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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.

rs4648356

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:2792599 (GRCh38.p13) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.390646 (103400/264690, TOPMED)
A=0.382783 (53572/139954, GnomAD)
A=0.44813 (35263/78690, PAGE_STUDY) (+ 19 more)
A=0.33947 (24297/71574, ALFA)
C=0.48920 (8199/16760, 8.3KJPN)
A=0.4681 (2344/5008, 1000G)
A=0.3196 (1432/4480, Estonian)
A=0.3313 (1277/3854, ALSPAC)
A=0.3350 (1242/3708, TWINSUK)
A=0.4720 (1383/2930, KOREAN)
A=0.4400 (917/2084, HGDP_Stanford)
A=0.4461 (844/1892, HapMap)
A=0.4771 (874/1832, Korea1K)
A=0.302 (301/998, GoNL)
C=0.487 (366/752, PRJEB37584)
A=0.383 (230/600, NorthernSweden)
C=0.293 (113/386, SGDP_PRJ)
A=0.417 (90/216, Qatari)
A=0.476 (101/212, Vietnamese)
A=0.22 (16/72, Ancient Sardinia)
A=0.23 (9/40, GENOME_DK)
C=0.31 (10/32, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTC34 : Intron Variant
Publications
6 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.2792599C>A
GRCh37.p13 chr 1 NC_000001.10:g.2709164C>A
Gene: TTC34, tetratricopeptide repeat domain 34 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TTC34 transcript NM_001242672.2:c.785-2253…

NM_001242672.2:c.785-2253G>T

N/A Intron Variant
TTC34 transcript variant X1 XM_016999990.1: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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 71574 C=0.66053 A=0.33947
European Sub 58842 C=0.68361 A=0.31639
African Sub 4534 C=0.5216 A=0.4784
African Others Sub 170 C=0.482 A=0.518
African American Sub 4364 C=0.5231 A=0.4769
Asian Sub 224 C=0.411 A=0.589
East Asian Sub 182 C=0.396 A=0.604
Other Asian Sub 42 C=0.48 A=0.52
Latin American 1 Sub 254 C=0.622 A=0.378
Latin American 2 Sub 1232 C=0.6347 A=0.3653
South Asian Sub 4962 C=0.5455 A=0.4545
Other Sub 1526 C=0.6212 A=0.3788


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=0.609354 A=0.390646
gnomAD - Genomes Global Study-wide 139954 C=0.617217 A=0.382783
gnomAD - Genomes European Sub 75812 C=0.67909 A=0.32091
gnomAD - Genomes African Sub 41908 C=0.52498 A=0.47502
gnomAD - Genomes American Sub 13640 C=0.57749 A=0.42251
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.6884 A=0.3116
gnomAD - Genomes East Asian Sub 3126 C=0.4498 A=0.5502
gnomAD - Genomes Other Sub 2146 C=0.6188 A=0.3812
The PAGE Study Global Study-wide 78690 C=0.55187 A=0.44813
The PAGE Study AfricanAmerican Sub 32510 C=0.53156 A=0.46844
The PAGE Study Mexican Sub 10806 C=0.60874 A=0.39126
The PAGE Study Asian Sub 8318 C=0.4721 A=0.5279
The PAGE Study PuertoRican Sub 7918 C=0.6215 A=0.3785
The PAGE Study NativeHawaiian Sub 4534 C=0.4638 A=0.5362
The PAGE Study Cuban Sub 4228 C=0.6403 A=0.3597
The PAGE Study Dominican Sub 3828 C=0.5961 A=0.4039
The PAGE Study CentralAmerican Sub 2450 C=0.5539 A=0.4461
The PAGE Study SouthAmerican Sub 1982 C=0.5293 A=0.4707
The PAGE Study NativeAmerican Sub 1260 C=0.6349 A=0.3651
The PAGE Study SouthAsian Sub 856 C=0.493 A=0.507
8.3KJPN JAPANESE Study-wide 16760 C=0.48920 A=0.51080
1000Genomes Global Study-wide 5008 C=0.5319 A=0.4681
1000Genomes African Sub 1322 C=0.4985 A=0.5015
1000Genomes East Asian Sub 1008 C=0.4385 A=0.5615
1000Genomes Europe Sub 1006 C=0.6918 A=0.3082
1000Genomes South Asian Sub 978 C=0.493 A=0.507
1000Genomes American Sub 694 C=0.555 A=0.445
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6804 A=0.3196
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6687 A=0.3313
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6650 A=0.3350
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5280 A=0.4720
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.5600 A=0.4400
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.470 A=0.530
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.599 A=0.401
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.651 A=0.349
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.697 A=0.303
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.579 A=0.421
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.435 A=0.565
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.18 A=0.82
HapMap Global Study-wide 1892 C=0.5539 A=0.4461
HapMap American Sub 770 C=0.586 A=0.414
HapMap African Sub 692 C=0.494 A=0.506
HapMap Asian Sub 254 C=0.504 A=0.496
HapMap Europe Sub 176 C=0.722 A=0.278
Korean Genome Project KOREAN Study-wide 1832 C=0.5229 A=0.4771
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.698 A=0.302
CNV burdens in cranial meningiomas Global Study-wide 752 C=0.487 A=0.513
CNV burdens in cranial meningiomas CRM Sub 752 C=0.487 A=0.513
Northern Sweden ACPOP Study-wide 600 C=0.617 A=0.383
SGDP_PRJ Global Study-wide 386 C=0.293 A=0.707
Qatari Global Study-wide 216 C=0.583 A=0.417
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.524 A=0.476
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 72 C=0.78 A=0.22
The Danish reference pan genome Danish Study-wide 40 C=0.78 A=0.23
Siberian Global Study-wide 32 C=0.31 A=0.69
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
GRCh38.p13 chr 1 NC_000001.11:g.2792599= NC_000001.11:g.2792599C>A
GRCh37.p13 chr 1 NC_000001.10:g.2709164= NC_000001.10:g.2709164C>A
TTC34 transcript NM_001242672.2:c.785-2253= NM_001242672.2:c.785-2253G>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#.

94 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396347 Feb 20, 2003 (111)
2 BCM_SSAHASNP ss9820758 Jul 11, 2003 (116)
3 ILLUMINA ss66716703 Dec 03, 2006 (127)
4 ILLUMINA ss67352857 Dec 03, 2006 (127)
5 ILLUMINA ss67743291 Dec 03, 2006 (127)
6 ILLUMINA ss70812957 May 27, 2008 (130)
7 ILLUMINA ss71393463 May 16, 2007 (127)
8 ILLUMINA ss75674713 Dec 06, 2007 (129)
9 ILLUMINA ss79187700 Dec 16, 2007 (130)
10 KRIBB_YJKIM ss84304105 Dec 16, 2007 (130)
11 BGI ss105113838 Dec 01, 2009 (131)
12 1000GENOMES ss107943019 Jan 22, 2009 (130)
13 1000GENOMES ss109954134 Jan 24, 2009 (130)
14 ILLUMINA ss122343282 Dec 01, 2009 (131)
15 ILLUMINA ss154304363 Dec 01, 2009 (131)
16 GMI ss154547118 Dec 01, 2009 (131)
17 ILLUMINA ss159481187 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss162994520 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss165997331 Jul 04, 2010 (132)
20 ILLUMINA ss171844694 Jul 04, 2010 (132)
21 ILLUMINA ss173767963 Jul 04, 2010 (132)
22 BUSHMAN ss197909560 Jul 04, 2010 (132)
23 1000GENOMES ss218197321 Jul 14, 2010 (132)
24 1000GENOMES ss230400367 Jul 14, 2010 (132)
25 1000GENOMES ss238119506 Jul 15, 2010 (132)
26 BL ss252874382 May 09, 2011 (134)
27 GMI ss275688004 May 04, 2012 (137)
28 GMI ss283989844 Apr 25, 2013 (138)
29 PJP ss290496698 May 09, 2011 (134)
30 ILLUMINA ss537252854 Sep 08, 2015 (146)
31 TISHKOFF ss553725524 Apr 25, 2013 (138)
32 SSMP ss647529262 Apr 25, 2013 (138)
33 ILLUMINA ss825518218 Apr 01, 2015 (144)
34 ILLUMINA ss832992618 Jul 12, 2019 (153)
35 EVA-GONL ss974785860 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1067620961 Aug 21, 2014 (142)
37 1000GENOMES ss1289412022 Aug 21, 2014 (142)
38 DDI ss1425690003 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1573856605 Apr 01, 2015 (144)
40 EVA_DECODE ss1584145434 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1599407510 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1642401543 Apr 01, 2015 (144)
43 EVA_SVP ss1712306195 Apr 01, 2015 (144)
44 HAMMER_LAB ss1793752933 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1917980629 Feb 12, 2016 (147)
46 ILLUMINA ss1958233331 Feb 12, 2016 (147)
47 GENOMED ss1966669637 Jul 19, 2016 (147)
48 JJLAB ss2019506635 Sep 14, 2016 (149)
49 ILLUMINA ss2094839988 Dec 20, 2016 (150)
50 ILLUMINA ss2094949650 Dec 20, 2016 (150)
51 ILLUMINA ss2094949653 Dec 20, 2016 (150)
52 USC_VALOUEV ss2147496393 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2159493571 Dec 20, 2016 (150)
54 TOPMED ss2321649436 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2624269178 Nov 08, 2017 (151)
56 GRF ss2697389849 Nov 08, 2017 (151)
57 GNOMAD ss2750866597 Nov 08, 2017 (151)
58 AFFY ss2985495521 Nov 08, 2017 (151)
59 SWEGEN ss2986185745 Nov 08, 2017 (151)
60 ILLUMINA ss3021046241 Nov 08, 2017 (151)
61 BIOINF_KMB_FNS_UNIBA ss3023517142 Nov 08, 2017 (151)
62 TOPMED ss3066895544 Nov 08, 2017 (151)
63 CSHL ss3343283865 Nov 08, 2017 (151)
64 ILLUMINA ss3626009748 Oct 11, 2018 (152)
65 ILLUMINA ss3637733287 Oct 11, 2018 (152)
66 ILLUMINA ss3638888025 Oct 11, 2018 (152)
67 ILLUMINA ss3639440734 Oct 11, 2018 (152)
68 ILLUMINA ss3640973439 Oct 11, 2018 (152)
69 ILLUMINA ss3641267252 Oct 11, 2018 (152)
70 ILLUMINA ss3642747516 Oct 11, 2018 (152)
71 ILLUMINA ss3651368678 Oct 11, 2018 (152)
72 ILLUMINA ss3651368679 Oct 11, 2018 (152)
73 EGCUT_WGS ss3654286724 Jul 12, 2019 (153)
74 EVA_DECODE ss3686027920 Jul 12, 2019 (153)
75 ILLUMINA ss3724989955 Jul 12, 2019 (153)
76 ACPOP ss3726731173 Jul 12, 2019 (153)
77 EVA ss3745742040 Jul 12, 2019 (153)
78 PAGE_CC ss3770779964 Jul 12, 2019 (153)
79 PACBIO ss3783306775 Jul 12, 2019 (153)
80 PACBIO ss3788983845 Jul 12, 2019 (153)
81 PACBIO ss3793856463 Jul 12, 2019 (153)
82 KHV_HUMAN_GENOMES ss3798764706 Jul 12, 2019 (153)
83 EVA ss3825989088 Apr 25, 2020 (154)
84 EVA ss3836381832 Apr 25, 2020 (154)
85 EVA ss3841785934 Apr 25, 2020 (154)
86 HGDP ss3847322285 Apr 25, 2020 (154)
87 SGDP_PRJ ss3848046380 Apr 25, 2020 (154)
88 KRGDB ss3892905400 Apr 25, 2020 (154)
89 KOGIC ss3943669794 Apr 25, 2020 (154)
90 EVA ss3984450972 Apr 25, 2021 (155)
91 EVA ss3984774470 Apr 25, 2021 (155)
92 EVA ss4016889696 Apr 25, 2021 (155)
93 TOPMED ss4437004218 Apr 25, 2021 (155)
94 TOMMO_GENOMICS ss5142155846 Apr 25, 2021 (155)
95 1000Genomes NC_000001.10 - 2709164 Oct 11, 2018 (152)
96 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 2709164 Oct 11, 2018 (152)
97 Genetic variation in the Estonian population NC_000001.10 - 2709164 Oct 11, 2018 (152)
98 The Danish reference pan genome NC_000001.10 - 2709164 Apr 25, 2020 (154)
99 gnomAD - Genomes NC_000001.11 - 2792599 Apr 25, 2021 (155)
100 Genome of the Netherlands Release 5 NC_000001.10 - 2709164 Apr 25, 2020 (154)
101 HGDP-CEPH-db Supplement 1 NC_000001.9 - 2699024 Apr 25, 2020 (154)
102 HapMap NC_000001.11 - 2792599 Apr 25, 2020 (154)
103 KOREAN population from KRGDB NC_000001.10 - 2709164 Apr 25, 2020 (154)
104 Korean Genome Project NC_000001.11 - 2792599 Apr 25, 2020 (154)
105 Northern Sweden NC_000001.10 - 2709164 Jul 12, 2019 (153)
106 The PAGE Study NC_000001.11 - 2792599 Jul 12, 2019 (153)
107 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 2709164 Apr 25, 2021 (155)
108 CNV burdens in cranial meningiomas NC_000001.10 - 2709164 Apr 25, 2021 (155)
109 Qatari NC_000001.10 - 2709164 Apr 25, 2020 (154)
110 SGDP_PRJ NC_000001.10 - 2709164 Apr 25, 2020 (154)
111 Siberian NC_000001.10 - 2709164 Apr 25, 2020 (154)
112 8.3KJPN NC_000001.10 - 2709164 Apr 25, 2021 (155)
113 TopMed NC_000001.11 - 2792599 Apr 25, 2021 (155)
114 UK 10K study - Twins NC_000001.10 - 2709164 Oct 11, 2018 (152)
115 A Vietnamese Genetic Variation Database NC_000001.10 - 2709164 Jul 12, 2019 (153)
116 ALFA NC_000001.11 - 2792599 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)
rs61607301 May 27, 2008 (130)
rs386594405 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638888025, ss3639440734 NC_000001.8:2732321:C:A NC_000001.11:2792598:C:A (self)
177, ss107943019, ss109954134, ss162994520, ss165997331, ss197909560, ss252874382, ss275688004, ss283989844, ss290496698, ss825518218, ss1584145434, ss1712306195, ss2094839988, ss3642747516, ss3847322285 NC_000001.9:2699023:C:A NC_000001.11:2792598:C:A (self)
78962, 32254, 24972, 1363839, 13579, 82794, 16038, 397, 272, 22559, 63360, 12747, 125153, 32254, 6599, ss218197321, ss230400367, ss238119506, ss537252854, ss553725524, ss647529262, ss832992618, ss974785860, ss1067620961, ss1289412022, ss1425690003, ss1573856605, ss1599407510, ss1642401543, ss1793752933, ss1917980629, ss1958233331, ss1966669637, ss2019506635, ss2094949650, ss2094949653, ss2147496393, ss2321649436, ss2624269178, ss2697389849, ss2750866597, ss2985495521, ss2986185745, ss3021046241, ss3343283865, ss3626009748, ss3637733287, ss3640973439, ss3641267252, ss3651368678, ss3651368679, ss3654286724, ss3726731173, ss3745742040, ss3783306775, ss3788983845, ss3793856463, ss3825989088, ss3836381832, ss3848046380, ss3892905400, ss3984450972, ss3984774470, ss4016889696, ss5142155846 NC_000001.10:2709163:C:A NC_000001.11:2792598:C:A (self)
605676, 1419, 47795, 1433, 375611, 610553, 5143438874, ss2159493571, ss3023517142, ss3066895544, ss3686027920, ss3724989955, ss3770779964, ss3798764706, ss3841785934, ss3943669794, ss4437004218 NC_000001.11:2792598:C:A NC_000001.11:2792598:C:A (self)
ss9820758 NT_004321.15:15939:C:A NC_000001.11:2792598:C:A (self)
ss6396347, ss66716703, ss67352857, ss67743291, ss70812957, ss71393463, ss75674713, ss79187700, ss84304105, ss105113838, ss122343282, ss154304363, ss154547118, ss159481187, ss171844694, ss173767963 NT_004350.19:2187795:C:A NC_000001.11:2792598:C:A (self)
Help

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

6 citations for rs4648356
PMID Title Author Year Journal
22164203 Perspectives on the use of multiple sclerosis risk genes for prediction. Jafari N et al. 2011 PloS one
22396755 Genomic regions associated with multiple sclerosis are active in B cells. Disanto G et al. 2012 PloS one
23730204 Progress in multiple sclerosis genetics. Goris A et al. 2012 Current genomics
24727690 Single nucleotide polymorphism (SNP)-strings: an alternative method for assessing genetic associations. Goodin DS et al. 2014 PloS one
27802296 A Risk Score for Predicting Multiple Sclerosis. Dobson R et al. 2016 PloS one
31482761 Breakdown of multiple sclerosis genetics to identify an integrated disease network and potential variant mechanisms. Shepard CJ et al. 2019 Physiological genomics
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.post596+ae089ad