{{Rsnum
|rsid=1800961
|Gene=HNF4A
|Chromosome=20
|position=44413724
|Orientation=plus
|ReferenceAllele=C
|MissenseAllele=T
|GMAF=0.02112
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(C;C)
|geno2=(C;T)
|geno3=(T;T)
|Gene_s=HNF4A
}}{{ population diversity
| geno1=(C;C)
| geno2=(C;T)
| geno3=(T;T)
| CEU | 92.9 | 7.1 | 0.0
| HCB | 96.4 | 3.6 | 0.0
| JPT | 99.1 | 0.9 | 0.0
| YRI | 100.0 | 0.0 | 0.0
| ASW | 0.0 | 0.0 | 0.0
| CHB | 96.4 | 3.6 | 0.0
| CHD | 95.4 | 4.6 | 0.0
| GIH | 95.0 | 5.0 | 0.0
| LWK | 0.0 | 0.0 | 0.0
| MEX | 98.3 | 1.7 | 0.0
| MKK | 0.0 | 0.0 | 0.0
| TSI | 97.1 | 2.9 | 0.0
| HapMapRevision=28
}}per the [http://blog.23andme.com/2008/12/08/new-papers-from-nature-genetics-yield-a-bounty-of-cholesterol-snps/ 23andMe blog], the minor allele of this SNP (T) was associated with decreased HDL [[cholesterol]]
 
{| border="1"
|-
!SNP
!Rarer allele
!LDL
!HDL
!TG
|-
| [[rs6544713]] || T || + || ||
|-
| [[rs2650000]] || A || + || ||
|-
| [[rs471364]] || C || || - ||
|-
| [[rs1800961]] || T || || - ||
|-
| [[rs7679]] || C || || - || +
|-
| [[rs2967605]] || T || || - ||
|-
| [[rs2409722]] || T || || || -
|-
| [[rs10903129]] || A || - || - || -
|-
| [[rs6756629]] || A || - || + || -
|-
| [[rs12670798]] || C || + || + || +
|-
| [[rs7395662]] || A || - || + || +
|-
| [[rs174570]] || T || - || - || +
|-
| [[rs2271293]] || A || - || + || -
|-
| [[rs2624265]] || C || || || +
|-
| [[rs2167079]] || T || || + ||
|-
| [[rs9891572]] || T || || + ||
|-
| [[rs4844614]] || T || + || ||
|-
| [[rs5031002]] || G || + || ||
|-
|}

{{PMID Auto GWAS
|PMID=19060906
|Trait=HDL cholesterol
|Title=Common variants at 30 loci contribute to polygenic dyslipidemia
|RiskAllele=T
|Pval=8E-10
|OR=0.19
|ORtxt=[0.09-0.29] SD decrease
|OA=1
}}

{{PMID Auto
|PMID=19748811
|Title=Influence of hepatocyte nuclear factor 4alpha (HNF4alpha) gene variants on the risk of type 2 diabetes: A meta-analysis in 49,577 individuals
}}

{{PharmGKB
|RSID=rs1800961
|Name_s=
|Gene_s=HNF4A
|Feature=
|Evidence=PubMed ID:19060906; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 20q13.2; Reported Gene(s): HNF4A; Risk Allele: rs1800961-T); (p-value= 0.0000000008).This variant is associated with HDL cholesterol.
|Drugs=
|Drug Classes=
|Diseases=
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA164740235
}}

{{PMID Auto GWAS
|PMID=21300955
|Trait=None
|Title=Meta-Analysis of Genome-Wide Association Studies in >80 000 Subjects Identifies Multiple Loci for C-Reactive Protein Levels
|RiskAllele=C
|Pval=2E-9
|OR=0.0880
|ORtxt=[0.06-0.12] unit increase
|OA=1
}}

{{PMID Auto GWAS
|PMID=20686565
|Trait=None
|Title=Biological, clinical and population relevance of 95 loci for blood lipids.
|RiskAllele=T
|Pval=1E-15
|OR=1.8800
|ORtxt=None
|OA=1
}}

{{PMID Auto
|PMID=16186411
|Title=Variants in hepatocyte nuclear factor 4alpha are modestly associated with type 2 diabetes in Pima Indians.
|OA=1
}}

{{PMID Auto
|PMID=18660489
|Title=Multiple genetic variants along candidate pathways influence plasma high-density lipoprotein cholesterol concentrations.
}}

{{PMID Auto
|PMID=19915572
|Title=Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
|OA=1
}}

{{PMID Auto
|PMID=19951432
|Title=Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease.
|OA=1
}}

{{PMID Auto
|PMID=20385826
|Title=Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC).
|OA=1
}}

{{GET Evidence
|gene=HNF4A
|aa_change=Thr139Ile
|aa_change_short=T139I
|impact=not reviewed
|qualified_impact=Insufficiently evaluated not reviewed
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs1800961
|overall_frequency_n=258
|overall_frequency_d=10758
|overall_frequency=0.0239822
|n_genomes=2
|n_genomes_annotated=0
|n_haplomes=2
|n_articles=0
|n_articles_annotated=0
|gene_in_genetests=Y
|pph2_score=0.014
|genetests_testable=Y
|nblosum100=3
|autoscore=1
|webscore=N
}}

{{PMID Auto GWAS
  |PMID=22939635
  |Trait=C-reactive protein
  |Title=Genome-wide association and population genetic analysis of C-reactive protein in African American and Hispanic American women.
  |RiskAllele=T
  |Pval=8E-6
  |OR=.27
  |ORtxt=[0.15-0.39] (unit decrease)
  |OA=1
}}

{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | Affy GenomeWide 6}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}