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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.

rs1230678

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:113755798 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.261604 (69244/264690, TOPMED)
G=0.247879 (34658/139818, GnomAD)
T=0.40951 (11571/28256, 14KJPN) (+ 16 more)
G=0.24815 (4687/18888, ALFA)
T=0.41277 (6918/16760, 8.3KJPN)
G=0.3153 (2019/6404, 1000G_30x)
G=0.3213 (1609/5008, 1000G)
G=0.2585 (1158/4480, Estonian)
G=0.2496 (962/3854, ALSPAC)
G=0.2416 (896/3708, TWINSUK)
T=0.3590 (1052/2930, KOREAN)
T=0.3597 (659/1832, Korea1K)
G=0.223 (223/998, GoNL)
G=0.235 (141/600, NorthernSweden)
T=0.388 (107/276, SGDP_PRJ)
G=0.324 (70/216, Qatari)
T=0.476 (98/206, Vietnamese)
G=0.28 (11/40, GENOME_DK)
T=0.38 (10/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PHTF1 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele
Total Global 18888 T=0.75185 G=0.24815
European Sub 14284 T=0.74678 G=0.25322
African Sub 2946 T=0.8337 G=0.1663
African Others Sub 114 T=0.798 G=0.202
African American Sub 2832 T=0.8351 G=0.1649
Asian Sub 112 T=0.464 G=0.536
East Asian Sub 86 T=0.38 G=0.62
Other Asian Sub 26 T=0.73 G=0.27
Latin American 1 Sub 146 T=0.699 G=0.301
Latin American 2 Sub 610 T=0.548 G=0.452
South Asian Sub 98 T=0.83 G=0.17
Other Sub 692 T=0.736 G=0.264


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 T=0.738396 G=0.261604
gnomAD - Genomes Global Study-wide 139818 T=0.752121 G=0.247879
gnomAD - Genomes European Sub 75760 T=0.74621 G=0.25379
gnomAD - Genomes African Sub 41882 T=0.82864 G=0.17136
gnomAD - Genomes American Sub 13596 T=0.63261 G=0.36739
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.7601 G=0.2399
gnomAD - Genomes East Asian Sub 3118 T=0.3881 G=0.6119
gnomAD - Genomes Other Sub 2144 T=0.7411 G=0.2589
14KJPN JAPANESE Study-wide 28256 T=0.40951 G=0.59049
Allele Frequency Aggregator Total Global 18888 T=0.75185 G=0.24815
Allele Frequency Aggregator European Sub 14284 T=0.74678 G=0.25322
Allele Frequency Aggregator African Sub 2946 T=0.8337 G=0.1663
Allele Frequency Aggregator Other Sub 692 T=0.736 G=0.264
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.548 G=0.452
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.699 G=0.301
Allele Frequency Aggregator Asian Sub 112 T=0.464 G=0.536
Allele Frequency Aggregator South Asian Sub 98 T=0.83 G=0.17
8.3KJPN JAPANESE Study-wide 16760 T=0.41277 G=0.58723
1000Genomes_30x Global Study-wide 6404 T=0.6847 G=0.3153
1000Genomes_30x African Sub 1786 T=0.8387 G=0.1613
1000Genomes_30x Europe Sub 1266 T=0.7409 G=0.2591
1000Genomes_30x South Asian Sub 1202 T=0.7762 G=0.2238
1000Genomes_30x East Asian Sub 1170 T=0.3889 G=0.6111
1000Genomes_30x American Sub 980 T=0.572 G=0.428
1000Genomes Global Study-wide 5008 T=0.6787 G=0.3213
1000Genomes African Sub 1322 T=0.8343 G=0.1657
1000Genomes East Asian Sub 1008 T=0.3948 G=0.6052
1000Genomes Europe Sub 1006 T=0.7406 G=0.2594
1000Genomes South Asian Sub 978 T=0.774 G=0.226
1000Genomes American Sub 694 T=0.571 G=0.429
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7415 G=0.2585
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7504 G=0.2496
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7584 G=0.2416
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.3590 C=0.0000, G=0.6410
Korean Genome Project KOREAN Study-wide 1832 T=0.3597 G=0.6403
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.777 G=0.223
Northern Sweden ACPOP Study-wide 600 T=0.765 G=0.235
SGDP_PRJ Global Study-wide 276 T=0.388 G=0.612
Qatari Global Study-wide 216 T=0.676 G=0.324
A Vietnamese Genetic Variation Database Global Study-wide 206 T=0.476 G=0.524
The Danish reference pan genome Danish Study-wide 40 T=0.72 G=0.28
Siberian Global Study-wide 26 T=0.38 G=0.62
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.113755798T>C
GRCh38.p14 chr 1 NC_000001.11:g.113755798T>G
GRCh37.p13 chr 1 NC_000001.10:g.114298420T>C
GRCh37.p13 chr 1 NC_000001.10:g.114298420T>G
Gene: PHTF1, putative homeodomain transcription factor 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PHTF1 transcript variant 2 NM_001323041.2:c.102+1901…

NM_001323041.2:c.102+1901A>G

N/A Intron Variant
PHTF1 transcript variant 3 NM_001323042.2:c.102+1901…

NM_001323042.2:c.102+1901A>G

N/A Intron Variant
PHTF1 transcript variant 4 NM_001323043.2:c.102+1901…

NM_001323043.2:c.102+1901A>G

N/A Intron Variant
PHTF1 transcript variant 5 NM_001323044.2:c.-109+190…

NM_001323044.2:c.-109+1901A>G

N/A Intron Variant
PHTF1 transcript variant 6 NM_001323045.2:c.-109+190…

NM_001323045.2:c.-109+1901A>G

N/A Intron Variant
PHTF1 transcript variant 7 NM_001323046.2:c.-368+190…

NM_001323046.2:c.-368+1901A>G

N/A Intron Variant
PHTF1 transcript variant 8 NM_001323047.2:c.102+1901…

NM_001323047.2:c.102+1901A>G

N/A Intron Variant
PHTF1 transcript variant 9 NM_001323048.2:c.102+1901…

NM_001323048.2:c.102+1901A>G

N/A Intron Variant
PHTF1 transcript variant 10 NM_001323049.2:c.102+1901…

NM_001323049.2:c.102+1901A>G

N/A Intron Variant
PHTF1 transcript variant 11 NM_001323050.2:c.-109+190…

NM_001323050.2:c.-109+1901A>G

N/A Intron Variant
PHTF1 transcript variant 12 NM_001323051.2:c.-109+190…

NM_001323051.2:c.-109+1901A>G

N/A Intron Variant
PHTF1 transcript variant 13 NM_001323052.2:c.102+1901…

NM_001323052.2:c.102+1901A>G

N/A Intron Variant
PHTF1 transcript variant 14 NM_001323053.2:c.102+1901…

NM_001323053.2:c.102+1901A>G

N/A Intron Variant
PHTF1 transcript variant 1 NM_006608.3:c.102+1901A>G N/A Intron Variant
PHTF1 transcript variant 15 NR_136564.2:n. N/A Intron Variant
PHTF1 transcript variant 16 NR_136565.2:n. N/A Intron Variant
PHTF1 transcript variant 17 NR_136566.2:n. N/A Intron Variant
PHTF1 transcript variant 18 NR_136567.2:n. N/A Intron Variant
PHTF1 transcript variant 19 NR_136568.2:n. 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 T= C G
GRCh38.p14 chr 1 NC_000001.11:g.113755798= NC_000001.11:g.113755798T>C NC_000001.11:g.113755798T>G
GRCh37.p13 chr 1 NC_000001.10:g.114298420= NC_000001.10:g.114298420T>C NC_000001.10:g.114298420T>G
PHTF1 transcript variant 2 NM_001323041.2:c.102+1901= NM_001323041.2:c.102+1901A>G NM_001323041.2:c.102+1901A>C
PHTF1 transcript variant 3 NM_001323042.2:c.102+1901= NM_001323042.2:c.102+1901A>G NM_001323042.2:c.102+1901A>C
PHTF1 transcript variant 4 NM_001323043.2:c.102+1901= NM_001323043.2:c.102+1901A>G NM_001323043.2:c.102+1901A>C
PHTF1 transcript variant 5 NM_001323044.2:c.-109+1901= NM_001323044.2:c.-109+1901A>G NM_001323044.2:c.-109+1901A>C
PHTF1 transcript variant 6 NM_001323045.2:c.-109+1901= NM_001323045.2:c.-109+1901A>G NM_001323045.2:c.-109+1901A>C
PHTF1 transcript variant 7 NM_001323046.2:c.-368+1901= NM_001323046.2:c.-368+1901A>G NM_001323046.2:c.-368+1901A>C
PHTF1 transcript variant 8 NM_001323047.2:c.102+1901= NM_001323047.2:c.102+1901A>G NM_001323047.2:c.102+1901A>C
PHTF1 transcript variant 9 NM_001323048.2:c.102+1901= NM_001323048.2:c.102+1901A>G NM_001323048.2:c.102+1901A>C
PHTF1 transcript variant 10 NM_001323049.2:c.102+1901= NM_001323049.2:c.102+1901A>G NM_001323049.2:c.102+1901A>C
PHTF1 transcript variant 11 NM_001323050.2:c.-109+1901= NM_001323050.2:c.-109+1901A>G NM_001323050.2:c.-109+1901A>C
PHTF1 transcript variant 12 NM_001323051.2:c.-109+1901= NM_001323051.2:c.-109+1901A>G NM_001323051.2:c.-109+1901A>C
PHTF1 transcript variant 13 NM_001323052.2:c.102+1901= NM_001323052.2:c.102+1901A>G NM_001323052.2:c.102+1901A>C
PHTF1 transcript variant 14 NM_001323053.2:c.102+1901= NM_001323053.2:c.102+1901A>G NM_001323053.2:c.102+1901A>C
PHTF1 transcript variant 1 NM_006608.2:c.102+1901= NM_006608.2:c.102+1901A>G NM_006608.2:c.102+1901A>C
PHTF1 transcript variant 1 NM_006608.3:c.102+1901= NM_006608.3:c.102+1901A>G NM_006608.3:c.102+1901A>C
PHTF1 transcript variant X1 XM_005270383.1:c.102+1901= XM_005270383.1:c.102+1901A>G XM_005270383.1:c.102+1901A>C
PHTF1 transcript variant X2 XM_005270384.1:c.102+1901= XM_005270384.1:c.102+1901A>G XM_005270384.1:c.102+1901A>C
PHTF1 transcript variant X4 XM_005270386.1:c.102+1901= XM_005270386.1:c.102+1901A>G XM_005270386.1:c.102+1901A>C
PHTF1 transcript variant X8 XM_005270387.1:c.102+1901= XM_005270387.1:c.102+1901A>G XM_005270387.1:c.102+1901A>C
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#.

63 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1826760 Oct 18, 2000 (87)
2 SC_JCM ss3961760 Sep 28, 2001 (100)
3 CSHL-HAPMAP ss17353614 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19853461 Feb 27, 2004 (120)
5 ABI ss41086773 Mar 14, 2006 (126)
6 BCMHGSC_JDW ss87727228 Mar 23, 2008 (129)
7 ENSEMBL ss138063440 Dec 01, 2009 (131)
8 GMI ss155552600 Dec 01, 2009 (131)
9 ENSEMBL ss161160623 Dec 01, 2009 (131)
10 1000GENOMES ss230698669 Jul 14, 2010 (132)
11 1000GENOMES ss238354934 Jul 15, 2010 (132)
12 GMI ss275984702 May 04, 2012 (137)
13 GMI ss284124175 Apr 25, 2013 (138)
14 PJP ss290602298 May 09, 2011 (134)
15 TISHKOFF ss554594838 Apr 25, 2013 (138)
16 SSMP ss648324057 Apr 25, 2013 (138)
17 EVA-GONL ss975588058 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1068205966 Aug 21, 2014 (142)
19 1000GENOMES ss1292500452 Aug 21, 2014 (142)
20 DDI ss1425942520 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1574334266 Apr 01, 2015 (144)
22 EVA_DECODE ss1584968925 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1601026424 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1644020457 Apr 01, 2015 (144)
25 WEILL_CORNELL_DGM ss1918788305 Feb 12, 2016 (147)
26 GENOMED ss1966845443 Jul 19, 2016 (147)
27 JJLAB ss2019918564 Sep 14, 2016 (149)
28 USC_VALOUEV ss2147937355 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2165853936 Dec 20, 2016 (150)
30 SYSTEMSBIOZJU ss2624468937 Nov 08, 2017 (151)
31 GRF ss2697867686 Nov 08, 2017 (151)
32 GNOMAD ss2759755267 Nov 08, 2017 (151)
33 SWEGEN ss2987466666 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3023723832 Nov 08, 2017 (151)
35 CSHL ss3343643033 Nov 08, 2017 (151)
36 EGCUT_WGS ss3655555552 Jul 12, 2019 (153)
37 EVA_DECODE ss3687564517 Jul 12, 2019 (153)
38 ACPOP ss3727403409 Jul 12, 2019 (153)
39 EVA ss3746693085 Jul 12, 2019 (153)
40 PACBIO ss3783524477 Jul 12, 2019 (153)
41 PACBIO ss3789165521 Jul 12, 2019 (153)
42 PACBIO ss3794038454 Jul 12, 2019 (153)
43 KHV_HUMAN_GENOMES ss3799695844 Jul 12, 2019 (153)
44 EVA ss3826378937 Apr 25, 2020 (154)
45 EVA ss3836581165 Apr 25, 2020 (154)
46 EVA ss3841989608 Apr 25, 2020 (154)
47 SGDP_PRJ ss3849685248 Apr 25, 2020 (154)
48 KRGDB ss3894783853 Apr 25, 2020 (154)
49 KOGIC ss3945282310 Apr 25, 2020 (154)
50 TOPMED ss4464206964 Apr 25, 2021 (155)
51 TOMMO_GENOMICS ss5145758764 Apr 25, 2021 (155)
52 1000G_HIGH_COVERAGE ss5243668527 Oct 12, 2022 (156)
53 EVA ss5321292262 Oct 12, 2022 (156)
54 HUGCELL_USP ss5444585958 Oct 12, 2022 (156)
55 EVA ss5506002874 Oct 12, 2022 (156)
56 1000G_HIGH_COVERAGE ss5516692184 Oct 12, 2022 (156)
57 SANFORD_IMAGENETICS ss5626332022 Oct 12, 2022 (156)
58 TOMMO_GENOMICS ss5671050670 Oct 12, 2022 (156)
59 YY_MCH ss5800946547 Oct 12, 2022 (156)
60 EVA ss5832506989 Oct 12, 2022 (156)
61 EVA ss5849074808 Oct 12, 2022 (156)
62 EVA ss5909868860 Oct 12, 2022 (156)
63 EVA ss5938199698 Oct 12, 2022 (156)
64 1000Genomes NC_000001.10 - 114298420 Oct 11, 2018 (152)
65 1000Genomes_30x NC_000001.11 - 113755798 Oct 12, 2022 (156)
66 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 114298420 Oct 11, 2018 (152)
67 Genetic variation in the Estonian population NC_000001.10 - 114298420 Oct 11, 2018 (152)
68 The Danish reference pan genome NC_000001.10 - 114298420 Apr 25, 2020 (154)
69 gnomAD - Genomes NC_000001.11 - 113755798 Apr 25, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000001.10 - 114298420 Apr 25, 2020 (154)
71 KOREAN population from KRGDB NC_000001.10 - 114298420 Apr 25, 2020 (154)
72 Korean Genome Project NC_000001.11 - 113755798 Apr 25, 2020 (154)
73 Northern Sweden NC_000001.10 - 114298420 Jul 12, 2019 (153)
74 Qatari NC_000001.10 - 114298420 Apr 25, 2020 (154)
75 SGDP_PRJ NC_000001.10 - 114298420 Apr 25, 2020 (154)
76 Siberian NC_000001.10 - 114298420 Apr 25, 2020 (154)
77 8.3KJPN NC_000001.10 - 114298420 Apr 25, 2021 (155)
78 14KJPN NC_000001.11 - 113755798 Oct 12, 2022 (156)
79 TopMed NC_000001.11 - 113755798 Apr 25, 2021 (155)
80 UK 10K study - Twins NC_000001.10 - 114298420 Oct 11, 2018 (152)
81 A Vietnamese Genetic Variation Database NC_000001.10 - 114298420 Jul 12, 2019 (153)
82 ALFA NC_000001.11 - 113755798 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
1961247, ss3894783853 NC_000001.10:114298419:T:C NC_000001.11:113755797:T:C (self)
ss87727228, ss275984702, ss284124175, ss290602298, ss1584968925 NC_000001.9:114099942:T:G NC_000001.11:113755797:T:G (self)
3278799, 1813959, 1293800, 1671803, 788882, 1961247, 688274, 830235, 1702228, 453709, 3728071, 1813959, 392767, ss230698669, ss238354934, ss554594838, ss648324057, ss975588058, ss1068205966, ss1292500452, ss1425942520, ss1574334266, ss1601026424, ss1644020457, ss1918788305, ss1966845443, ss2019918564, ss2147937355, ss2624468937, ss2697867686, ss2759755267, ss2987466666, ss3343643033, ss3655555552, ss3727403409, ss3746693085, ss3783524477, ss3789165521, ss3794038454, ss3826378937, ss3836581165, ss3849685248, ss3894783853, ss5145758764, ss5321292262, ss5506002874, ss5626332022, ss5832506989, ss5938199698 NC_000001.10:114298419:T:G NC_000001.11:113755797:T:G (self)
4218119, 23191597, 1660311, 4887774, 27813299, 9438363634, ss2165853936, ss3023723832, ss3687564517, ss3799695844, ss3841989608, ss3945282310, ss4464206964, ss5243668527, ss5444585958, ss5516692184, ss5671050670, ss5800946547, ss5849074808, ss5909868860 NC_000001.11:113755797:T:G NC_000001.11:113755797:T:G (self)
ss17353614, ss19853461 NT_019273.16:5294367:T:G NC_000001.11:113755797:T:G (self)
ss1826760, ss3961760, ss41086773, ss138063440, ss155552600, ss161160623 NT_032977.9:84270337:T:G NC_000001.11:113755797:T:G (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 rs1230678

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.post774+babeb33