rs16836497

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LOC101928306 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0197 (5918/29970,GnomAD)
C=0203 (5923/29118,TOPMED)
C=0190 (954/5008,1000G)
C=0210 (809/3854,ALSPAC)
C=0196 (725/3708,TWINSUK)

Position: chr4:4950950 (GRCh38.p7) (4p16.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 56 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.4950950T>C
GRCh37.p13 chr 4	NC_000004.11:g.4952677T>C

Gene: LOC101928306, uncharacterized LOC101928306(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928306 transcript	NR_125893.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.797	C=0.203
1000Genomes	American	Sub	694	T=0.740	C=0.260
1000Genomes	East Asian	Sub	1008	T=0.774	C=0.226
1000Genomes	Europe	Sub	1006	T=0.817	C=0.183
1000Genomes	Global	Study-wide	5008	T=0.810	C=0.190
1000Genomes	South Asian	Sub	978	T=0.910	C=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.790	C=0.210
The Genome Aggregation Database	African	Sub	8724	T=0.800	C=0.200
The Genome Aggregation Database	American	Sub	838	T=0.720	C=0.280
The Genome Aggregation Database	East Asian	Sub	1622	T=0.756	C=0.244
The Genome Aggregation Database	Europe	Sub	18484	T=0.811	C=0.188
The Genome Aggregation Database	Global	Study-wide	29970	T=0.802	C=0.197
The Genome Aggregation Database	Other	Sub	302	T=0.820	C=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.796	C=0.203
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.804	C=0.196

PMID	Title	Author	Journal
22613542	ANKRD7 and CYTL1 are novel risk genes for alcohol drinking behavior.	Chen XD	Chin Med J (Engl)

SNP ID	p-value	Traits	Study
rs16836497	7.46E-05	alcohol consumption	22613542

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

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 )
chr4	4952086	4952253	E067	-424
chr4	4952380	4952651	E067	-26
chr4	4952729	4953211	E067	52
chr4	4996883	4997299	E068	44206
chr4	4945407	4946213	E069	-6464
chr4	4952086	4952253	E069	-424
chr4	4952380	4952651	E069	-26
chr4	4952729	4953211	E069	52
chr4	4992325	4993493	E069	39648
chr4	4952086	4952253	E070	-424
chr4	4952380	4952651	E070	-26
chr4	4952729	4953211	E070	52
chr4	4953627	4953677	E070	950
chr4	4996883	4997299	E070	44206
chr4	4997493	4997543	E070	44816
chr4	4997672	4997916	E070	44995
chr4	4952086	4952253	E071	-424
chr4	4952380	4952651	E071	-26
chr4	4952729	4953211	E071	52
chr4	4992325	4993493	E071	39648
chr4	4996771	4996882	E071	44094
chr4	4996883	4997299	E071	44206
chr4	4952729	4953211	E072	52
chr4	4992325	4993493	E072	39648
chr4	4996883	4997299	E072	44206
chr4	4997493	4997543	E072	44816
chr4	4952086	4952253	E073	-424
chr4	4952380	4952651	E073	-26
chr4	4952729	4953211	E073	52
chr4	4996883	4997299	E073	44206
chr4	4997493	4997543	E073	44816
chr4	4914859	4915598	E081	-37079
chr4	4915910	4916061	E081	-36616
chr4	4916242	4916389	E081	-36288
chr4	4916558	4916778	E081	-35899
chr4	4945407	4946213	E081	-6464
chr4	4946391	4946578	E081	-6099
chr4	4952380	4952651	E081	-26
chr4	4952729	4953211	E081	52
chr4	4953627	4953677	E081	950
chr4	4996883	4997299	E081	44206
chr4	4997493	4997543	E081	44816
chr4	4997672	4997916	E081	44995
chr4	4945407	4946213	E082	-6464
chr4	4952380	4952651	E082	-26
chr4	4954106	4954156	E082	1429
chr4	4982396	4982516	E082	29719
chr4	4982622	4982794	E082	29945
chr4	4982803	4983001	E082	30126
chr4	4983040	4983139	E082	30363
chr4	4983250	4983438	E082	30573
chr4	4983469	4983525	E082	30792
chr4	4996771	4996882	E082	44094
chr4	4996883	4997299	E082	44206
chr4	4997493	4997543	E082	44816
chr4	4997672	4997916	E082	44995

rs16836497

Genomic Coordinates

Gene: LOC101928306, uncharacterized LOC101928306(plus strand)

Population Frequency

P-Value

eQTL of rs16836497 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs16836497 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)