	G=0.0265
1000Genomes_30x	American	Sub	980	C=0.932	G=0.068
1000Genomes	Global	Study-wide	5008	C=0.8836	G=0.1164
1000Genomes	African	Sub	1322	C=0.7080	G=0.2920
1000Genomes	East Asian	Sub	1008	C=0.9772	G=0.0228
1000Genomes	Europe	Sub	1006	C=0.8966	G=0.1034
1000Genomes	South Asian	Sub	978	C=0.982	G=0.018
1000Genomes	American	Sub	694	C=0.925	G=0.075
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9134	G=0.0866
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9056	G=0.0944
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9059	G=0.0941
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9860	G=0.0140
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.904	G=0.096
Northern Sweden	ACPOP	Study-wide	600	C=0.848	G=0.152
Qatari	Global	Study-wide	216	C=0.926	G=0.074
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.958	G=0.042
SGDP_PRJ	Global	Study-wide	72	C=0.49	G=0.51
The Danish reference pan genome	Danish	Study-wide	40	C=0.90	G=0.10
Siberian	Global	Study-wide	6	C=0.5	G=0.5

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 18	NC_000018.10:g.79068471C>G
GRCh37.p13 chr 18	NC_000018.9:g.76828471C>G
GRCh38.p14 chr 18 alt locus HSCHR18_2_CTG2_1	NW_003315961.1:g.139021C>G
GRCh38.p14 chr 18 alt locus HSCHR18_ALT2_CTG2_1	NT_187666.1:g.137184C>G

Gene: ATP9B, ATPase phospholipid transporting 9B (putative) (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ATP9B transcript variant 2	NM_001306085.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant 1	NM_198531.5:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant 3	NR_148360.2:n.	N/A	Upstream Transcript Variant
ATP9B transcript variant X1	XM_011525963.3:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X2	XM_011525964.3:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X3	XM_017025726.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X4	XM_017025727.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X6	XM_017025728.3:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X7	XM_017025729.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X8	XM_017025730.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X11	XM_017025731.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X13	XM_017025732.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X16	XM_017025733.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X18	XM_017025734.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X19	XM_017025735.3:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X21	XM_017025736.3:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X24	XM_017025737.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X34	XM_017025742.2:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X5	XM_047437489.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X14	XM_047437492.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X17	XM_047437494.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X20	XM_047437495.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X22	XM_047437496.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X23	XM_047437497.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X25	XM_047437498.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X26	XM_047437499.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X27	XM_047437500.1:c.	N/A	Upstream Transcript Variant
ATP9B transcript variant X10	XM_011525966.3:c.	N/A	N/A
ATP9B transcript variant X28	XM_011525971.3:c.	N/A	N/A
ATP9B transcript variant X29	XM_011525972.3:c.	N/A	N/A
ATP9B transcript variant X30	XM_011525973.3:c.	N/A	N/A
ATP9B transcript variant X31	XM_011525974.3:c.	N/A	N/A
ATP9B transcript variant X9	XM_047437490.1:c.	N/A	N/A
ATP9B transcript variant X12	XM_047437491.1:c.	N/A	N/A
ATP9B transcript variant X15	XM_047437493.1:c.	N/A	N/A
ATP9B transcript variant X32	XM_047437501.1:c.	N/A	N/A
ATP9B transcript variant X33	XM_047437502.1:c.	N/A	N/A

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	C=	G
GRCh38.p14 chr 18	NC_000018.10:g.79068471=	NC_000018.10:g.79068471C>G
GRCh37.p13 chr 18	NC_000018.9:g.76828471=	NC_000018.9:g.76828471C>G
GRCh38.p14 chr 18 alt locus HSCHR18_2_CTG2_1	NW_003315961.1:g.139021=	NW_003315961.1:g.139021C>G
GRCh38.p14 chr 18 alt locus HSCHR18_ALT2_CTG2_1	NT_187666.1:g.137184=	NT_187666.1:g.137184C>G

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#.

60 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss808590	Aug 11, 2000 (83)
2	TSC-CSHL	ss3086745	Jun 15, 2001 (96)
3	WUGSC_SSAHASNP	ss14428878	Dec 05, 2003 (119)
4	CSHL-HAPMAP	ss17599693	Feb 27, 2004 (120)
5	ABI	ss44106731	Mar 14, 2006 (126)
6	1000GENOMES	ss110945089	Jan 25, 2009 (130)
7	ILLUMINA	ss160770599	Dec 01, 2009 (131)
8	ENSEMBL	ss161867447	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss172059800	Jul 04, 2010 (132)
10	1000GENOMES	ss227996080	Jul 14, 2010 (132)
11	1000GENOMES	ss237568467	Jul 15, 2010 (132)
12	GMI	ss287329940	Apr 25, 2013 (138)
13	PJP	ss292118142	May 09, 2011 (134)
14	ILLUMINA	ss482241675	Sep 08, 2015 (146)
15	TISHKOFF	ss565793153	Apr 25, 2013 (138)
16	SSMP	ss661640325	Apr 25, 2013 (138)
17	EVA-GONL	ss993984885	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1081695645	Aug 21, 2014 (142)
19	1000GENOMES	ss1361959241	Aug 21, 2014 (142)
20	EVA_GENOME_DK	ss1578514746	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1637384379	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1680378412	Apr 01, 2015 (144)
23	EVA_DECODE	ss1698049041	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1809162358	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1937456578	Feb 12, 2016 (147)
26	GENOMED	ss1968588563	Jul 19, 2016 (147)
27	JJLAB	ss2029505003	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2158013383	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2223496142	Dec 20, 2016 (150)
30	GRF	ss2702615719	Nov 08, 2017 (151)
31	ILLUMINA	ss2710874059	Nov 08, 2017 (151)
32	GNOMAD	ss2959283382	Nov 08, 2017 (151)
33	SWEGEN	ss3016912308	Nov 08, 2017 (151)
34	CSHL	ss3352144706	Nov 08, 2017 (151)
35	ILLUMINA	ss3636407929	Oct 12, 2018 (152)
36	BIOINF_KMB_FNS_UNIBA	ss3645502337	Oct 12, 2018 (152)
37	EGCUT_WGS	ss3683767492	Jul 13, 2019 (153)
38	EVA_DECODE	ss3702128939	Jul 13, 2019 (153)
39	ACPOP	ss3742762603	Jul 13, 2019 (153)
40	EVA	ss3755689932	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3820945236	Jul 13, 2019 (153)
42	EVA	ss3835297213	Apr 27, 2020 (154)
43	EVA	ss3841271135	Apr 27, 2020 (154)
44	EVA	ss3846774716	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3887521187	Apr 27, 2020 (154)
46	KRGDB	ss3937432080	Apr 27, 2020 (154)
47	TOPMED	ss5064754567	Apr 27, 2021 (155)
48	TOMMO_GENOMICS	ss5226215877	Apr 27, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5306112454	Oct 16, 2022 (156)
50	EVA	ss5432925890	Oct 16, 2022 (156)
51	HUGCELL_USP	ss5498804502	Oct 16, 2022 (156)
52	EVA	ss5512023318	Oct 16, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5611368367	Oct 16, 2022 (156)
54	SANFORD_IMAGENETICS	ss5661771973	Oct 16, 2022 (156)
55	TOMMO_GENOMICS	ss5784304702	Oct 16, 2022 (156)
56	YY_MCH	ss5817311990	Oct 16, 2022 (156)
57	EVA	ss5827878234	Oct 16, 2022 (156)
58	EVA	ss5852164437	Oct 16, 2022 (156)
59	EVA	ss5875029106	Oct 16, 2022 (156)
60	EVA	ss5953207963	Oct 16, 2022 (156)
61	1000Genomes	NC_000018.9 - 76828471	Oct 12, 2018 (152)
62	1000Genomes_30x	NC_000018.10 - 79068471	Oct 16, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 76828471	Oct 12, 2018 (152)
64	Genetic variation in the Estonian population	NC_000018.9 - 76828471	Oct 12, 2018 (152)
65	The Danish reference pan genome	NC_000018.9 - 76828471	Apr 27, 2020 (154)
66	gnomAD - Genomes	NC_000018.10 - 79068471	Apr 27, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000018.9 - 76828471	Apr 27, 2020 (154)
68	KOREAN population from KRGDB	NC_000018.9 - 76828471	Apr 27, 2020 (154)
69	Northern Sweden	NC_000018.9 - 76828471	Jul 13, 2019 (153)
70	Qatari	NC_000018.9 - 76828471	Apr 27, 2020 (154)
71	SGDP_PRJ	NC_000018.9 - 76828471	Apr 27, 2020 (154)
72	Siberian	NC_000018.9 - 76828471	Apr 27, 2020 (154)
73	8.3KJPN	NC_000018.9 - 76828471	Apr 27, 2021 (155)
74	14KJPN	NC_000018.10 - 79068471	Oct 16, 2022 (156)
75	TopMed	NC_000018.10 - 79068471	Apr 27, 2021 (155)
76	UK 10K study - Twins	NC_000018.9 - 76828471	Oct 12, 2018 (152)
77	A Vietnamese Genetic Variation Database	NC_000018.9 - 76828471	Jul 13, 2019 (153)
78	ALFA	NC_000018.10 - 79068471	Apr 27, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss110945089, ss160770599, ss172059800, ss287329940, ss292118142, ss1698049041	NC_000018.8:74929458:C:G	NC_000018.10:79068470:C:G	(self)
75322056, 41758464, 29505740, 4702333, 18606282, 44609474, 16047468, 19498500, 39538167, 10529737, 84185184, 41758464, 9235481, ss227996080, ss237568467, ss482241675, ss565793153, ss661640325, ss993984885, ss1081695645, ss1361959241, ss1578514746, ss1637384379, ss1680378412, ss1809162358, ss1937456578, ss1968588563, ss2029505003, ss2158013383, ss2702615719, ss2710874059, ss2959283382, ss3016912308, ss3352144706, ss3636407929, ss3683767492, ss3742762603, ss3755689932, ss3835297213, ss3841271135, ss3887521187, ss3937432080, ss5226215877, ss5432925890, ss5512023318, ss5661771973, ss5827878234, ss5953207963	NC_000018.9:76828470:C:G	NC_000018.10:79068470:C:G	(self)
98894302, 531163431, 118141806, 280300230, 5357788895, ss2223496142, ss3645502337, ss3702128939, ss3820945236, ss3846774716, ss5064754567, ss5306112454, ss5498804502, ss5611368367, ss5784304702, ss5817311990, ss5852164437, ss5875029106	NC_000018.10:79068470:C:G	NC_000018.10:79068470:C:G	(self)
ss14428878, ss17599693	NT_010879.14:1056650:C:G	NC_000018.10:79068470:C:G	(self)
ss808590, ss3086745, ss44106731, ss161867447	NT_025028.14:24619334:C:G	NC_000018.10:79068470:C:G	(self)

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

No publications for rs635900

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

rs635900