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.
rs2395029
Current Build 157
Released September 3, 2024
- Organism
- Homo sapiens
- Position
-
chr6:31464003 (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>G
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
G=0.030284 (10437/344632, GnomAD_exomes)G=0.033694 (9288/275660, ALFA)G=0.023877 (6320/264690, TOPMED) (+ 26 more)
- Clinical Significance
- Reported in ClinVar
- Gene : Consequence
- HCP5 : Non Coding Transcript Variant
- Publications
- 72 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 | Ref HMOZ | Alt HMOZ | HTRZ | HWEP |
|---|---|---|---|---|---|---|---|---|
| Total | Global | 275660 | T=0.966306 | G=0.033694 | 0.934078 | 0.001466 | 0.064456 | 8 |
| European | Sub | 230526 | T=0.963288 | G=0.036712 | 0.928121 | 0.001544 | 0.070335 | 2 |
| African | Sub | 13680 | T=0.99254 | G=0.00746 | 0.985965 | 0.000877 | 0.013158 | 32 |
| African Others | Sub | 510 | T=1.000 | G=0.000 | 1.0 | 0.0 | 0.0 | N/A |
| African American | Sub | 13170 | T=0.99226 | G=0.00774 | 0.985421 | 0.000911 | 0.013667 | 32 |
| Asian | Sub | 6372 | T=0.9931 | G=0.0069 | 0.98619 | 0.0 | 0.01381 | 0 |
| East Asian | Sub | 4540 | T=0.9932 | G=0.0068 | 0.986344 | 0.0 | 0.013656 | 0 |
| Other Asian | Sub | 1832 | T=0.9929 | G=0.0071 | 0.985808 | 0.0 | 0.014192 | 0 |
| Latin American 1 | Sub | 914 | T=0.982 | G=0.018 | 0.964989 | 0.0 | 0.035011 | 0 |
| Latin American 2 | Sub | 1654 | T=0.9903 | G=0.0097 | 0.981862 | 0.001209 | 0.016929 | 7 |
| South Asian | Sub | 5136 | T=0.9616 | G=0.0384 | 0.926402 | 0.003115 | 0.070483 | 3 |
| Other | Sub | 17378 | T=0.97411 | G=0.02589 | 0.949246 | 0.001036 | 0.049718 | 1 |
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 |
|---|---|---|---|---|---|
| gnomAD v4 - Exomes | Global | Study-wide | 344632 | T=0.969716 | G=0.030284 |
| gnomAD v4 - Exomes | European | Sub | 214788 | T=0.969654 | G=0.030346 |
| gnomAD v4 - Exomes | South Asian | Sub | 63524 | T=0.95307 | G=0.04693 |
| gnomAD v4 - Exomes | American | Sub | 31010 | T=0.99049 | G=0.00951 |
| gnomAD v4 - Exomes | East Asian | Sub | 12266 | T=0.99755 | G=0.00245 |
| gnomAD v4 - Exomes | Ashkenazi Jewish | Sub | 10656 | T=0.95693 | G=0.04307 |
| gnomAD v4 - Exomes | African | Sub | 9604 | T=0.9901 | G=0.0099 |
| gnomAD v4 - Exomes | Middle Eastern | sub | 2784 | T=0.9788 | G=0.0212 |
| Allele Frequency Aggregator | Total | Global | 275660 | T=0.966306 | G=0.033694 |
| Allele Frequency Aggregator | European | Sub | 230526 | T=0.963288 | G=0.036712 |
| Allele Frequency Aggregator | Other | Sub | 17378 | T=0.97411 | G=0.02589 |
| Allele Frequency Aggregator | African | Sub | 13680 | T=0.99254 | G=0.00746 |
| Allele Frequency Aggregator | Asian | Sub | 6372 | T=0.9931 | G=0.0069 |
| Allele Frequency Aggregator | South Asian | Sub | 5136 | T=0.9616 | G=0.0384 |
| Allele Frequency Aggregator | Latin American 2 | Sub | 1654 | T=0.9903 | G=0.0097 |
| Allele Frequency Aggregator | Latin American 1 | Sub | 914 | T=0.982 | G=0.018 |
| TopMed | Global | Study-wide | 264690 | T=0.976123 | G=0.023877 |
| gnomAD v4 - Genomes | Global | Study-wide | 148980 | T=0.976124 | G=0.023876 |
| gnomAD v4 - Genomes | European | Sub | 78622 | T=0.96701 | G=0.03299 |
| gnomAD v4 - Genomes | African | Sub | 41396 | T=0.99234 | G=0.00766 |
| gnomAD v4 - Genomes | American | Sub | 15238 | T=0.98609 | G=0.01391 |
| gnomAD v4 - Genomes | East Asian | Sub | 5160 | T=0.9915 | G=0.0085 |
| gnomAD v4 - Genomes | South Asian | Sub | 4810 | T=0.9516 | G=0.0484 |
| gnomAD v4 - Genomes | Ashkenazi Jewish | Sub | 3460 | T=0.9572 | G=0.0428 |
| gnomAD v4 - Genomes | Middle Eastern | sub | 294 | T=0.969 | G=0.031 |
| ExAC | Global | Study-wide | 117162 | T=0.971740 | G=0.028260 |
| ExAC | Europe | Sub | 72210 | T=0.96917 | G=0.03083 |
| ExAC | Asian | Sub | 22272 | T=0.95964 | G=0.04036 |
| ExAC | American | Sub | 11472 | T=0.99207 | G=0.00793 |
| ExAC | African | Sub | 10340 | T=0.99197 | G=0.00803 |
| ExAC | Other | Sub | 868 | T=0.986 | G=0.014 |
| 38KJPN | JAPANESE | Study-wide | 77390 | T=0.99999 | G=0.00001 |
| GO Exome Sequencing Project | Global | Study-wide | 13006 | T=0.97101 | G=0.02899 |
| GO Exome Sequencing Project | European American | Sub | 8600 | T=0.9606 | G=0.0394 |
| GO Exome Sequencing Project | African American | Sub | 4406 | T=0.9914 | G=0.0086 |
| Korean Genome Project 4K | KOREAN | Study-wide | 7228 | T=0.9970 | G=0.0030 |
| 1000Genomes_30X | Global | Study-wide | 6404 | T=0.9692 | G=0.0308 |
| 1000Genomes_30X | African | Sub | 1786 | T=0.9972 | G=0.0028 |
| 1000Genomes_30X | Europe | Sub | 1266 | T=0.9589 | G=0.0411 |
| 1000Genomes_30X | South Asian | Sub | 1202 | T=0.9126 | G=0.0874 |
| 1000Genomes_30X | East Asian | Sub | 1170 | T=0.9855 | G=0.0145 |
| 1000Genomes_30X | American | Sub | 980 | T=0.982 | G=0.018 |
| 1000Genomes | Global | Study-wide | 5008 | T=0.9667 | G=0.0333 |
| 1000Genomes | African | Sub | 1322 | T=0.9955 | G=0.0045 |
| 1000Genomes | East Asian | Sub | 1008 | T=0.9881 | G=0.0119 |
| 1000Genomes | Europe | Sub | 1006 | T=0.9563 | G=0.0437 |
| 1000Genomes | South Asian | Sub | 978 | T=0.907 | G=0.093 |
| 1000Genomes | American | Sub | 694 | T=0.980 | G=0.020 |
| Genetic variation in the Estonian population | Estonian | Study-wide | 4480 | T=0.9761 | G=0.0239 |
| The Avon Longitudinal Study of Parents and Children | PARENT AND CHILD COHORT | Study-wide | 3854 | T=0.9611 | G=0.0389 |
| UK 10K study - Twins | TWIN COHORT | Study-wide | 3708 | T=0.9676 | G=0.0324 |
| KOREAN population from KRGDB | KOREAN | Study-wide | 2922 | T=0.9983 | G=0.0017 |
| HGDP-CEPH-db Supplement 1 | Global | Study-wide | 2080 | T=0.9803 | G=0.0197 |
| HGDP-CEPH-db Supplement 1 | Est_Asia | Sub | 470 | T=0.989 | G=0.011 |
| HGDP-CEPH-db Supplement 1 | Central_South_Asia | Sub | 414 | T=0.978 | G=0.022 |
| HGDP-CEPH-db Supplement 1 | Middle_Est | Sub | 348 | T=0.983 | G=0.017 |
| HGDP-CEPH-db Supplement 1 | Europe | Sub | 320 | T=0.947 | G=0.053 |
| HGDP-CEPH-db Supplement 1 | Africa | Sub | 242 | T=0.983 | G=0.017 |
| HGDP-CEPH-db Supplement 1 | America | Sub | 216 | T=1.000 | G=0.000 |
| HGDP-CEPH-db Supplement 1 | Oceania | Sub | 70 | T=1.00 | G=0.00 |
| HapMap | Global | Study-wide | 1700 | T=0.9406 | G=0.0594 |
| HapMap | American | Sub | 770 | T=0.935 | G=0.065 |
| HapMap | African | Sub | 586 | T=0.923 | G=0.077 |
| HapMap | Europe | Sub | 176 | T=0.966 | G=0.034 |
| HapMap | Asian | Sub | 168 | T=1.000 | G=0.000 |
| Genome-wide autozygosity in Daghestan | Global | Study-wide | 1128 | T=0.9583 | G=0.0417 |
| Genome-wide autozygosity in Daghestan | Daghestan | Sub | 626 | T=0.958 | G=0.042 |
| Genome-wide autozygosity in Daghestan | Near_East | Sub | 144 | T=0.979 | G=0.021 |
| Genome-wide autozygosity in Daghestan | Central Asia | Sub | 120 | T=0.967 | G=0.033 |
| Genome-wide autozygosity in Daghestan | Europe | Sub | 106 | T=0.953 | G=0.047 |
| Genome-wide autozygosity in Daghestan | South Asian | Sub | 96 | T=0.91 | G=0.09 |
| Genome-wide autozygosity in Daghestan | Caucasus | Sub | 36 | T=1.00 | G=0.00 |
| Genome of the Netherlands Release 5 | Genome of the Netherlands | Study-wide | 998 | T=0.968 | G=0.032 |
| CNV burdens in cranial meningiomas | Global | Study-wide | 788 | T=0.981 | G=0.019 |
| CNV burdens in cranial meningiomas | CRM | Sub | 788 | T=0.981 | G=0.019 |
| Northern Sweden | ACPOP | Study-wide | 600 | T=0.992 | G=0.008 |
| A Vietnamese Genetic Variation Database | Global | Study-wide | 598 | T=0.987 | G=0.013 |
| Medical Genome Project healthy controls from Spanish population | Spanish controls | Study-wide | 534 | T=0.981 | G=0.019 |
| FINRISK | Finnish from FINRISK project | Study-wide | 304 | T=0.997 | G=0.003 |
| Qatari | Global | Study-wide | 216 | T=0.981 | G=0.019 |
| Ancient Sardinia genome-wide 1240k capture data generation and analysis | Global | Study-wide | 102 | T=0.980 | G=0.020 |
| SGDP_PRJ | Global | Study-wide | 20 | T=0.50 | G=0.50 |
| Siberian | Global | Study-wide | 2 | T=0.5 | G=0.5 |
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 6 | NC_000006.12:g.31464003T>G |
| GRCh37.p13 chr 6 | NC_000006.11:g.31431780T>G |
| GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 | NT_113891.3:g.2941328T>G |
| GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 | NT_113891.2:g.2941434T>G |
| GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 | NT_167249.2:g.2763252T>G |
| GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 | NT_167249.1:g.2762550T>G |
Gene: HCP5, HLA complex P5
(plus strand)
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| HCP5 transcript | NR_040662.1:n.733T>G | N/A | Non Coding 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.
Allele: G (allele ID:
29949
)
| ClinVar Accession | Disease Names | Clinical Significance |
|---|---|---|
| RCV000016042.3 | Abacavir hypersensitivity | Risk-Factor |
| RCV000016043.26 | Drug-induced liver injury due to flucloxacillin | Pathogenic |
| RCV003313923.3 | Autism spectrum disorder | Likely-Risk-Allele |
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= | G |
|---|---|---|
| GRCh38.p14 chr 6 | NC_000006.12:g.31464003= | NC_000006.12:g.31464003T>G |
| GRCh37.p13 chr 6 | NC_000006.11:g.31431780= | NC_000006.11:g.31431780T>G |
| GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 | NT_113891.3:g.2941328= | NT_113891.3:g.2941328T>G |
| GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 | NT_113891.2:g.2941434= | NT_113891.2:g.2941434T>G |
| GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 | NT_167249.2:g.2763252= | NT_167249.2:g.2763252T>G |
| GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 | NT_167249.1:g.2762550= | NT_167249.1:g.2762550T>G |
| HCP5 transcript | NM_006674.3:c.*568= | NM_006674.3:c.*568T>G |
| HCP5 transcript | NM_006674.2:c.335= | NM_006674.2:c.335T>G |
| HCP5 transcript | NR_040662.1:n.733= | NR_040662.1:n.733T>G |
| HCP5 transcript | NM_006674.1:c.421= | NM_006674.1:c.421T>G |
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#.
131 SubSNP,
27 Frequency,
3 ClinVar
submissions
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | TSC-CSHL | ss3357812 | Sep 28, 2001 (100) |
| 2 | TSC-CSHL | ss5320801 | Oct 10, 2002 (117) |
| 3 | KRIBB_YJKIM | ss65844405 | Nov 30, 2006 (127) |
| 4 | ILLUMINA | ss66557192 | Nov 30, 2006 (127) |
| 5 | ILLUMINA | ss67251545 | Nov 30, 2006 (127) |
| 6 | ILLUMINA | ss67649309 | Nov 30, 2006 (127) |
| 7 | PERLEGEN | ss68971560 | May 17, 2007 (127) |
| 8 | ILLUMINA | ss70729885 | May 25, 2008 (130) |
| 9 | ILLUMINA | ss71299225 | May 17, 2007 (127) |
| 10 | ILLUMINA | ss75006599 | Dec 06, 2007 (129) |
| 11 | ILLUMINA | ss79133249 | Dec 15, 2007 (130) |
| 12 | KRIBB_YJKIM | ss84045131 | Dec 15, 2007 (130) |
| 13 | ILLUMINA | ss122024861 | Dec 01, 2009 (131) |
| 14 | ILLUMINA | ss153909329 | Dec 01, 2009 (131) |
| 15 | ILLUMINA | ss159387181 | Dec 01, 2009 (131) |
| 16 | ILLUMINA | ss171238093 | Jul 04, 2010 (135) |
| 17 | ILLUMINA | ss173324651 | Jul 04, 2010 (135) |
| 18 | 1000GENOMES | ss233398423 | Jul 14, 2010 (136) |
| 19 | GMI | ss278726096 | May 04, 2012 (137) |
| 20 | NHLBI-ESP | ss342206514 | May 09, 2011 (136) |
| 21 | ILLUMINA | ss410922790 | Sep 17, 2011 (136) |
| 22 | ILLUMINA | ss479488851 | May 04, 2012 (137) |
| 23 | ILLUMINA | ss485227649 | May 04, 2012 (137) |
| 24 | EXOME_CHIP | ss491381778 | May 04, 2012 (137) |
| 25 | CLINSEQ_SNP | ss491885021 | May 04, 2012 (137) |
| 26 | ILLUMINA | ss533031097 | Sep 08, 2015 (146) |
| 27 | TISHKOFF | ss559113405 | Apr 25, 2013 (138) |
| 28 | SSMP | ss653034414 | Apr 25, 2013 (138) |
| 29 | ILLUMINA | ss779478188 | Sep 08, 2015 (146) |
| 30 | ILLUMINA | ss780683408 | Sep 08, 2015 (146) |
| 31 | ILLUMINA | ss780994048 | Sep 08, 2015 (146) |
| 32 | ILLUMINA | ss783356804 | Sep 08, 2015 (146) |
| 33 | ILLUMINA | ss825463767 | Apr 01, 2015 (144) |
| 34 | ILLUMINA | ss832898940 | Jul 13, 2019 (153) |
| 35 | ILLUMINA | ss834948177 | Sep 08, 2015 (146) |
| 36 | EVA-GONL | ss982764853 | Aug 21, 2014 (142) |
| 37 | JMKIDD_LAB | ss1067477106 | Aug 21, 2014 (142) |
| 38 | JMKIDD_LAB | ss1073505076 | Aug 21, 2014 (142) |
| 39 | 1000GENOMES | ss1319555611 | Aug 21, 2014 (142) |
| 40 | HAMMER_LAB | ss1397449754 | Sep 08, 2015 (146) |
| 41 | EVA_FINRISK | ss1584045171 | Apr 01, 2015 (144) |
| 42 | EVA_DECODE | ss1592308880 | Apr 01, 2015 (144) |
| 43 | EVA_UK10K_ALSPAC | ss1615275939 | Apr 01, 2015 (144) |
| 44 | EVA_UK10K_TWINSUK | ss1658269972 | Apr 01, 2015 (144) |
| 45 | EVA_EXAC | ss1688229396 | Apr 01, 2015 (144) |
| 46 | EVA_MGP | ss1711120929 | Apr 01, 2015 (144) |
| 47 | EVA_SVP | ss1712850830 | Apr 01, 2015 (144) |
| 48 | ILLUMINA | ss1752628383 | Sep 08, 2015 (146) |
| 49 | ILLUMINA | ss1917802355 | Feb 12, 2016 (147) |
| 50 | WEILL_CORNELL_DGM | ss1926017269 | Feb 12, 2016 (147) |
| 51 | ILLUMINA | ss1946173250 | Feb 12, 2016 (147) |
| 52 | ILLUMINA | ss1958887926 | Feb 12, 2016 (147) |
| 53 | ILLUMINA | ss2094824578 | Dec 20, 2016 (150) |
| 54 | ILLUMINA | ss2095177813 | Dec 20, 2016 (150) |
| 55 | USC_VALOUEV | ss2151807822 | Dec 20, 2016 (150) |
| 56 | HUMAN_LONGEVITY | ss2282941692 | Dec 20, 2016 (150) |
| 57 | ILLUMINA | ss2634429445 | Nov 08, 2017 (151) |
| 58 | ILLUMINA | ss2634429446 | Nov 08, 2017 (151) |
| 59 | ILLUMINA | ss2634429447 | Nov 08, 2017 (151) |
| 60 | GRF | ss2707401445 | Nov 08, 2017 (151) |
| 61 | GNOMAD | ss2735646584 | Nov 08, 2017 (151) |
| 62 | GNOMAD | ss2747581096 | Nov 08, 2017 (151) |
| 63 | GNOMAD | ss2837420187 | Nov 08, 2017 (151) |
| 64 | AFFY | ss2985361663 | Nov 08, 2017 (151) |
| 65 | AFFY | ss2985993860 | Nov 08, 2017 (151) |
| 66 | SWEGEN | ss2998794240 | Nov 08, 2017 (151) |
| 67 | ILLUMINA | ss3022599142 | Nov 08, 2017 (151) |
| 68 | ILLUMINA | ss3629502754 | Oct 12, 2018 (152) |
| 69 | ILLUMINA | ss3629502755 | Oct 12, 2018 (152) |
| 70 | ILLUMINA | ss3632348078 | Oct 12, 2018 (152) |
| 71 | ILLUMINA | ss3635056711 | Oct 12, 2018 (152) |
| 72 | ILLUMINA | ss3638619585 | Oct 12, 2018 (152) |
| 73 | ILLUMINA | ss3639311478 | Oct 12, 2018 (152) |
| 74 | ILLUMINA | ss3639681163 | Oct 12, 2018 (152) |
| 75 | ILLUMINA | ss3640764010 | Oct 12, 2018 (152) |
| 76 | ILLUMINA | ss3643560978 | Oct 12, 2018 (152) |
| 77 | ILLUMINA | ss3644906316 | Oct 12, 2018 (152) |
| 78 | OMUKHERJEE_ADBS | ss3646334654 | Oct 12, 2018 (152) |
| 79 | ILLUMINA | ss3653111643 | Oct 12, 2018 (152) |
| 80 | ILLUMINA | ss3653111644 | Oct 12, 2018 (152) |
| 81 | ILLUMINA | ss3654127986 | Oct 12, 2018 (152) |
| 82 | EGCUT_WGS | ss3666709354 | Jul 13, 2019 (153) |
| 83 | EVA_DECODE | ss3716906925 | Jul 13, 2019 (153) |
| 84 | ILLUMINA | ss3726329825 | Jul 13, 2019 (153) |
| 85 | ACPOP | ss3733360595 | Jul 13, 2019 (153) |
| 86 | ILLUMINA | ss3744549770 | Jul 13, 2019 (153) |
| 87 | ILLUMINA | ss3745356720 | Jul 13, 2019 (153) |
| 88 | EVA | ss3764821301 | Jul 13, 2019 (153) |
| 89 | ILLUMINA | ss3772850423 | Jul 13, 2019 (153) |
| 90 | KHV_HUMAN_GENOMES | ss3807976717 | Jul 13, 2019 (153) |
| 91 | EVA | ss3824169976 | Apr 26, 2020 (154) |
| 92 | EVA | ss3825694120 | Apr 26, 2020 (154) |
| 93 | HGDP | ss3847829179 | Apr 26, 2020 (154) |
| 94 | SGDP_PRJ | ss3864253193 | Apr 26, 2020 (154) |
| 95 | KRGDB | ss3911027898 | Apr 26, 2020 (154) |
| 96 | EVA | ss3984565602 | Apr 26, 2021 (155) |
| 97 | EVA | ss3985212966 | Apr 26, 2021 (155) |
| 98 | EVA | ss4017266152 | Apr 26, 2021 (155) |
| 99 | VINODS | ss4025188208 | Apr 26, 2021 (155) |
| 100 | VINODS | ss4025287179 | Apr 26, 2021 (155) |
| 101 | TOPMED | ss4698371586 | Apr 26, 2021 (155) |
| 102 | TOMMO_GENOMICS | ss6063284667 | Oct 31, 2024 (157) |
| 103 | EVA | ss6234902377 | Oct 31, 2024 (157) |
| 104 | EVA | ss6297856630 | Oct 31, 2024 (157) |
| 105 | EVA | ss6322269078 | Oct 31, 2024 (157) |
| 106 | YEGNASUBRAMANIAN_LAB | ss6339489986 | Oct 31, 2024 (157) |
| 107 | EVA | ss6349665218 | Oct 31, 2024 (157) |
| 108 | KOGIC | ss6369791961 | Oct 31, 2024 (157) |
| 109 | EVA | ss6404348858 | Oct 31, 2024 (157) |
| 110 | GNOMAD | ss6427139180 | Oct 31, 2024 (157) |
| 111 | GNOMAD | ss6710841975 | Oct 31, 2024 (157) |
| 112 | EVA | ss8237394528 | Oct 31, 2024 (157) |
| 113 | EVA | ss8237645688 | Oct 31, 2024 (157) |
| 114 | 1000G_HIGH_COVERAGE | ss8267934296 | Oct 31, 2024 (157) |
| 115 | EVA | ss8315141949 | Oct 31, 2024 (157) |
| 116 | EVA | ss8364719227 | Oct 31, 2024 (157) |
| 117 | HUGCELL_USP | ss8465668878 | Oct 31, 2024 (157) |
| 118 | EVA | ss8512473855 | Oct 31, 2024 (157) |
| 119 | 1000G_HIGH_COVERAGE | ss8553589766 | Oct 31, 2024 (157) |
| 120 | SANFORD_IMAGENETICS | ss8624623592 | Oct 31, 2024 (157) |
| 121 | SANFORD_IMAGENETICS | ss8640087897 | Oct 31, 2024 (157) |
| 122 | YY_MCH | ss8807306347 | Oct 31, 2024 (157) |
| 123 | EVA | ss8842025515 | Oct 31, 2024 (157) |
| 124 | EVA | ss8847290807 | Oct 31, 2024 (157) |
| 125 | EVA | ss8848651232 | Oct 31, 2024 (157) |
| 126 | EVA | ss8855283310 | Oct 31, 2024 (157) |
| 127 | EVA | ss8883241619 | Oct 31, 2024 (157) |
| 128 | EVA | ss8936530672 | Oct 31, 2024 (157) |
| 129 | EVA | ss8968589855 | Oct 31, 2024 (157) |
| 130 | EVA | ss8979779940 | Oct 31, 2024 (157) |
| 131 | EVA | ss8982525077 | Oct 31, 2024 (157) |
| 132 | 1000Genomes | NC_000006.11 - 31431780 | Oct 12, 2018 (152) |
| 133 | 1000Genomes_30X | NC_000006.12 - 31464003 | Oct 31, 2024 (157) |
| 134 | The Avon Longitudinal Study of Parents and Children | NC_000006.11 - 31431780 | Oct 12, 2018 (152) |
| 135 | Genome-wide autozygosity in Daghestan | NC_000006.10 - 31539759 | Apr 26, 2020 (154) |
| 136 | Genetic variation in the Estonian population | NC_000006.11 - 31431780 | Oct 12, 2018 (152) |
| 137 | ExAC | NC_000006.11 - 31431780 | Oct 12, 2018 (152) |
| 138 | FINRISK | NC_000006.11 - 31431780 | Apr 26, 2020 (154) |
| 139 | gnomAD v4 - Exomes | NC_000006.12 - 31464003 | Oct 31, 2024 (157) |
| 140 | gnomAD v4 - Genomes | NC_000006.12 - 31464003 | Oct 31, 2024 (157) |
| 141 | GO Exome Sequencing Project | NC_000006.11 - 31431780 | Oct 12, 2018 (152) |
| 142 | Genome of the Netherlands Release 5 | NC_000006.11 - 31431780 | Apr 26, 2020 (154) |
| 143 | HGDP-CEPH-db Supplement 1 | NC_000006.10 - 31539759 | Apr 26, 2020 (154) |
| 144 | HapMap | NC_000006.12 - 31464003 | Apr 26, 2020 (154) |
| 145 | KOREAN population from KRGDB | NC_000006.11 - 31431780 | Apr 26, 2020 (154) |
| 146 | Korean Genome Project 4K | NC_000006.12 - 31464003 | Oct 31, 2024 (157) |
| 147 | Medical Genome Project healthy controls from Spanish population | NC_000006.11 - 31431780 | Apr 26, 2020 (154) |
| 148 | Northern Sweden | NC_000006.11 - 31431780 | Jul 13, 2019 (153) |
| 149 | Ancient Sardinia genome-wide 1240k capture data generation and analysis | NC_000006.11 - 31431780 | Apr 26, 2021 (155) |
| 150 | CNV burdens in cranial meningiomas | NC_000006.11 - 31431780 | Apr 26, 2021 (155) |
| 151 | Qatari | NC_000006.11 - 31431780 | Apr 26, 2020 (154) |
| 152 | SGDP_PRJ | NC_000006.11 - 31431780 | Apr 26, 2020 (154) |
| 153 | Siberian | NC_000006.11 - 31431780 | Apr 26, 2020 (154) |
| 154 | 38KJPN | NC_000006.12 - 31464003 | Oct 31, 2024 (157) |
| 155 | TopMed | NC_000006.12 - 31464003 | Apr 26, 2021 (155) |
| 156 | UK 10K study - Twins | NC_000006.11 - 31431780 | Oct 12, 2018 (152) |
| 157 | A Vietnamese Genetic Variation Database | NC_000006.11 - 31431780 | Jul 13, 2019 (153) |
| 158 | ALFA | NC_000006.12 - 31464003 | Oct 31, 2024 (157) |
| 159 | ClinVar | RCV000016042.3 | Oct 13, 2022 (156) |
| 160 | ClinVar | RCV000016043.26 | Oct 13, 2022 (156) |
| 161 | ClinVar | RCV003313923.3 | Oct 31, 2024 (157) |
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) |
|---|---|
| rs3997925 | Aug 27, 2003 (117) |
| rs60378661 | May 25, 2008 (130) |
| rs111645003 | Sep 17, 2011 (135) |
| rs114783691 | Mar 28, 2012 (136) |
Added to this RefSNP Cluster:
| Submission IDs | Observation SPDI | Canonical SPDI | Source RSIDs |
|---|---|---|---|
| ss3639311478, ss3639681163 | NC_000006.9:31539758:T:G | NC_000006.12:31464002:T:G | (self) |
| 424406, 507071, ss278726096, ss485227649, ss491885021, ss825463767, ss1397449754, ss1592308880, ss1712850830, ss3643560978, ss3847829179 | NC_000006.10:31539758:T:G | NC_000006.12:31464002:T:G | (self) |
| 31322905, 17465250, 12447602, 8254602, 41632, 628019, 7763703, 18205292, 236689, 6645460, 438893, 115005, 8059199, 16270173, 4324176, 17465250, 3872963, ss233398423, ss342206514, ss479488851, ss491381778, ss533031097, ss559113405, ss653034414, ss779478188, ss780683408, ss780994048, ss783356804, ss832898940, ss834948177, ss982764853, ss1067477106, ss1073505076, ss1319555611, ss1584045171, ss1615275939, ss1658269972, ss1688229396, ss1711120929, ss1752628383, ss1917802355, ss1926017269, ss1946173250, ss1958887926, ss2094824578, ss2095177813, ss2151807822, ss2634429445, ss2634429446, ss2634429447, ss2707401445, ss2735646584, ss2747581096, ss2837420187, ss2985361663, ss2985993860, ss2998794240, ss3022599142, ss3629502754, ss3629502755, ss3632348078, ss3635056711, ss3638619585, ss3640764010, ss3644906316, ss3646334654, ss3653111643, ss3653111644, ss3654127986, ss3666709354, ss3733360595, ss3744549770, ss3745356720, ss3764821301, ss3772850423, ss3824169976, ss3825694120, ss3864253193, ss3911027898, ss3984565602, ss3985212966, ss4017266152, ss6234902377, ss6297856630, ss6322269078, ss6339489986, ss6349665218, ss8237394528, ss8315141949, ss8364719227, ss8512473855, ss8624623592, ss8640087897, ss8842025515, ss8847290807, ss8848651232, ss8936530672, ss8968589855, ss8979779940, ss8982525077 | NC_000006.11:31431779:T:G | NC_000006.12:31464002:T:G | (self) |
| RCV000016042.3, RCV000016043.26, RCV003313923.3, 41115701, 22450733, 237620069, 3099751, 19643859, 80660487, 535749144, 3644264163, ss2282941692, ss3716906925, ss3726329825, ss3807976717, ss4698371586, ss6063284667, ss6369791961, ss6404348858, ss6427139180, ss6710841975, ss8237645688, ss8267934296, ss8465668878, ss8553589766, ss8807306347, ss8855283310, ss8883241619 | NC_000006.12:31464002:T:G | NC_000006.12:31464002:T:G | (self) |
| ss3357812, ss5320801, ss65844405, ss66557192, ss67251545, ss67649309, ss68971560, ss70729885, ss71299225, ss75006599, ss79133249, ss84045131, ss122024861, ss153909329, ss159387181, ss171238093, ss173324651, ss410922790 | NT_007592.15:31371779:T:G | NC_000006.12:31464002:T:G | (self) |
| ss4025188208 | NT_113891.3:2941327:T:G | NC_000006.12:31464002:T:G | (self) |
| ss4025287179 | NT_167249.2:2763251:T:G | NC_000006.12:31464002: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.
72
citations for rs2395029
| PMID | Title | Author | Year | Journal |
|---|---|---|---|---|
| 17641165 | A whole-genome association study of major determinants for host control of HIV-1. | Fellay J et al. | 2007 | Science (New York, N.Y.) |
| 18256235 | WGAViewer: software for genomic annotation of whole genome association studies. | Ge D et al. | 2008 | Genome research |
| 18369459 | A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. | Liu Y et al. | 2008 | PLoS genetics |
| 18684101 | The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir. | Colombo S et al. | 2008 | The Journal of infectious diseases |
| 18982067 | HIV-1 disease-influencing effects associated with ZNRD1, HCP5 and HLA-C alleles are attributable mainly to either HLA-A10 or HLA-B*57 alleles. | Catano G et al. | 2008 | PloS one |
| 19050382 | Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection. | van Manen D et al. | 2009 | AIDS (London, England) |
| 19107206 | Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. | Dalmasso C et al. | 2008 | PloS one |
| 19115949 | Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). | Limou S et al. | 2009 | The Journal of infectious diseases |
| 19182814 | New insights into the pathogenesis and genetics of psoriatic arthritis. | Nograles KE et al. | 2009 | Nature clinical practice. Rheumatology |
| 19276793 | Host genetics and HIV-1 viral load set-point in African-Americans. | Shrestha S et al. | 2009 | AIDS (London, England) |
| 19474294 | Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. | Hindorff LA et al. | 2009 | Proceedings of the National Academy of Sciences of the United States of America |
| 19483685 | HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. | Daly AK et al. | 2009 | Nature genetics |
| 19679225 | X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women. | Siddiqui RA et al. | 2009 | American journal of human genetics |
| 19693088 | The HLA-B/-C haplotype block contains major determinants for host control of HIV. | Trachtenberg E et al. | 2009 | Genes and immunity |
| 19935381 | A polymorphism in the HCP5 gene associated with HLA-B*5701 does not restrict HIV-1 in vitro. | Yoon W et al. | 2010 | AIDS (London, England) |
| 20041166 | Common genetic variation and the control of HIV-1 in humans. | Fellay J et al. | 2009 | PLoS genetics |
| 20149939 | Host genes associated with HIV/AIDS: advances in gene discovery. | An P et al. | 2010 | Trends in genetics |
| 20205591 | Host determinants of HIV-1 control in African Americans. | Pelak K et al. | 2010 | The Journal of infectious diseases |
| 20394749 | Risk factors for idiosyncratic drug-induced liver injury. | Chalasani N et al. | 2010 | Gastroenterology |
| 20487506 | A whole genome association study of mother-to-child transmission of HIV in Malawi. | Joubert BR et al. | 2010 | Genome medicine |
| 20534626 | Use of the HCP5 single nucleotide polymorphism to predict hypersensitivity reactions to abacavir: correlation with HLA-B*5701. | Rodríguez-Nóvoa S et al. | 2010 | The Journal of antimicrobial chemotherapy |
| 20552027 | Host and viral genetic correlates of clinical definitions of HIV-1 disease progression. | Casado C et al. | 2010 | PloS one |
| 20704485 | Multiple-cohort genetic association study reveals CXCR6 as a new chemokine receptor involved in long-term nonprogression to AIDS. | Limou S et al. | 2010 | The Journal of infectious diseases |
| 20876667 | Genome-wide significant associations for variants with minor allele frequency of 5% or less--an overview: A HuGE review. | Panagiotou OA et al. | 2010 | American journal of epidemiology |
| 20976252 | Host genetics and HIV-1: the final phase? | Fellay J et al. | 2010 | PLoS pathogens |
| 21051598 | The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. | Pereyra F et al. | 2010 | Science (New York, N.Y.) |
| 21107268 | Screening low-frequency SNPS from genome-wide association study reveals a new risk allele for progression to AIDS. | Le Clerc S et al. | 2011 | Journal of acquired immune deficiency syndromes (1999) |
| 21221856 | The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery. | Aouizerat BE et al. | 2011 | Current HIV/AIDS reports |
| 21253569 | Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? | Casto AM et al. | 2011 | PLoS genetics |
| 21296743 | Exploring the potential relevance of human-specific genes to complex disease. | Cooper DN et al. | 2011 | Human genomics |
| 21502085 | Genome-wide association study implicates PARD3B-based AIDS restriction. | Troyer JL et al. | 2011 | The Journal of infectious diseases |
| 21514285 | Rapid HCP5 single-nucleotide polymorphism genotyping: a simple allele-specific PCR method for prediction of hypersensitivity reaction to Abacavir. | Galván CA et al. | 2011 | Clinica chimica acta; international journal of clinical chemistry |
| 21689440 | Natural selection among Eurasians at genomic regions associated with HIV-1 control. | Klimentidis YC et al. | 2011 | BMC evolutionary biology |
| 21811574 | Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course. | van Manen D et al. | 2011 | PloS one |
| 21854194 | Distribution of polymorphisms in cytochrome P450 2B6, histocompatibility complex P5, chemokine coreceptor 5, and interleukin 28B genes in inhabitants from the central area of Argentina. | Galván CA et al. | 2012 | Genetic testing and molecular biomarkers |
| 21860345 | Rising HIV-1 viral load set point at a population level coincides with a fading impact of host genetic factors on HIV-1 control. | van Manen D et al. | 2011 | AIDS (London, England) |
| 22128242 | The role of toll-like receptor variants in acute anterior uveitis. | Pratap DS et al. | 2011 | Molecular vision |
| 22310811 | Genetic correlates influencing immunopathogenesis of HIV infection. | Sharma G et al. | 2011 | The Indian journal of medical research |
| 22362864 | Multicohort genomewide association study reveals a new signal of protection against HIV-1 acquisition. | Limou S et al. | 2012 | The Journal of infectious diseases |
| 22384103 | Low-replicating viruses and strong anti-viral immune response associated with prolonged disease control in a superinfected HIV-1 LTNP elite controller. | Pernas M et al. | 2012 | PloS one |
| 22437317 | Protective effect of human endogenous retrovirus K dUTPase variants on psoriasis susceptibility. | Lai OY et al. | 2012 | The Journal of investigative dermatology |
| 22474614 | Host genes important to HIV replication and evolution. | Telenti A et al. | 2012 | Cold Spring Harbor perspectives in medicine |
| 22577363 | Psoriasis patients are enriched for genetic variants that protect against HIV-1 disease. | Chen H et al. | 2012 | PLoS genetics |
| 22920050 | Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics. | van Manen D et al. | 2012 | Retrovirology |
| 22934000 | Current State and Future Prospects of Direct-to-Consumer Pharmacogenetics. | Chua EW et al. | 2012 | Frontiers in pharmacology |
| 22938532 | Sequencing and analysis of a South Asian-Indian personal genome. | Gupta R et al. | 2012 | BMC genomics |
| 23300409 | Chapter 7: Pharmacogenomics. | Karczewski KJ et al. | 2012 | PLoS computational biology |
| 23403273 | Novel genetic association of TNF-α-238 and PDCD1-7209 polymorphisms with long-term non-progressive HIV-1 infection. | Nasi M et al. | 2013 | International journal of infectious diseases |
| 23772624 | Immunogenetics of HIV disease. | Martin MP et al. | 2013 | Immunological reviews |
| 24270849 | Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. | Denny JC et al. | 2013 | Nature biotechnology |
| 24842830 | Regulatory variation in HIV-1 dependency factor ZNRD1 associates with host resistance to HIV-1 acquisition. | An P et al. | 2014 | The Journal of infectious diseases |
| 24861233 | Development of multiplex pyrosequencing for HLA-B*57:01 screening using single nucleotide polymorphism haplotype. | Sankuntaw N et al. | 2014 | Journal of clinical pharmacy and therapeutics |
| 24939907 | Evidence after imputation for a role of MICA variants in nonprogression and elite control of HIV type 1 infection. | Le Clerc S et al. | 2014 | The Journal of infectious diseases |
| 24944790 | Screening for 392 polymorphisms in 141 pharmacogenes. | Kim JY et al. | 2014 | Biomedical reports |
| 24971308 | Genetic variations of cytokines and cytokine receptors in psoriasis patients from china. | Li XL et al. | 2014 | International journal of genomics |
| 25264125 | Investigating the genetic association of HCP5, SPATA2, TNIP1, TNFAIP3 and COG6 with psoriasis in Chinese population. | Li XL et al. | 2014 | International journal of immunogenetics |
| 25369137 | A multilocus genetic study in a cohort of Italian SLE patients confirms the association with STAT4 gene and describes a new association with HCP5 gene. | Ciccacci C et al. | 2014 | PloS one |
| 26083016 | Accuracy of SNPs to predict risk of HLA alleles associated with drug-induced hypersensitivity events across racial groups. | He Y et al. | 2015 | Pharmacogenomics |
| 26100217 | [Prevalence study of the genetic markers associated with slow progression of human inmunodefiency virus type 1 in the Galician population (Northwest of Spain)]. | Rodríguez-Da Silva A et al. | 2017 | Enfermedades infecciosas y microbiologia clinica |
| 26369774 | Impact of New Genomic Technologies on Understanding Adverse Drug Reactions. | Maggo SD et al. | 2016 | Clinical pharmacokinetics |
| 26613086 | Polymorphisms Associated with Age at Onset in Patients with Moderate-to-Severe Plaque Psoriasis. | Prieto-Pérez R et al. | 2015 | Journal of immunology research |
| 27083073 | Impact of polymorphisms in the HCP5 and HLA-C, and ZNRD1 genes on HIV viral load. | Thørner LW et al. | 2016 | Infection, genetics and evolution |
| 27546346 | Validation of two commercial real-time PCR assays for rapid screening of the HLA-B*57:01 allele in the HIV clinical laboratory. | Avidor B et al. | 2016 | Journal of virological methods |
| 28449694 | The MHC locus and genetic susceptibility to autoimmune and infectious diseases. | Matzaraki V et al. | 2017 | Genome biology |
| 31137555 | Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. | Kulski JK et al. | 2019 | Cells |
| 31148855 | Evaluation of HCP5 and Chemokine C Receptor type 5 Gene Polymorphisms in Indian Psoriatic Patients. | Rajesh D et al. | 2019 | Indian journal of dermatology |
| 31393887 | Novel association of five HLA alleles with HIV-1 progression in Spanish long-term non progressor patients. | Ramírez de Arellano E et al. | 2019 | PloS one |
| 31421661 | The utility of surrogate markers in predicting HLA alleles associated with adverse drug reactions in Vietnamese. | Nguyen DV et al. | 2022 | Asian Pacific journal of allergy and immunology |
| 33044391 | HCP5 rs2395029 is a rapid and inexpensive alternative to HLA-B*57:01 genotyping to predict abacavir hypersensitivity reaction in Spain. | Zubiaur P et al. | 2021 | Pharmacogenetics and genomics |
| 36164570 | Prevalence of exposure to pharmacogenetic drugs by the Saudis treated at the health care centers of the Ministry of National Guard. | Alshabeeb MA et al. | 2022 | Saudi pharmaceutical journal |
| 37372997 | Genetic Influence on Treatment Response in Psoriasis: New Insights into Personalized Medicine. | Berna-Rico E et al. | 2023 | International journal of molecular sciences |
| 37614503 | The genetic variant rs55986091 HLA-DQB1 is associated with a protective effect against cervical cancer. | Vinokurov MA et al. | 2023 | Frontiers in oncology |
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
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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.
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.