Which Databases Carry Named Gene Variants Like Apoe4

Question

[Jeremy Leipzig]

Where can I download raw databases that can tell me which SNPs comprise a "named allele" or "named variant" like ApoE4?

[Rm]

@Jeremy Leipzig: do you have any update on this ; I am similarly looking for a tool to map named variants (for example: UGT1A128 , DPYD3 ) to variant coordinates or rsid?.

Biobase PGMD supports the same but need subscription I believe.

Answer 1

[Larry_Parnell]

I've commented on this longstanding issue before. It is indeed a real problem to determine the SNP identifier for some RFLP band or "SNP 3" in an older paper into something unique and searchable. Some sources to consider include OMIM (under the genetic variants heading), specialized gene family databases (eg, CYP or P450 genes (important in drug development/toxicity) and mitochondrial genomics) as well as a data table I published on SNPs involved in cardiovascular and metabolic diseases. What one would look for is the link between common SNP name and unique identifier.

An added problem arises with your APOE example. E4 is not a SNP per se, but a haplotype of two SNPs. In short, my experience has been to take the painstaking approach to look through the literature to recreate electronically the PCR, restriction enzyme digests and other SNP detection methods to unequivocally identify the common name to rs identifier link, but my goal was quite focused. If you're trying to do this for all commonly studied variants in the days before dbSNP was widely accepted, it will be a lot of work.

Answer 2

[JC]

you can use SNPedia: http://snpedia.com/index.php/ApoE4

[Jeremy Leipzig]

how do i query this programmatically?

Answer 3

[Jeremy Leipzig]

I see there are some downloadable resources at http://www.hugenavigator.net

A lot of these look rather apocryphal and don't tell me what sequences actually indicate ApoE4, although I suppose once you have the rs ids and gene location you can determine that.

A grep of 'APOE':

Common Name      Rs Number   Gene Symbol     Source URL      Source
    -491    rs449647    APOE    10213175,11343837,9811931,18317248,12095653,12167762,9425904,10961667,10563653,15106838,10454160,12782964,16608402,10525981,11099722,16176061,9700208,12105308,15245790,10208564,12232782,10462111,18057979,15455263,12951193,16314757,11378846,9875528,121161alzgene
    -427    rs769446    APOE    9811931,10961667,16608402,9700208,18057979,15455263,12951193,16314757,11378846,15364690,11113217,12962909,10980578  alzgene
    113 rs440446    APOE    10961667,9467014,8710077,15455263,10505604,12962909 alzgene
    Th1/E47cs   rs405509    APOE    18317248,12095653,12167762,16399900,10961667,15106838,11418222,17317784,11095526,9467014,9700208,12105308,15245790,15455263,16013913,12951193,10505604,15364690,12480755,11113217,11173875,12962909,11315514,10980578   alzgene
    E2/E3/E4    rs429358    APOE    12707932,16567081,18060780  hn
    E2/E3/E4    rs7412  APOE    12707932,16567081,18060780  hn
    Th1/E47cs   rs405509    APOE    17052657,10319883   pdgene
    -491    rs449647    APOE    10624815    pdgene
    Arg158Cys   rs7412  APOE    SI001124I   alfred
    Cys112Arg   rs429358    APOE    SI001123H   alfred
    SNP92-APOE  rs429358    APOE    SI000455O   alfred
    SNP93-APOE  rs405509    APOE    SI000456P   alfred
    491A/T  rs449647    APOE    13129656,9832216    szgene
    IVS2+78G>A  rs769449    APOE    NULL    snp500
    IVS2+520G>A rs769450    APOE    NULL    snp500
    IVS1+69C>G  rs440446    APOE    NULL    snp500
    IVS1+185C>A rs877973    APOE    NULL    snp500
    IVS1+15C>T  rs9282609   APOE    NULL    snp500
    Ex4+290C>T  rs7412  APOE    NULL    snp500
    Ex4+152T>C  rs429358    APOE    NULL    snp500
    -1045T>G    rs405509    APOE    NULL    snp500
    3937T>C; p.Cys112Arg; (g.7903T>C; c.388T>C; p.Cys130Arg in dbSNP build 130) rs429358    APOE    NULL    pharm
    4075C>T; p.Arg158Cys; (g.8041C>T; c.526C>T; p.Arg176Cys in dbSNP build 130) rs7412  APOE    NULL    pharm
    Arg158Cys (g.8041C>T; c.526C>T; p.Arg176Cys in dbSNP build 130) rs7412  APOE    NULL    pharm
    Arg158Cys (g.8041C>T; c.526C>T; p.Arg176Cys in dbSNP build 130) rs7412  APOE    NULL    pharm
    Arg158Cys (g.8041C>T; c.526C>T; p.Arg176Cys in dbSNP build 130) rs7412  APOE    NULL    pharm
    Arg158Cys (g.8041C>T; c.526C>T; p.Arg176Cys in dbSNP build 130) rs7412  APOE    NULL    pharm
    Arg158Cys; 2198C>T; ApoE epsilon 2  rs7412  APOE    NULL    pharm
    Cys112Arg (g.7903T>C; c.388T>C; p.Cys130Arg in dbSNP build 130) rs429358    APOE    NULL    pharm
    Cys112Arg (g.7903T>C; c.388T>C; p.Cys130Arg in dbSNP build 130) rs429358    APOE    NULL    pharm
    Cys112Arg (g.7903T>C; c.388T>C; p.Cys130Arg in dbSNP build 130) rs429358    APOE    NULL    pharm
    Cys112Arg (g.7903T>C; c.388T>C; p.Cys130Arg in dbSNP build 130) rs429358    APOE    NULL    pharm
    epsilon3; defined as rs429358 T 130Cys + rs7412 C 176Arg    rs7412  APOE    NULL    pharm
    epsilon3; defined as rs429358 T 130Cys + rs7412 C 176Arg    rs429358    APOE    NULL    pharm
    -219G-->T   rs405509    APOE    NULL    pharm
    Cys112Arg; 2060T>C; ApoE epsilon 4  rs429358    APOE    NULL    pharm
    IVS1+69     rs440446    APOE    <http://www.snpedia.com/index.php/rs440446> snpedia