PMID: 20876667

Genome-wide significant associations for variants with minor allele frequency of 5% or less--an overview: A HuGE review.

American journal of epidemiology
OA Panagiotou, E Evangelou, JP Ioannidis
2010-10-15

82 variants were identified in this publication


Variant ID Gene cDNA Protein Consequence Exon Intron
9-107560785-G-A ABCA1 c.5038C>T p.Arg1680Trp Missense 37/50 -
15-28263548-G-A OCA2 c.802C>T p.Gln268* Nonsense 7/24 -
15-28171315-C-G OCA2 c.2037G>C p.Trp679Cys Missense 19/24 -
16-89986141-C-A MC1R c.475C>A p.Pro159Thr Missense 1/1 -
16-50739582-C-G NOD2 c.541-2184C>G - IntronicSNV - 2/11
20-43030106-C-T HNF4A c.94C>T p.Gln32* Nonsense 1/10 -
16-89986117-C-A MC1R c.451C>A p.Arg151Ser Missense 1/1 -
11-116661530-G-A APOA5 c.415C>T p.Gln139* Nonsense 4/4 -
10-17388143-C-T ST8SIA6 c.377+13370G>A - IntronicSNV - 4/7
16-89986117-C-G MC1R c.451C>G p.Arg151Gly Missense 1/1 -
11-116774201-G-A SIK3 c.617-6168C>T - intron_variant - 4/23
11-116619073-C-G BUD13 c.*125G>C - 3-UTRSNV 10/10 -
1-201262432-C-G PKP1 c.203-638C>G - IntronicSNV - 1/14
11-116619073-C-T BUD13 c.*125G>A - 3-UTRSNV 10/10 -
9-107658385-G-A ABCA1 c.67-6909C>T - IntronicSNV - 2/49
15-28234747-C-T OCA2 c.1182G>A p.Met394Ile Missense 11/24 -
10-114796048-A-G TCF7L2 c.382-3736A>G - IntronicSNV - 3/13
5-33944889-G-A SLC45A2 c.1457C>T p.Ala486Val Missense 7/7 -
11-116732512-G-T SIK3 c.2171+45C>A - intron_variant - 17/23
11-116621963-T-G BUD13 c.1767-2672A>C - IntronicSNV - 9/9
10-114915214-G-T TCF7L2 c.1201-2566G>T - IntronicSNV - 10/13
9-107664301-C-T ABCA1 c.66+1594G>A - IntronicSNV - 2/49
10-114913559-A-T TCF7L2 c.1200+1360A>T - IntronicSNV - 10/13
16-50756540-G-T NOD2 c.2722G>T p.Gly908Cys Missense 8/12 -
10-114914913-T-G TCF7L2 c.1200+2714T>G - IntronicSNV - 10/13
6-138195723-C-G TNFAIP3 c.296-259C>G - IntronicSNV - 2/8
9-107647655-G-A ABCA1 c.161-806C>T - IntronicSNV - 3/49
11-116655600-G-A ZPR1 c.791C>T p.Ala264Val Missense 8/14 -
11-116655600-G-C ZPR1 c.791C>G p.Ala264Gly Missense 8/14 -
1-55529215-C-A PCSK9 c.2037C>A p.Cys679* Nonsense 12/12 -
15-28530182-C-A HERC2 c.323-4749G>T - IntronicSNV - 4/92
15-28530182-C-T HERC2 c.323-4749G>A - IntronicSNV - 4/92
3-37522828-G-A ITGA9 c.421-147G>A - IntronicSNV - 3/27
16-50756881-A-G NOD2 c.2798+265A>G - IntronicSNV - 8/11
16-89986136-C-T MC1R c.470C>T p.Thr157Ile Missense 1/1 -
11-116652207-C-T ZPR1 c.1179+667G>A - IntronicSNV - 12/13
6-138196066-T-C TNFAIP3 c.380T>C p.Phe127Ser Missense 3/9 -
11-116943354-A-C SIK3 c.273+25505T>G - intron_variant - 1/23
16-50756774-C-G NOD2 c.2798+158C>G - IntronicSNV - 8/11
11-117531731-C-T DSCAML1 c.511+115775G>A - intron_variant - 3/32
10-114732882-T-C TCF7L2 c.381+21516T>C - IntronicSNV - 3/13
16-50756774-C-T NOD2 c.2798+158C>T - IntronicSNV - 8/11
16-89986133-T-A MC1R c.467T>A p.Val156Glu Missense 1/1 -
9-107620835-G-A ABCA1 c.688C>T p.Arg230Cys Missense 7/50 -
20-43042364-C-T HNF4A c.416C>T p.Thr139Ile Missense 4/10 -
6-26093144-A-C HFE c.848A>C p.Gln283Pro Missense 4/6 -
1-201262432-C-T PKP1 c.203-638C>T - IntronicSNV - 1/14
11-116752219-A-G SIK3 c.866-4461T>C - intron_variant - 6/23
11-116652423-G-A ZPR1 c.1179+451C>T - IntronicSNV - 12/13
11-116652423-G-T ZPR1 c.1179+451C>A - IntronicSNV - 12/13
15-28228529-T-C OCA2 c.1465A>G p.Asn489Asp Missense 14/24 -
9-107647655-G-T ABCA1 c.161-806C>A - IntronicSNV - 3/49
1-55512222-C-G PCSK9 c.426C>G p.Tyr142* Nonsense 3/12 -
9-107657070-G-A ABCA1 c.67-5594C>T - IntronicSNV - 2/49
11-116752219-A-T SIK3 c.866-4461T>A - intron_variant - 6/23
11-116652423-G-C ZPR1 c.1179+451C>G - IntronicSNV - 12/13
12-117002658-G-A MAP1LC3B2 c.-102+5420G>A - intron_variant - 1/1
16-50745199-C-T NOD2 c.1377C>T p.Arg459Arg Synonymous 4/12 -
16-50745199-C-A NOD2 c.1377C>A p.Arg459Arg Synonymous 4/12 -
3-37518545-T-A ITGA9 c.420+3594T>A - IntronicSNV - 3/27
9-107647220-C-T ABCA1 c.161-371G>A - IntronicSNV - 3/49
11-116856642-T-C SIK3 c.274-28862A>G - intron_variant - 1/23
5-33982434-C-T SLC45A2 c.469G>A p.Asp157Asn Missense 2/7 -
15-28259965-G-A OCA2 c.1001C>T p.Ala334Val Missense 9/24 -
1-55505647-G-A PCSK9 c.137G>A p.Arg46His Missense 1/12 -
9-107648652-C-T ABCA1 c.161-1803G>A - IntronicSNV - 3/49
6-26093443-G-T HFE c.989G>T p.Arg330Met Missense 5/6 -
15-28116316-G-A OCA2 c.2228C>T p.Pro743Leu Missense 21/24 -
9-107639414-G-A ABCA1 c.421+5906C>T - IntronicSNV - 5/49
15-28483811-C-T HERC2 c.3685G>A p.Asp1229Asn Missense 24/93 -
10-114756041-A-T TCF7L2 c.382-43743A>T - IntronicSNV - 3/13
11-116662407-G-A APOA5 c.56C>T p.Ser19Leu Missense 3/4 -
15-28234747-C-A OCA2 c.1182G>T p.Met394Ile Missense 11/24 -
15-28344238-A-G OCA2 c.-22+132T>C - intron_variant - 1/23
13-43180696-T-A TNFSF11 c.596T>A p.Met199Lys Missense 5/5 -
13-42875512-C-T AKAP11 c.2630C>T p.Ala877Val Missense 8/13 -
5-33955673-T-C SLC45A2 c.889-1064A>G - IntronicSNV - 3/6
9-107593379-G-C ABCA1 c.1719C>G p.Tyr573* Nonsense 14/50 -
6-138196066-T-G TNFAIP3 c.380T>G p.Phe127Cys Missense 3/9 -
10-114756041-A-G TCF7L2 c.382-43743A>G - IntronicSNV - 3/13
9-107593379-G-T ABCA1 c.1719C>A p.Tyr573* Nonsense 14/50 -
15-28234747-C-G OCA2 c.1182G>C p.Met394Ile Missense 11/24 -