rs544049

Homo sapiens
G>A
LOXHD1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0144 (4334/29910,GnomAD)
A=0170 (4974/29118,TOPMED)
A=0144 (719/5008,1000G)
A=0115 (443/3854,ALSPAC)
A=0120 (445/3708,TWINSUK)
chr18:46624750 (GRCh38.p7) (18q21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
66 Enhancers around
1 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 18NC_000018.10:g.46624750G>A
GRCh37.p13 chr 18NC_000018.9:g.44204713G>A
LOXHD1 RefSeqGeneNG_016646.1:g.37284C>T

Gene: LOXHD1, lipoxygenase homology domains 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOXHD1 transcript variant 1NM_144612.6:c.N/AIntron Variant
LOXHD1 transcript variant 2NM_001145472.2:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant 3NM_001145473.2:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant 4NM_001173129.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant 5NM_001308013.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X13XM_017025548.1:c.N/AIntron Variant
LOXHD1 transcript variant X3XM_006722388.3:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X4XM_006722389.3:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X5XM_006722390.3:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X7XM_006722391.3:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X2XM_011525804.2:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X14XM_011525807.2:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X11XM_011525810.2:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X12XM_011525811.2:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X1XM_017025540.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X2XM_017025541.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X3XM_017025542.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X4XM_017025543.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X5XM_017025544.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X6XM_017025545.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X8XM_017025546.1:c.N/AGenic Upstream Transcript Variant
LOXHD1 transcript variant X9XM_017025547.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.707A=0.293
1000GenomesAmericanSub694G=0.870A=0.130
1000GenomesEast AsianSub1008G=0.993A=0.007
1000GenomesEuropeSub1006G=0.880A=0.120
1000GenomesGlobalStudy-wide5008G=0.856A=0.144
1000GenomesSouth AsianSub978G=0.880A=0.120
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.885A=0.115
The Genome Aggregation DatabaseAfricanSub8682G=0.767A=0.233
The Genome Aggregation DatabaseAmericanSub838G=0.880A=0.120
The Genome Aggregation DatabaseEast AsianSub1622G=0.998A=0.002
The Genome Aggregation DatabaseEuropeSub18466G=0.883A=0.117
The Genome Aggregation DatabaseGlobalStudy-wide29910G=0.855A=0.144
The Genome Aggregation DatabaseOtherSub302G=0.830A=0.170
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.829A=0.170
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.880A=0.120
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs5440490.000339alcohol dependence21314694

eQTL of rs544049 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs544049 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr184424073944240829E06736026
chr184424102944241263E06736316
chr184424129644241346E06736583
chr184420305244203317E068-1396
chr184420338444203519E068-1194
chr184420354944204343E068-370
chr184421239744212729E0687684
chr184424073944240829E06936026
chr184424102944241263E06936316
chr184424129644241346E06936583
chr184424139944241630E06936686
chr184424073944240829E07036026
chr184424102944241263E07036316
chr184424129644241346E07036583
chr184424139944241630E07036686
chr184424780744247965E07043094
chr184424799944248079E07043286
chr184424812544248434E07043412
chr184424073944240829E07136026
chr184424102944241263E07136316
chr184424129644241346E07136583
chr184424139944241630E07136686
chr184420292344202973E072-1740
chr184420305244203317E072-1396
chr184420338444203519E072-1194
chr184424102944241263E07236316
chr184424129644241346E07236583
chr184424139944241630E07236686
chr184424754644247644E07242833
chr184424770844247759E07242995
chr184424780744247965E07243094
chr184424799944248079E07243286
chr184424102944241263E07336316
chr184424129644241346E07336583
chr184424139944241630E07336686
chr184424180944241859E07337096
chr184424748344247533E07342770
chr184424754644247644E07342833
chr184424770844247759E07342995
chr184424780744247965E07343094
chr184424799944248079E07343286
chr184424102944241263E07436316
chr184424129644241346E07436583
chr184424139944241630E07436686
chr184419995844200051E081-4662
chr184420016144200215E081-4498
chr184420030044200533E081-4180
chr184420075144200795E081-3918
chr184420082644200866E081-3847
chr184420103644201100E081-3613
chr184420116344201213E081-3500
chr184420292344202973E081-1740
chr184420305244203317E081-1396
chr184420338444203519E081-1194
chr184420354944204343E081-370
chr184420447144204595E081-118
chr184421030244210450E0815589
chr184421123344211362E0816520
chr184421141644211470E0816703
chr184421163644211690E0816923
chr184421185244212112E0817139
chr184421239744212729E0817684
chr184421276444213003E0818051
chr184424073944240829E08136026
chr184424102944241263E08136316
chr184425214444252805E08147431









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr184423647744236517E06831764