rs12932948

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC400499 : Missense Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0432 (12940/29928,GnomAD)
A=0394 (11497/29118,TOPMED)
A=0456 (6174/13532,ExAC)
A=0322 (1611/5008,1000G)
G==0410 (1581/3854,ALSPAC)
G==0409 (1518/3708,TWINSUK)

Position: chr16:11450817 (GRCh38.p7) (16p13.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 57 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 16	NC_000016.10:g.11450817G>A
GRCh37.p13 chr 16	NC_000016.9:g.11544673G>A

Gene: LOC400499, uncharacterized LOC400499(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC400499 transcript variant X21	XM_017023947.1:c.	N/A	5 Prime UTR Variant
LOC400499 transcript variant X1	XM_017023929.1:c....XM_017023929.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X1	XP_016879418.1:p....XP_016879418.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X2	XM_017023930.1:c....XM_017023930.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X2	XP_016879419.1:p....XP_016879419.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X3	XM_017023931.1:c....XM_017023931.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X3	XP_016879420.1:p....XP_016879420.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X4	XM_017023932.1:c....XM_017023932.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X4	XP_016879421.1:p....XP_016879421.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X5	XM_017023933.1:c....XM_017023933.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X5	XP_016879422.1:p....XP_016879422.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X6	XM_017023934.1:c....XM_017023934.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X6	XP_016879423.1:p....XP_016879423.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X7	XM_017023935.1:c....XM_017023935.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X7	XP_016879424.1:p....XP_016879424.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X8	XM_017023936.1:c....XM_017023936.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X8	XP_016879425.1:p....XP_016879425.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X9	XM_017023937.1:c....XM_017023937.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X9	XP_016879426.1:p....XP_016879426.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X10	XM_017023938.1:c....XM_017023938.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X10	XP_016879427.1:p....XP_016879427.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X11	XM_017023939.1:c....XM_017023939.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X11	XP_016879428.1:p....XP_016879428.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X12	XM_017023940.1:c....XM_017023940.1:c.2849C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X12	XP_016879429.1:p....XP_016879429.1:p.Ala950Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X13	XM_017023941.1:c....XM_017023941.1:c.2054C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X13	XP_016879430.1:p....XP_016879430.1:p.Ala685Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X14	XM_017023942.1:c....XM_017023942.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X14	XP_016879431.1:p....XP_016879431.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X15	XM_017023943.1:c....XM_017023943.1:c.1019C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X15	XP_016879432.1:p....XP_016879432.1:p.Ala340Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X16	XM_017023944.1:c....XM_017023944.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X16	XP_016879433.1:p....XP_016879433.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X17	XM_017023945.1:c....XM_017023945.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X17	XP_016879434.1:p....XP_016879434.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X20	XM_017023946.1:c....XM_017023946.1:c.833C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X18	XP_016879435.1:p....XP_016879435.1:p.Ala278Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X22	XM_017023948.1:c....XM_017023948.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X20	XP_016879437.1:p....XP_016879437.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X23	XM_017023949.1:c....XM_017023949.1:c.3944C>T	A [GCC]> V [GTC]	Coding Sequence Variant
putative uncharacterized protein LOC400499 isoform X21	XP_016879438.1:p....XP_016879438.1:p.Ala1315Val	A [Ala]> V [Val]	Missense Variant
LOC400499 transcript variant X18	XR_001752082.1:n....XR_001752082.1:n.4334C>T	C>T	Non Coding Transcript Variant
LOC400499 transcript variant X19	XR_001752083.1:n....XR_001752083.1:n.4334C>T	C>T	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.862	A=0.138
1000Genomes	American	Sub	694	G=0.690	A=0.310
1000Genomes	East Asian	Sub	1008	G=0.747	A=0.253
1000Genomes	Europe	Sub	1006	G=0.435	A=0.565
1000Genomes	Global	Study-wide	5008	G=0.678	A=0.322
1000Genomes	South Asian	Sub	978	G=0.600	A=0.400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.410	A=0.590
The Exome Aggregation Consortium	American	Sub	702	G=0.750	A=0.250
The Exome Aggregation Consortium	Asian	Sub	7764	G=0.588	A=0.412
The Exome Aggregation Consortium	Europe	Sub	4906	G=0.447	A=0.553
The Exome Aggregation Consortium	Global	Study-wide	13532	G=0.543	A=0.456
The Exome Aggregation Consortium	Other	Sub	160	G=0.480	A=0.520
The Genome Aggregation Database	African	Sub	8716	G=0.795	A=0.205
The Genome Aggregation Database	American	Sub	836	G=0.700	A=0.300
The Genome Aggregation Database	East Asian	Sub	1608	G=0.757	A=0.243
The Genome Aggregation Database	Europe	Sub	18466	G=0.439	A=0.561
The Genome Aggregation Database	Global	Study-wide	29928	G=0.567	A=0.432
The Genome Aggregation Database	Other	Sub	302	G=0.490	A=0.510
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.605	A=0.394
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.409	A=0.591

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs12932948	1.17E-05	alcohol dependence	21703634

eQTL of rs12932948 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 rs12932948 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 )
chr16	11589985	11590042	E067	45312
chr16	11590244	11590317	E067	45571
chr16	11590387	11592192	E067	45714
chr16	11504634	11504871	E068	-39802
chr16	11504882	11504945	E068	-39728
chr16	11505009	11505293	E068	-39380
chr16	11589985	11590042	E068	45312
chr16	11590244	11590317	E068	45571
chr16	11590387	11592192	E068	45714
chr16	11504634	11504871	E069	-39802
chr16	11504882	11504945	E069	-39728
chr16	11505009	11505293	E069	-39380
chr16	11589266	11589883	E069	44593
chr16	11589985	11590042	E069	45312
chr16	11590244	11590317	E069	45571
chr16	11590387	11592192	E069	45714
chr16	11504634	11504871	E071	-39802
chr16	11504882	11504945	E071	-39728
chr16	11505009	11505293	E071	-39380
chr16	11589128	11589227	E071	44455
chr16	11589266	11589883	E071	44593
chr16	11589985	11590042	E071	45312
chr16	11590244	11590317	E071	45571
chr16	11590387	11592192	E071	45714
chr16	11592398	11592974	E071	47725
chr16	11504634	11504871	E072	-39802
chr16	11504882	11504945	E072	-39728
chr16	11505009	11505293	E072	-39380
chr16	11590387	11592192	E072	45714
chr16	11504634	11504871	E073	-39802
chr16	11504882	11504945	E073	-39728
chr16	11589128	11589227	E073	44455
chr16	11590244	11590317	E073	45571
chr16	11590387	11592192	E073	45714
chr16	11495564	11495608	E074	-49065
chr16	11495727	11495773	E074	-48900
chr16	11495834	11495890	E074	-48783
chr16	11504311	11504517	E074	-40156
chr16	11504634	11504871	E074	-39802
chr16	11504882	11504945	E074	-39728
chr16	11505009	11505293	E074	-39380
chr16	11507609	11507680	E074	-36993
chr16	11507736	11508270	E074	-36403
chr16	11589128	11589227	E074	44455
chr16	11589266	11589883	E074	44593
chr16	11589985	11590042	E074	45312
chr16	11590244	11590317	E074	45571
chr16	11590387	11592192	E074	45714
chr16	11592398	11592974	E074	47725
chr16	11593144	11593796	E074	48471
chr16	11508798	11508978	E081	-35695
chr16	11509053	11509124	E081	-35549
chr16	11523098	11523326	E081	-21347
chr16	11523678	11524091	E081	-20582
chr16	11544028	11544397	E081	-276
chr16	11590387	11592192	E081	45714
chr16	11523098	11523326	E082	-21347