rs10079478

Homo sapiens
T>C
LOC101927934 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0228 (6853/29958,GnomAD)
C=0208 (6059/29118,TOPMED)
C=0265 (1325/5008,1000G)
C=0241 (929/3854,ALSPAC)
C=0233 (863/3708,TWINSUK)
chr5:134505105 (GRCh38.p7) (5q31.1)
AD
GWASdb2
1   publication(s)
See rs on genome
166 Enhancers around
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.134505105T>C
GRCh37.p13 chr 5NC_000005.9:g.133840796T>C

Gene: LOC101927934, uncharacterized LOC101927934(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LINC01843 transcriptNR_105045.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.840C=0.160
1000GenomesAmericanSub694T=0.640C=0.360
1000GenomesEast AsianSub1008T=0.647C=0.353
1000GenomesEuropeSub1006T=0.752C=0.248
1000GenomesGlobalStudy-wide5008T=0.735C=0.265
1000GenomesSouth AsianSub978T=0.730C=0.270
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.759C=0.241
The Genome Aggregation DatabaseAfricanSub8730T=0.834C=0.166
The Genome Aggregation DatabaseAmericanSub836T=0.600C=0.400
The Genome Aggregation DatabaseEast AsianSub1618T=0.604C=0.396
The Genome Aggregation DatabaseEuropeSub18472T=0.764C=0.235
The Genome Aggregation DatabaseGlobalStudy-wide29958T=0.771C=0.228
The Genome Aggregation DatabaseOtherSub302T=0.750C=0.250
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.791C=0.208
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.767C=0.233
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
rs100794780.000911alcohol dependence21314694

eQTL of rs10079478 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 rs10079478 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 )
chr5133838757133840017E067-779
chr5133846500133848623E0675704
chr5133864332133864445E06723536
chr5133864746133864876E06723950
chr5133865080133865155E06724284
chr5133865195133865721E06724399
chr5133865894133866905E06725098
chr5133866948133866988E06726152
chr5133868926133869407E06728130
chr5133869461133869563E06728665
chr5133869763133869820E06728967
chr5133869944133870012E06729148
chr5133870476133870516E06729680
chr5133879393133879633E06738597
chr5133882596133882759E06741800
chr5133882811133882883E06742015
chr5133883035133883591E06742239
chr5133883817133883995E06743021
chr5133884210133884275E06743414
chr5133889384133889469E06748588
chr5133889529133889955E06748733
chr5133800740133800827E068-39969
chr5133838757133840017E068-779
chr5133841599133842924E068803
chr5133859048133859217E06818252
chr5133859227133859582E06818431
chr5133864746133864876E06823950
chr5133865080133865155E06824284
chr5133865195133865721E06824399
chr5133865894133866905E06825098
chr5133866948133866988E06826152
chr5133867793133867959E06826997
chr5133868509133868559E06827713
chr5133879681133880141E06838885
chr5133882596133882759E06841800
chr5133882811133882883E06842015
chr5133883035133883591E06842239
chr5133883817133883995E06843021
chr5133884210133884275E06843414
chr5133884607133884676E06843811
chr5133885410133885694E06844614
chr5133885992133886043E06845196
chr5133886069133886235E06845273
chr5133886278133886514E06845482
chr5133886551133886772E06845755
chr5133889529133889955E06848733
chr5133800740133800827E069-39969
chr5133838757133840017E069-779
chr5133859048133859217E06918252
chr5133859227133859582E06918431
chr5133864332133864445E06923536
chr5133864746133864876E06923950
chr5133865080133865155E06924284
chr5133865195133865721E06924399
chr5133865894133866905E06925098
chr5133866948133866988E06926152
chr5133867793133867959E06926997
chr5133868509133868559E06927713
chr5133868926133869407E06928130
chr5133869461133869563E06928665
chr5133869763133869820E06928967
chr5133869944133870012E06929148
chr5133870476133870516E06929680
chr5133870670133870725E06929874
chr5133882596133882759E06941800
chr5133882811133882883E06942015
chr5133883035133883591E06942239
chr5133883817133883995E06943021
chr5133884210133884275E06943414
chr5133887649133888425E06946853
chr5133889384133889469E06948588
chr5133889529133889955E06948733
chr5133866948133866988E07026152
chr5133882596133882759E07041800
chr5133882811133882883E07042015
chr5133883035133883591E07042239
chr5133883817133883995E07043021
chr5133884210133884275E07043414
chr5133800569133800609E071-40187
chr5133800740133800827E071-39969
chr5133803237133803318E071-37478
chr5133803534133803604E071-37192
chr5133838757133840017E071-779
chr5133864746133864876E07123950
chr5133865080133865155E07124284
chr5133865195133865721E07124399
chr5133865894133866905E07125098
chr5133866948133866988E07126152
chr5133867793133867959E07126997
chr5133868509133868559E07127713
chr5133868926133869407E07128130
chr5133869461133869563E07128665
chr5133869763133869820E07128967
chr5133869944133870012E07129148
chr5133882596133882759E07141800
chr5133882811133882883E07142015
chr5133883035133883591E07142239
chr5133883817133883995E07143021
chr5133884210133884275E07143414
chr5133884607133884676E07143811
chr5133886069133886235E07145273
chr5133887649133888425E07146853
chr5133889529133889955E07148733
chr5133793926133794618E072-46178
chr5133800740133800827E072-39969
chr5133838757133840017E072-779
chr5133846500133848623E0725704
chr5133864746133864876E07223950
chr5133865080133865155E07224284
chr5133865195133865721E07224399
chr5133865894133866905E07225098
chr5133866948133866988E07226152
chr5133868509133868559E07227713
chr5133882811133882883E07242015
chr5133883035133883591E07242239
chr5133884210133884275E07243414
chr5133889384133889469E07248588
chr5133889529133889955E07248733
chr5133864332133864445E07323536
chr5133864746133864876E07323950
chr5133865080133865155E07324284
chr5133865195133865721E07324399
chr5133865894133866905E07325098
chr5133866948133866988E07326152
chr5133867793133867959E07326997
chr5133868509133868559E07327713
chr5133882596133882759E07341800
chr5133882811133882883E07342015
chr5133883035133883591E07342239
chr5133884210133884275E07343414
chr5133886069133886235E07345273
chr5133886278133886514E07345482
chr5133886551133886772E07345755
chr5133889529133889955E07348733
chr5133800569133800609E074-40187
chr5133800740133800827E074-39969
chr5133838757133840017E074-779
chr5133859227133859582E07418431
chr5133864332133864445E07423536
chr5133864746133864876E07423950
chr5133865080133865155E07424284
chr5133865195133865721E07424399
chr5133865894133866905E07425098
chr5133866948133866988E07426152
chr5133868509133868559E07427713
chr5133868926133869407E07428130
chr5133869461133869563E07428665
chr5133869763133869820E07428967
chr5133869944133870012E07429148
chr5133882596133882759E07441800
chr5133882811133882883E07442015
chr5133883035133883591E07442239
chr5133883817133883995E07443021
chr5133884210133884275E07443414
chr5133884607133884676E07443811
chr5133889384133889469E07448588
chr5133889529133889955E07448733
chr5133851543133851615E08110747
chr5133851624133851948E08110828
chr5133858772133858903E08117976
chr5133883035133883591E08142239
chr5133883817133883995E08143021
chr5133864332133864445E08223536
chr5133864746133864876E08223950
chr5133866948133866988E08226152
chr5133885992133886043E08245196










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5133859591133864281E06718795
chr5133859591133864281E06818795
chr5133859591133864281E06918795
chr5133859591133864281E07118795
chr5133859591133864281E07218795
chr5133859591133864281E07318795
chr5133859591133864281E07418795
chr5133859591133864281E08218795