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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.

rs9494142

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr6:135110502 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.201160 (53245/264690, TOPMED)
C=0.211415 (29610/140056, GnomAD)
C=0.18240 (14353/78690, PAGE_STUDY) (+ 17 more)
C=0.21152 (6479/30630, ALFA)
C=0.36754 (6160/16760, 8.3KJPN)
C=0.1815 (909/5008, 1000G)
C=0.2538 (1137/4480, Estonian)
C=0.2540 (979/3854, ALSPAC)
C=0.2478 (919/3708, TWINSUK)
C=0.3457 (1013/2930, KOREAN)
C=0.3483 (638/1832, Korea1K)
C=0.1840 (209/1136, Daghestan)
C=0.242 (242/998, GoNL)
C=0.312 (187/600, NorthernSweden)
C=0.207 (68/328, HapMap)
C=0.153 (33/216, Qatari)
C=0.243 (52/214, Vietnamese)
T=0.438 (92/210, SGDP_PRJ)
C=0.25 (10/40, GENOME_DK)
T=0.32 (11/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105378010 : 500B Downstream Variant
Publications
10 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 30630 T=0.78848 C=0.21152
European Sub 15880 T=0.75176 C=0.24824
African Sub 6314 T=0.8692 C=0.1308
African Others Sub 198 T=0.899 C=0.101
African American Sub 6116 T=0.8682 C=0.1318
Asian Sub 166 T=0.687 C=0.313
East Asian Sub 136 T=0.684 C=0.316
Other Asian Sub 30 T=0.70 C=0.30
Latin American 1 Sub 222 T=0.820 C=0.180
Latin American 2 Sub 4710 T=0.8134 C=0.1866
South Asian Sub 120 T=0.850 C=0.150
Other Sub 3218 T=0.7756 C=0.2244


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=0.798840 C=0.201160
gnomAD - Genomes Global Study-wide 140056 T=0.788585 C=0.211415
gnomAD - Genomes European Sub 75844 T=0.74540 C=0.25460
gnomAD - Genomes African Sub 41986 T=0.86445 C=0.13555
gnomAD - Genomes American Sub 13638 T=0.80430 C=0.19570
gnomAD - Genomes Ashkenazi Jewish Sub 3316 T=0.7856 C=0.2144
gnomAD - Genomes East Asian Sub 3122 T=0.7422 C=0.2578
gnomAD - Genomes Other Sub 2150 T=0.8028 C=0.1972
The PAGE Study Global Study-wide 78690 T=0.81760 C=0.18240
The PAGE Study AfricanAmerican Sub 32506 T=0.86538 C=0.13462
The PAGE Study Mexican Sub 10810 T=0.80574 C=0.19426
The PAGE Study Asian Sub 8318 T=0.6422 C=0.3578
The PAGE Study PuertoRican Sub 7918 T=0.7950 C=0.2050
The PAGE Study NativeHawaiian Sub 4534 T=0.8487 C=0.1513
The PAGE Study Cuban Sub 4228 T=0.8146 C=0.1854
The PAGE Study Dominican Sub 3828 T=0.8339 C=0.1661
The PAGE Study CentralAmerican Sub 2450 T=0.8278 C=0.1722
The PAGE Study SouthAmerican Sub 1982 T=0.8073 C=0.1927
The PAGE Study NativeAmerican Sub 1260 T=0.7786 C=0.2214
The PAGE Study SouthAsian Sub 856 T=0.896 C=0.104
8.3KJPN JAPANESE Study-wide 16760 T=0.63246 C=0.36754
1000Genomes Global Study-wide 5008 T=0.8185 C=0.1815
1000Genomes African Sub 1322 T=0.8699 C=0.1301
1000Genomes East Asian Sub 1008 T=0.7411 C=0.2589
1000Genomes Europe Sub 1006 T=0.7515 C=0.2485
1000Genomes South Asian Sub 978 T=0.899 C=0.101
1000Genomes American Sub 694 T=0.817 C=0.183
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7462 C=0.2538
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7460 C=0.2540
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7522 C=0.2478
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.6543 C=0.3457
Korean Genome Project KOREAN Study-wide 1832 T=0.6517 C=0.3483
Genome-wide autozygosity in Daghestan Global Study-wide 1136 T=0.8160 C=0.1840
Genome-wide autozygosity in Daghestan Daghestan Sub 628 T=0.803 C=0.197
Genome-wide autozygosity in Daghestan Near_East Sub 144 T=0.875 C=0.125
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=0.779 C=0.221
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.759 C=0.241
Genome-wide autozygosity in Daghestan South Asian Sub 98 T=0.95 C=0.05
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.75 C=0.25
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.758 C=0.242
Northern Sweden ACPOP Study-wide 600 T=0.688 C=0.312
HapMap Global Study-wide 328 T=0.793 C=0.207
HapMap African Sub 120 T=0.892 C=0.108
HapMap American Sub 120 T=0.808 C=0.192
HapMap Asian Sub 88 T=0.64 C=0.36
Qatari Global Study-wide 216 T=0.847 C=0.153
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.757 C=0.243
SGDP_PRJ Global Study-wide 210 T=0.438 C=0.562
The Danish reference pan genome Danish Study-wide 40 T=0.75 C=0.25
Siberian Global Study-wide 34 T=0.32 C=0.68
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 6 NC_000006.12:g.135110502T>C
GRCh37.p13 chr 6 NC_000006.11:g.135431640T>C
Gene: LOC105378010, uncharacterized LOC105378010 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC105378010 transcript variant X2 XR_001743891.1:n. N/A Downstream Transcript Variant
LOC105378010 transcript variant X1 XR_943010.2:n. N/A Downstream 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 T= C
GRCh38.p13 chr 6 NC_000006.12:g.135110502= NC_000006.12:g.135110502T>C
GRCh37.p13 chr 6 NC_000006.11:g.135431640= NC_000006.11:g.135431640T>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#.

65 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13138280 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss17870213 Feb 27, 2004 (126)
3 SC_SNP ss18349029 Feb 27, 2004 (126)
4 SSAHASNP ss22369790 Apr 05, 2004 (126)
5 PERLEGEN ss24195391 Sep 20, 2004 (126)
6 ABI ss44699877 Mar 13, 2006 (126)
7 PERLEGEN ss68992436 May 17, 2007 (127)
8 CGM_KYOTO ss76875250 Dec 07, 2007 (129)
9 BCMHGSC_JDW ss93565727 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss98544201 Feb 06, 2009 (130)
11 1000GENOMES ss110968582 Feb 13, 2009 (130)
12 1000GENOMES ss115161855 Jan 25, 2009 (130)
13 GMI ss157627753 Dec 01, 2009 (131)
14 ILLUMINA ss161089467 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss162839575 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss164644374 Jul 04, 2010 (132)
17 BUSHMAN ss202456234 Jul 04, 2010 (132)
18 1000GENOMES ss222696947 Jul 14, 2010 (132)
19 1000GENOMES ss233699208 Jul 15, 2010 (132)
20 1000GENOMES ss240709805 Jul 15, 2010 (132)
21 GMI ss279036612 May 04, 2012 (137)
22 GMI ss285511047 Apr 25, 2013 (138)
23 ILLUMINA ss479218330 Sep 08, 2015 (146)
24 TISHKOFF ss559550246 Apr 25, 2013 (138)
25 SSMP ss653824740 Apr 25, 2013 (138)
26 EVA-GONL ss983542864 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1074065917 Aug 21, 2014 (142)
28 1000GENOMES ss1322432282 Aug 21, 2014 (142)
29 HAMMER_LAB ss1397472225 Sep 08, 2015 (146)
30 DDI ss1430907164 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1581913541 Apr 01, 2015 (144)
32 EVA_DECODE ss1593112913 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1616781935 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1659775968 Apr 01, 2015 (144)
35 WEILL_CORNELL_DGM ss1926787615 Feb 12, 2016 (147)
36 ILLUMINA ss1958953434 Feb 12, 2016 (147)
37 JJLAB ss2024051876 Sep 14, 2016 (149)
38 USC_VALOUEV ss2152244610 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2288727194 Dec 20, 2016 (150)
40 TOPMED ss2457400285 Dec 20, 2016 (150)
41 SYSTEMSBIOZJU ss2626519374 Nov 08, 2017 (151)
42 GRF ss2707876618 Nov 08, 2017 (151)
43 GNOMAD ss2845579474 Nov 08, 2017 (151)
44 SWEGEN ss3000015378 Nov 08, 2017 (151)
45 ILLUMINA ss3022669943 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3025818609 Nov 08, 2017 (151)
47 CSHL ss3347247191 Nov 08, 2017 (151)
48 TOPMED ss3512941742 Nov 08, 2017 (151)
49 ILLUMINA ss3636815776 Oct 12, 2018 (152)
50 URBANLAB ss3648479753 Oct 12, 2018 (152)
51 ILLUMINA ss3653192702 Oct 12, 2018 (152)
52 EGCUT_WGS ss3667935847 Jul 13, 2019 (153)
53 EVA_DECODE ss3718357013 Jul 13, 2019 (153)
54 ILLUMINA ss3726387496 Jul 13, 2019 (153)
55 ACPOP ss3734018647 Jul 13, 2019 (153)
56 EVA ss3765718270 Jul 13, 2019 (153)
57 PAGE_CC ss3771325499 Jul 13, 2019 (153)
58 KHV_HUMAN_GENOMES ss3808876197 Jul 13, 2019 (153)
59 EVA ss3830212734 Apr 26, 2020 (154)
60 SGDP_PRJ ss3865793513 Apr 26, 2020 (154)
61 KRGDB ss3912754194 Apr 26, 2020 (154)
62 KOGIC ss3960145521 Apr 26, 2020 (154)
63 TOPMED ss4723250792 Apr 26, 2021 (155)
64 TOMMO_GENOMICS ss5180110633 Apr 26, 2021 (155)
65 EVA ss5237407744 Apr 26, 2021 (155)
66 1000Genomes NC_000006.11 - 135431640 Oct 12, 2018 (152)
67 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 135431640 Oct 12, 2018 (152)
68 Genome-wide autozygosity in Daghestan NC_000006.10 - 135473333 Apr 26, 2020 (154)
69 Genetic variation in the Estonian population NC_000006.11 - 135431640 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000006.11 - 135431640 Apr 26, 2020 (154)
71 gnomAD - Genomes NC_000006.12 - 135110502 Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000006.11 - 135431640 Apr 26, 2020 (154)
73 HapMap NC_000006.12 - 135110502 Apr 26, 2020 (154)
74 KOREAN population from KRGDB NC_000006.11 - 135431640 Apr 26, 2020 (154)
75 Korean Genome Project NC_000006.12 - 135110502 Apr 26, 2020 (154)
76 Northern Sweden NC_000006.11 - 135431640 Jul 13, 2019 (153)
77 The PAGE Study NC_000006.12 - 135110502 Jul 13, 2019 (153)
78 Qatari NC_000006.11 - 135431640 Apr 26, 2020 (154)
79 SGDP_PRJ NC_000006.11 - 135431640 Apr 26, 2020 (154)
80 Siberian NC_000006.11 - 135431640 Apr 26, 2020 (154)
81 8.3KJPN NC_000006.11 - 135431640 Apr 26, 2021 (155)
82 TopMed NC_000006.12 - 135110502 Apr 26, 2021 (155)
83 UK 10K study - Twins NC_000006.11 - 135431640 Oct 12, 2018 (152)
84 A Vietnamese Genetic Variation Database NC_000006.11 - 135431640 Jul 13, 2019 (153)
85 ALFA NC_000006.12 - 135110502 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).

Associated ID History Updated (Build)
rs11154792 Oct 15, 2006 (127)
rs17720631 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
446636, ss93565727, ss110968582, ss115161855, ss161089467, ss162839575, ss164644374, ss202456234, ss279036612, ss285511047, ss1397472225, ss1593112913 NC_000006.10:135473332:T:C NC_000006.12:135110501:T:C (self)
34307388, 19121962, 13674095, 8078480, 8516745, 19931588, 7303512, 8829545, 17810493, 4760964, 38079940, 19121962, 4256801, ss222696947, ss233699208, ss240709805, ss479218330, ss559550246, ss653824740, ss983542864, ss1074065917, ss1322432282, ss1430907164, ss1581913541, ss1616781935, ss1659775968, ss1926787615, ss1958953434, ss2024051876, ss2152244610, ss2457400285, ss2626519374, ss2707876618, ss2845579474, ss3000015378, ss3022669943, ss3347247191, ss3636815776, ss3653192702, ss3667935847, ss3734018647, ss3765718270, ss3830212734, ss3865793513, ss3912754194, ss5180110633, ss5237407744 NC_000006.11:135431639:T:C NC_000006.12:135110501:T:C (self)
242281390, 3258042, 16523522, 546968, 350672722, 560628350, 7397857867, ss2288727194, ss3025818609, ss3512941742, ss3648479753, ss3718357013, ss3726387496, ss3771325499, ss3808876197, ss3960145521, ss4723250792 NC_000006.12:135110501:T:C NC_000006.12:135110501:T:C (self)
ss13138280 NT_025741.12:39536068:T:C NC_000006.12:135110501:T:C (self)
ss17870213, ss18349029, ss22369790 NT_025741.13:39536068:T:C NC_000006.12:135110501:T:C (self)
ss24195391, ss44699877, ss68992436, ss76875250, ss98544201, ss157627753 NT_025741.15:39601096:T:C NC_000006.12:135110501:T:C (self)
Help

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

10 citations for rs9494142
PMID Title Author Year Journal
17592125 Intergenic variants of HBS1L-MYB are responsible for a major quantitative trait locus on chromosome 6q23 influencing fetal hemoglobin levels in adults. Thein SL et al. 2007 Proceedings of the National Academy of Sciences of the United States of America
19148297 Genetic variation on chromosome 6 influences F cell levels in healthy individuals of African descent and HbF levels in sickle cell patients. Creary LE et al. 2009 PloS one
19853236 Sequence variants in three loci influence monocyte counts and erythrocyte volume. Ferreira MA et al. 2009 American journal of human genetics
20401335 Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype. Driss A et al. 2009 Genomics insights
20886046 Experimental generation of SNP haplotype signatures in patients with sickle cell anaemia. Menzel S et al. 2010 PloS one
21385855 A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression. Farrell JJ et al. 2011 Blood
24614105 HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers. Stadhouders R et al. 2014 The Journal of clinical investigation
24978191 The co-inheritance of alpha-thalassemia and sickle cell anemia is associated with better hematological indices and lower consultations rate in Cameroonian patients and could improve their survival. Rumaney MB et al. 2014 PloS one
28280727 Existence of HbF Enhancer Haplotypes at <i>HBS1L-MYB</i> Intergenic Region in Transfusion-Dependent Saudi <i>β</i>-Thalassemia Patients. Cyrus C et al. 2017 BioMed research international
29437638 <i>g(HbF)</i>: a genetic model of fetal hemoglobin in sickle cell disease. Gardner K et al. 2018 Blood advances
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.post629+eb05767