rs10402506

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LOC107985347 : Intron Variant
LOC105372461 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0242 (7261/29924,GnomAD)
G=0285 (8298/29118,TOPMED)
G=0294 (1472/5008,1000G)
G=0133 (513/3854,ALSPAC)
G=0124 (459/3708,TWINSUK)

Position: chr19:54563023 (GRCh38.p7) (19q13.42)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 175 Enhancers around

Promoter: 49 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.54563023A>G
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.537390A>G
GRCh38.p7 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.545584A>G
GRCh37.p13 chr 19	NC_000019.9:g.55074470A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.467899A>G
GRCh38.p7 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.469417A>G

Gene: LOC107985347, uncharacterized LOC107985347(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985347 transcript variant X1	XR_001754007.1:n.	N/A	Intron Variant
LOC107985347 transcript variant X3	XR_001754009.1:n.	N/A	Intron Variant
LOC107985347 transcript variant X4	XR_001754010.1:n.	N/A	Intron Variant
LOC107985347 transcript variant X2	XR_001754008.1:n.	N/A	Genic Downstream Transcript Variant

Gene: LOC105372461, uncharacterized LOC105372461(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372461 transcript	XR_936073.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.499	G=0.501
1000Genomes	American	Sub	694	A=0.720	G=0.280
1000Genomes	East Asian	Sub	1008	A=0.725	G=0.275
1000Genomes	Europe	Sub	1006	A=0.873	G=0.127
1000Genomes	Global	Study-wide	5008	A=0.706	G=0.294
1000Genomes	South Asian	Sub	978	A=0.780	G=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.867	G=0.133
The Genome Aggregation Database	African	Sub	8690	A=0.535	G=0.465
The Genome Aggregation Database	American	Sub	838	A=0.750	G=0.250
The Genome Aggregation Database	East Asian	Sub	1614	A=0.690	G=0.310
The Genome Aggregation Database	Europe	Sub	18482	A=0.866	G=0.133
The Genome Aggregation Database	Global	Study-wide	29924	A=0.757	G=0.242
The Genome Aggregation Database	Other	Sub	300	A=0.860	G=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.715	G=0.285
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.876	G=0.124

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

P-Value

SNP ID	p-value	Traits	Study
rs10402506	0.000989	alcohol dependence	21314694

eQTL of rs10402506 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 rs10402506 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 )
chr19	534509	534565	E067	-2825
chr19	534777	534827	E067	-2563
chr19	534901	535052	E067	-2338
chr19	535090	535426	E067	-1964
chr19	535533	535846	E067	-1544
chr19	551174	551336	E067	13784
chr19	551366	551552	E067	13976
chr19	574107	574278	E067	36717
chr19	576737	576824	E067	39347
chr19	576862	577212	E067	39472
chr19	577228	577350	E067	39838
chr19	577399	577504	E067	40009
chr19	577519	577623	E067	40129
chr19	577665	577879	E067	40275
chr19	577905	577955	E067	40515
chr19	578009	578184	E067	40619
chr19	579826	579966	E067	42436
chr19	580036	580097	E067	42646
chr19	580161	580257	E067	42771
chr19	487867	487927	E068	-49463
chr19	490223	490284	E068	-47106
chr19	490308	490408	E068	-46982
chr19	534509	534565	E068	-2825
chr19	551174	551336	E068	13784
chr19	551366	551552	E068	13976
chr19	576737	576824	E068	39347
chr19	576862	577212	E068	39472
chr19	577228	577350	E068	39838
chr19	577399	577504	E068	40009
chr19	583747	585118	E068	46357
chr19	487867	487927	E069	-49463
chr19	490466	490531	E069	-46859
chr19	490543	490656	E069	-46734
chr19	534509	534565	E069	-2825
chr19	534777	534827	E069	-2563
chr19	534901	535052	E069	-2338
chr19	535090	535426	E069	-1964
chr19	535533	535846	E069	-1544
chr19	537974	538060	E069	584
chr19	538186	538356	E069	796
chr19	538422	538476	E069	1032
chr19	558802	559122	E069	21412
chr19	559207	559257	E069	21817
chr19	559311	559411	E069	21921
chr19	576737	576824	E069	39347
chr19	577399	577504	E069	40009
chr19	577519	577623	E069	40129
chr19	579478	579638	E069	42088
chr19	579705	579785	E069	42315
chr19	579826	579966	E069	42436
chr19	580036	580097	E069	42646
chr19	580161	580257	E069	42771
chr19	580365	580598	E069	42975
chr19	583747	585118	E069	46357
chr19	534901	535052	E070	-2338
chr19	535090	535426	E070	-1964
chr19	535533	535846	E070	-1544
chr19	535898	535948	E070	-1442
chr19	576737	576824	E070	39347
chr19	490466	490531	E071	-46859
chr19	491138	491205	E071	-46185
chr19	534509	534565	E071	-2825
chr19	534777	534827	E071	-2563
chr19	534901	535052	E071	-2338
chr19	535090	535426	E071	-1964
chr19	535533	535846	E071	-1544
chr19	574107	574278	E071	36717
chr19	576737	576824	E071	39347
chr19	576862	577212	E071	39472
chr19	577228	577350	E071	39838
chr19	577399	577504	E071	40009
chr19	577519	577623	E071	40129
chr19	577665	577879	E071	40275
chr19	577905	577955	E071	40515
chr19	578009	578184	E071	40619
chr19	578233	578277	E071	40843
chr19	578341	578393	E071	40951
chr19	579208	579268	E071	41818
chr19	579478	579638	E071	42088
chr19	579705	579785	E071	42315
chr19	579826	579966	E071	42436
chr19	580036	580097	E071	42646
chr19	580161	580257	E071	42771
chr19	580365	580598	E071	42975
chr19	583747	585118	E071	46357
chr19	487867	487927	E072	-49463
chr19	490466	490531	E072	-46859
chr19	490543	490656	E072	-46734
chr19	534509	534565	E072	-2825
chr19	534777	534827	E072	-2563
chr19	534901	535052	E072	-2338
chr19	535090	535426	E072	-1964
chr19	537974	538060	E072	584
chr19	538186	538356	E072	796
chr19	551366	551552	E072	13976
chr19	574107	574278	E072	36717
chr19	577228	577350	E072	39838
chr19	577399	577504	E072	40009
chr19	577519	577623	E072	40129
chr19	577665	577879	E072	40275
chr19	577905	577955	E072	40515
chr19	578009	578184	E072	40619
chr19	578233	578277	E072	40843
chr19	578341	578393	E072	40951
chr19	578520	578601	E072	41130
chr19	578612	578687	E072	41222
chr19	578938	578988	E072	41548
chr19	579208	579268	E072	41818
chr19	579478	579638	E072	42088
chr19	579705	579785	E072	42315
chr19	579826	579966	E072	42436
chr19	580036	580097	E072	42646
chr19	580161	580257	E072	42771
chr19	580365	580598	E072	42975
chr19	487867	487927	E073	-49463
chr19	494969	495135	E073	-42255
chr19	495165	495275	E073	-42115
chr19	534509	534565	E073	-2825
chr19	534777	534827	E073	-2563
chr19	534901	535052	E073	-2338
chr19	535090	535426	E073	-1964
chr19	535533	535846	E073	-1544
chr19	538958	539008	E073	1568
chr19	539021	539078	E073	1631
chr19	539157	539275	E073	1767
chr19	539377	539483	E073	1987
chr19	556697	556915	E073	19307
chr19	556944	556988	E073	19554
chr19	559207	559257	E073	21817
chr19	559311	559411	E073	21921
chr19	578009	578184	E073	40619
chr19	578233	578277	E073	40843
chr19	578341	578393	E073	40951
chr19	578520	578601	E073	41130
chr19	578612	578687	E073	41222
chr19	578938	578988	E073	41548
chr19	579208	579268	E073	41818
chr19	579478	579638	E073	42088
chr19	579705	579785	E073	42315
chr19	579826	579966	E073	42436
chr19	580036	580097	E073	42646
chr19	580161	580257	E073	42771
chr19	580365	580598	E073	42975
chr19	580624	580806	E073	43234
chr19	581834	581994	E073	44444
chr19	582070	582185	E073	44680
chr19	583747	585118	E073	46357
chr19	487867	487927	E074	-49463
chr19	534901	535052	E074	-2338
chr19	535090	535426	E074	-1964
chr19	574107	574278	E074	36717
chr19	575910	576488	E074	38520
chr19	576737	576824	E074	39347
chr19	576862	577212	E074	39472
chr19	579826	579966	E074	42436
chr19	580036	580097	E074	42646
chr19	580161	580257	E074	42771
chr19	583747	585118	E074	46357
chr19	490223	490284	E081	-47106
chr19	490308	490408	E081	-46982
chr19	490466	490531	E081	-46859
chr19	534509	534565	E081	-2825
chr19	534777	534827	E081	-2563
chr19	534901	535052	E081	-2338
chr19	535090	535426	E081	-1964
chr19	551174	551336	E081	13784
chr19	551366	551552	E081	13976
chr19	574107	574278	E081	36717
chr19	575910	576488	E081	38520
chr19	576737	576824	E081	39347
chr19	576862	577212	E081	39472
chr19	534901	535052	E082	-2338
chr19	535090	535426	E082	-1964
chr19	535533	535846	E082	-1544
chr19	535898	535948	E082	-1442

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	488101	488299	E067	-49091
chr19	488487	490098	E067	-47292
chr19	506372	509364	E067	-28026
chr19	530689	534451	E067	-2939
chr19	570959	573974	E067	33569
chr19	488101	488299	E068	-49091
chr19	488487	490098	E068	-47292
chr19	506372	509364	E068	-28026
chr19	530689	534451	E068	-2939
chr19	570799	570868	E068	33409
chr19	570959	573974	E068	33569
chr19	488101	488299	E069	-49091
chr19	488487	490098	E069	-47292
chr19	506372	509364	E069	-28026
chr19	530689	534451	E069	-2939
chr19	570959	573974	E069	33569
chr19	488487	490098	E070	-47292
chr19	497445	497597	E070	-39793
chr19	506372	509364	E070	-28026
chr19	530689	534451	E070	-2939
chr19	570959	573974	E070	33569
chr19	488101	488299	E071	-49091
chr19	488487	490098	E071	-47292
chr19	506372	509364	E071	-28026
chr19	530689	534451	E071	-2939
chr19	570959	573974	E071	33569
chr19	488101	488299	E072	-49091
chr19	488487	490098	E072	-47292
chr19	506372	509364	E072	-28026
chr19	530689	534451	E072	-2939
chr19	570959	573974	E072	33569
chr19	488101	488299	E073	-49091
chr19	488487	490098	E073	-47292
chr19	506372	509364	E073	-28026
chr19	530689	534451	E073	-2939
chr19	570959	573974	E073	33569
chr19	488101	488299	E074	-49091
chr19	488487	490098	E074	-47292
chr19	506372	509364	E074	-28026
chr19	530689	534451	E074	-2939
chr19	570959	573974	E074	33569
chr19	570959	573974	E081	33569
chr19	488101	488299	E082	-49091
chr19	488487	490098	E082	-47292
chr19	497053	497183	E082	-40207
chr19	497445	497597	E082	-39793
chr19	506372	509364	E082	-28026
chr19	530689	534451	E082	-2939
chr19	570959	573974	E082	33569