rs11646835

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC400499 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0295 (8833/29944,GnomAD)
A=0297 (8650/29118,TOPMED)
A=0297 (1486/5008,1000G)
A=0309 (1189/3854,ALSPAC)
A=0288 (1068/3708,TWINSUK)

Position: chr16:11519313 (GRCh38.p7) (16p13.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 151 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.11519313G>A
GRCh37.p13 chr 16	NC_000016.9:g.11613169G>A

Gene: LOC400499, uncharacterized LOC400499(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC400499 transcript variant X1	XM_017023929.1:c.	N/A	Intron Variant
LOC400499 transcript variant X2	XM_017023930.1:c.	N/A	Intron Variant
LOC400499 transcript variant X3	XM_017023931.1:c.	N/A	Intron Variant
LOC400499 transcript variant X4	XM_017023932.1:c.	N/A	Intron Variant
LOC400499 transcript variant X5	XM_017023933.1:c.	N/A	Intron Variant
LOC400499 transcript variant X6	XM_017023934.1:c.	N/A	Intron Variant
LOC400499 transcript variant X7	XM_017023935.1:c.	N/A	Intron Variant
LOC400499 transcript variant X8	XM_017023936.1:c.	N/A	Intron Variant
LOC400499 transcript variant X9	XM_017023937.1:c.	N/A	Intron Variant
LOC400499 transcript variant X10	XM_017023938.1:c.	N/A	Intron Variant
LOC400499 transcript variant X11	XM_017023939.1:c.	N/A	Intron Variant
LOC400499 transcript variant X14	XM_017023942.1:c.	N/A	Intron Variant
LOC400499 transcript variant X16	XM_017023944.1:c.	N/A	Intron Variant
LOC400499 transcript variant X17	XM_017023945.1:c.	N/A	Intron Variant
LOC400499 transcript variant X22	XM_017023948.1:c.	N/A	Intron Variant
LOC400499 transcript variant X23	XM_017023949.1:c.	N/A	Intron Variant
LOC400499 transcript variant X12	XM_017023940.1:c.	N/A	Genic Upstream Transcript Variant
LOC400499 transcript variant X13	XM_017023941.1:c.	N/A	Genic Upstream Transcript Variant
LOC400499 transcript variant X15	XM_017023943.1:c.	N/A	Genic Upstream Transcript Variant
LOC400499 transcript variant X20	XM_017023946.1:c.	N/A	Genic Upstream Transcript Variant
LOC400499 transcript variant X21	XM_017023947.1:c.	N/A	Genic Upstream Transcript Variant
LOC400499 transcript variant X18	XR_001752082.1:n.	N/A	Intron Variant
LOC400499 transcript variant X19	XR_001752083.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.651	A=0.349
1000Genomes	American	Sub	694	G=0.780	A=0.220
1000Genomes	East Asian	Sub	1008	G=0.675	A=0.325
1000Genomes	Europe	Sub	1006	G=0.703	A=0.297
1000Genomes	Global	Study-wide	5008	G=0.703	A=0.297
1000Genomes	South Asian	Sub	978	G=0.750	A=0.250
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.691	A=0.309
The Genome Aggregation Database	African	Sub	8714	G=0.661	A=0.339
The Genome Aggregation Database	American	Sub	836	G=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1614	G=0.691	A=0.309
The Genome Aggregation Database	Europe	Sub	18478	G=0.723	A=0.276
The Genome Aggregation Database	Global	Study-wide	29944	G=0.705	A=0.295
The Genome Aggregation Database	Other	Sub	302	G=0.630	A=0.370
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.702	A=0.297
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.712	A=0.288

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs11646835	0.000955	alcohol dependence	21314694

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 )
chr16	11589985	11590042	E067	-23127
chr16	11590244	11590317	E067	-22852
chr16	11590387	11592192	E067	-20977
chr16	11639236	11639336	E067	26067
chr16	11639394	11639564	E067	26225
chr16	11652353	11652420	E067	39184
chr16	11652558	11652792	E067	39389
chr16	11657298	11657765	E067	44129
chr16	11589985	11590042	E068	-23127
chr16	11590244	11590317	E068	-22852
chr16	11590387	11592192	E068	-20977
chr16	11597905	11598036	E068	-15133
chr16	11598064	11598210	E068	-14959
chr16	11639236	11639336	E068	26067
chr16	11639394	11639564	E068	26225
chr16	11640027	11640067	E068	26858
chr16	11640197	11641890	E068	27028
chr16	11641934	11641986	E068	28765
chr16	11642136	11642222	E068	28967
chr16	11647208	11647258	E068	34039
chr16	11647377	11647445	E068	34208
chr16	11647471	11647530	E068	34302
chr16	11647672	11647760	E068	34503
chr16	11651511	11651629	E068	38342
chr16	11652222	11652269	E068	39053
chr16	11652353	11652420	E068	39184
chr16	11652558	11652792	E068	39389
chr16	11589266	11589883	E069	-23286
chr16	11589985	11590042	E069	-23127
chr16	11590244	11590317	E069	-22852
chr16	11590387	11592192	E069	-20977
chr16	11640197	11641890	E069	27028
chr16	11641934	11641986	E069	28765
chr16	11642136	11642222	E069	28967
chr16	11646326	11646628	E069	33157
chr16	11647208	11647258	E069	34039
chr16	11647377	11647445	E069	34208
chr16	11647471	11647530	E069	34302
chr16	11647672	11647760	E069	34503
chr16	11650786	11651474	E069	37617
chr16	11651511	11651629	E069	38342
chr16	11651672	11652045	E069	38503
chr16	11652353	11652420	E069	39184
chr16	11652558	11652792	E069	39389
chr16	11658076	11658137	E069	44907
chr16	11658162	11658227	E069	44993
chr16	11658295	11658414	E069	45126
chr16	11658471	11658610	E069	45302
chr16	11640027	11640067	E070	26858
chr16	11640197	11641890	E070	27028
chr16	11641934	11641986	E070	28765
chr16	11642136	11642222	E070	28967
chr16	11642829	11642879	E070	29660
chr16	11647471	11647530	E070	34302
chr16	11647672	11647760	E070	34503
chr16	11652108	11652169	E070	38939
chr16	11652222	11652269	E070	39053
chr16	11652353	11652420	E070	39184
chr16	11589128	11589227	E071	-23942
chr16	11589266	11589883	E071	-23286
chr16	11589985	11590042	E071	-23127
chr16	11590244	11590317	E071	-22852
chr16	11590387	11592192	E071	-20977
chr16	11592398	11592974	E071	-20195
chr16	11597905	11598036	E071	-15133
chr16	11640027	11640067	E071	26858
chr16	11640197	11641890	E071	27028
chr16	11642136	11642222	E071	28967
chr16	11650786	11651474	E071	37617
chr16	11652558	11652792	E071	39389
chr16	11657036	11657115	E071	43867
chr16	11657298	11657765	E071	44129
chr16	11657853	11657893	E071	44684
chr16	11657913	11657953	E071	44744
chr16	11658076	11658137	E071	44907
chr16	11658162	11658227	E071	44993
chr16	11658295	11658414	E071	45126
chr16	11658471	11658610	E071	45302
chr16	11658720	11658845	E071	45551
chr16	11590387	11592192	E072	-20977
chr16	11640197	11641890	E072	27028
chr16	11641934	11641986	E072	28765
chr16	11642136	11642222	E072	28967
chr16	11643070	11643130	E072	29901
chr16	11647208	11647258	E072	34039
chr16	11647377	11647445	E072	34208
chr16	11647471	11647530	E072	34302
chr16	11647672	11647760	E072	34503
chr16	11651511	11651629	E072	38342
chr16	11651672	11652045	E072	38503
chr16	11657853	11657893	E072	44684
chr16	11657913	11657953	E072	44744
chr16	11658076	11658137	E072	44907
chr16	11658162	11658227	E072	44993
chr16	11658295	11658414	E072	45126
chr16	11658471	11658610	E072	45302
chr16	11658720	11658845	E072	45551
chr16	11589128	11589227	E073	-23942
chr16	11590244	11590317	E073	-22852
chr16	11590387	11592192	E073	-20977
chr16	11658076	11658137	E073	44907
chr16	11658162	11658227	E073	44993
chr16	11658295	11658414	E073	45126
chr16	11658471	11658610	E073	45302
chr16	11658720	11658845	E073	45551
chr16	11589128	11589227	E074	-23942
chr16	11589266	11589883	E074	-23286
chr16	11589985	11590042	E074	-23127
chr16	11590244	11590317	E074	-22852
chr16	11590387	11592192	E074	-20977
chr16	11592398	11592974	E074	-20195
chr16	11593144	11593796	E074	-19373
chr16	11638848	11639134	E074	25679
chr16	11639236	11639336	E074	26067
chr16	11639394	11639564	E074	26225
chr16	11639565	11639631	E074	26396
chr16	11640027	11640067	E074	26858
chr16	11640197	11641890	E074	27028
chr16	11641934	11641986	E074	28765
chr16	11642136	11642222	E074	28967
chr16	11643070	11643130	E074	29901
chr16	11647208	11647258	E074	34039
chr16	11647377	11647445	E074	34208
chr16	11647471	11647530	E074	34302
chr16	11647672	11647760	E074	34503
chr16	11649773	11650242	E074	36604
chr16	11650258	11650310	E074	37089
chr16	11650451	11650701	E074	37282
chr16	11650786	11651474	E074	37617
chr16	11651511	11651629	E074	38342
chr16	11651672	11652045	E074	38503
chr16	11652108	11652169	E074	38939
chr16	11652222	11652269	E074	39053
chr16	11652353	11652420	E074	39184
chr16	11652558	11652792	E074	39389
chr16	11657298	11657765	E074	44129
chr16	11657853	11657893	E074	44684
chr16	11657913	11657953	E074	44744
chr16	11658076	11658137	E074	44907
chr16	11658162	11658227	E074	44993
chr16	11658295	11658414	E074	45126
chr16	11658471	11658610	E074	45302
chr16	11658720	11658845	E074	45551
chr16	11590387	11592192	E081	-20977
chr16	11636130	11636241	E081	22961
chr16	11636259	11636562	E081	23090
chr16	11640197	11641890	E081	27028
chr16	11636259	11636562	E082	23090
chr16	11640197	11641890	E082	27028
chr16	11641934	11641986	E082	28765
chr16	11651511	11651629	E082	38342

rs11646835

Genomic Coordinates

Gene: LOC400499, uncharacterized LOC400499(minus strand)

Population Frequency

P-Value

eQTL of rs11646835 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs11646835 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)