rs7251960

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

CEACAM3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0496 (14819/29856,GnomAD)
T==0442 (12884/29118,TOPMED)
T==0450 (2256/5008,1000G)
C=0382 (1473/3854,ALSPAC)
C=0394 (1460/3708,TWINSUK)

Position: chr19:41802111 (GRCh38.p7) (19q13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 202 Enhancers around

Promoter: 15 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.41802111C>T
GRCh37.p13 chr 19 fix patch HG1350_HG959_PATCH	NW_004775434.1:g.371150C>T
GRCh37.p13 chr 19	NC_000019.9:g.42306043T>C

Gene: CEACAM3, carcinoembryonic antigen related cell adhesion molecule 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CEACAM3 transcript variant 2	NM_001277163.2:c.	N/A	Intron Variant
CEACAM3 transcript variant 1	NM_001815.4:c.	N/A	Intron Variant
CEACAM3 transcript variant 3	NR_102333.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.144	C==0.856
1000Genomes	American	Sub	694	T=0.510	C==0.490
1000Genomes	East Asian	Sub	1008	T=0.479	C==0.521
1000Genomes	Europe	Sub	1006	T=0.624	C==0.376
1000Genomes	Global	Study-wide	5008	T=0.450	C==0.550
1000Genomes	South Asian	Sub	978	T=0.620	C==0.380
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.618	C==0.382
The Genome Aggregation Database	African	Sub	8690	T=0.217	C==0.783
The Genome Aggregation Database	American	Sub	836	T=0.570	C==0.430
The Genome Aggregation Database	East Asian	Sub	1612	T=0.431	C==0.569
The Genome Aggregation Database	Europe	Sub	18416	T=0.627	C==0.372
The Genome Aggregation Database	Global	Study-wide	29856	T=0.496	C==0.503
The Genome Aggregation Database	Other	Sub	302	T=0.660	C==0.340
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.442	C==0.557
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.606	C==0.394

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
rs7251960	0.000266	alcohol dependence	21314694

eQTL of rs7251960 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 rs7251960 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	340637	340866	E067	-30284
chr19	341036	341102	E067	-30048
chr19	341268	341364	E067	-29786
chr19	341410	341555	E067	-29595
chr19	341640	341716	E067	-29434
chr19	341809	341927	E067	-29223
chr19	342038	342121	E067	-29029
chr19	342131	342440	E067	-28710
chr19	342494	342560	E067	-28590
chr19	371478	371602	E067	328
chr19	371622	371770	E067	472
chr19	371843	372122	E067	693
chr19	372202	372294	E067	1052
chr19	372358	372637	E067	1208
chr19	372762	372814	E067	1612
chr19	372987	373037	E067	1837
chr19	403545	403777	E067	32395
chr19	341036	341102	E068	-30048
chr19	341268	341364	E068	-29786
chr19	341410	341555	E068	-29595
chr19	341640	341716	E068	-29434
chr19	341809	341927	E068	-29223
chr19	342038	342121	E068	-29029
chr19	342131	342440	E068	-28710
chr19	342494	342560	E068	-28590
chr19	371478	371602	E068	328
chr19	371622	371770	E068	472
chr19	371843	372122	E068	693
chr19	372202	372294	E068	1052
chr19	372358	372637	E068	1208
chr19	383005	383071	E068	11855
chr19	403545	403777	E068	32395
chr19	340637	340866	E069	-30284
chr19	341036	341102	E069	-30048
chr19	341268	341364	E069	-29786
chr19	341410	341555	E069	-29595
chr19	341640	341716	E069	-29434
chr19	341809	341927	E069	-29223
chr19	342038	342121	E069	-29029
chr19	342131	342440	E069	-28710
chr19	342494	342560	E069	-28590
chr19	371478	371602	E069	328
chr19	371622	371770	E069	472
chr19	371843	372122	E069	693
chr19	372202	372294	E069	1052
chr19	372358	372637	E069	1208
chr19	372762	372814	E069	1612
chr19	372987	373037	E069	1837
chr19	383870	384771	E069	12720
chr19	412267	412681	E069	41117
chr19	340637	340866	E070	-30284
chr19	341036	341102	E070	-30048
chr19	341268	341364	E070	-29786
chr19	341410	341555	E070	-29595
chr19	342131	342440	E070	-28710
chr19	342494	342560	E070	-28590
chr19	368193	368306	E070	-2844
chr19	368311	368933	E070	-2217
chr19	371005	371189	E070	0
chr19	371260	371300	E070	110
chr19	371478	371602	E070	328
chr19	371622	371770	E070	472
chr19	372202	372294	E070	1052
chr19	372358	372637	E070	1208
chr19	372762	372814	E070	1612
chr19	372987	373037	E070	1837
chr19	373043	373089	E070	1893
chr19	373111	373151	E070	1961
chr19	373415	373479	E070	2265
chr19	373566	373616	E070	2416
chr19	373689	373745	E070	2539
chr19	401263	401352	E070	30113
chr19	401431	401542	E070	30281
chr19	402792	402842	E070	31642
chr19	405623	405750	E070	34473
chr19	405814	405901	E070	34664
chr19	406019	406225	E070	34869
chr19	407351	407463	E070	36201
chr19	407562	407746	E070	36412
chr19	336130	336564	E071	-34586
chr19	340637	340866	E071	-30284
chr19	341036	341102	E071	-30048
chr19	341268	341364	E071	-29786
chr19	341410	341555	E071	-29595
chr19	341640	341716	E071	-29434
chr19	341809	341927	E071	-29223
chr19	342038	342121	E071	-29029
chr19	342131	342440	E071	-28710
chr19	342494	342560	E071	-28590
chr19	371478	371602	E071	328
chr19	371622	371770	E071	472
chr19	371843	372122	E071	693
chr19	372202	372294	E071	1052
chr19	372358	372637	E071	1208
chr19	372762	372814	E071	1612
chr19	336712	336819	E072	-34331
chr19	340637	340866	E072	-30284
chr19	341036	341102	E072	-30048
chr19	341268	341364	E072	-29786
chr19	341410	341555	E072	-29595
chr19	341640	341716	E072	-29434
chr19	341809	341927	E072	-29223
chr19	342038	342121	E072	-29029
chr19	342131	342440	E072	-28710
chr19	342494	342560	E072	-28590
chr19	371478	371602	E072	328
chr19	371622	371770	E072	472
chr19	372202	372294	E072	1052
chr19	372358	372637	E072	1208
chr19	372762	372814	E072	1612
chr19	372987	373037	E072	1837
chr19	373043	373089	E072	1893
chr19	373111	373151	E072	1961
chr19	383870	384771	E072	12720
chr19	403545	403777	E072	32395
chr19	412267	412681	E072	41117
chr19	412717	412975	E072	41567
chr19	340637	340866	E073	-30284
chr19	341036	341102	E073	-30048
chr19	341268	341364	E073	-29786
chr19	341410	341555	E073	-29595
chr19	341640	341716	E073	-29434
chr19	341809	341927	E073	-29223
chr19	342038	342121	E073	-29029
chr19	342131	342440	E073	-28710
chr19	364614	364664	E073	-6486
chr19	364955	365046	E073	-6104
chr19	365111	365169	E073	-5981
chr19	371478	371602	E073	328
chr19	371622	371770	E073	472
chr19	371843	372122	E073	693
chr19	372202	372294	E073	1052
chr19	372358	372637	E073	1208
chr19	372762	372814	E073	1612
chr19	372987	373037	E073	1837
chr19	373043	373089	E073	1893
chr19	373111	373151	E073	1961
chr19	403237	403391	E073	32087
chr19	403545	403777	E073	32395
chr19	341036	341102	E074	-30048
chr19	341268	341364	E074	-29786
chr19	341410	341555	E074	-29595
chr19	341640	341716	E074	-29434
chr19	341809	341927	E074	-29223
chr19	342038	342121	E074	-29029
chr19	342131	342440	E074	-28710
chr19	342494	342560	E074	-28590
chr19	371843	372122	E074	693
chr19	372202	372294	E074	1052
chr19	412717	412975	E074	41567
chr19	340637	340866	E081	-30284
chr19	341036	341102	E081	-30048
chr19	341268	341364	E081	-29786
chr19	341410	341555	E081	-29595
chr19	341640	341716	E081	-29434
chr19	341809	341927	E081	-29223
chr19	342038	342121	E081	-29029
chr19	342131	342440	E081	-28710
chr19	342494	342560	E081	-28590
chr19	370613	370668	E081	-482
chr19	370737	370777	E081	-373
chr19	370949	370999	E081	-151
chr19	371005	371189	E081	0
chr19	371260	371300	E081	110
chr19	371478	371602	E081	328
chr19	371622	371770	E081	472
chr19	371843	372122	E081	693
chr19	372202	372294	E081	1052
chr19	372358	372637	E081	1208
chr19	372762	372814	E081	1612
chr19	372987	373037	E081	1837
chr19	373043	373089	E081	1893
chr19	373111	373151	E081	1961
chr19	373415	373479	E081	2265
chr19	373566	373616	E081	2416
chr19	373689	373745	E081	2539
chr19	383870	384771	E081	12720
chr19	402203	402543	E081	31053
chr19	403058	403123	E081	31908
chr19	403237	403391	E081	32087
chr19	403545	403777	E081	32395
chr19	403854	403967	E081	32704
chr19	405623	405750	E081	34473
chr19	405814	405901	E081	34664
chr19	406019	406225	E081	34869
chr19	406340	406419	E081	35190
chr19	406567	406687	E081	35417
chr19	406956	407021	E081	35806
chr19	407351	407463	E081	36201
chr19	407562	407746	E081	36412
chr19	341268	341364	E082	-29786
chr19	341410	341555	E082	-29595
chr19	342131	342440	E082	-28710
chr19	342494	342560	E082	-28590
chr19	371478	371602	E082	328
chr19	371622	371770	E082	472
chr19	371843	372122	E082	693
chr19	372202	372294	E082	1052
chr19	372358	372637	E082	1208
chr19	372762	372814	E082	1612
chr19	372987	373037	E082	1837
chr19	406019	406225	E082	34869

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	342620	345624	E067	-25526
chr19	408520	410093	E067	37370
chr19	342620	345624	E068	-25526
chr19	342620	345624	E069	-25526
chr19	408520	410093	E069	37370
chr19	342620	345624	E070	-25526
chr19	345861	346000	E070	-25150
chr19	342620	345624	E071	-25526
chr19	342620	345624	E072	-25526
chr19	408520	410093	E072	37370
chr19	342620	345624	E073	-25526
chr19	408520	410093	E073	37370
chr19	342620	345624	E074	-25526
chr19	342620	345624	E082	-25526
chr19	408520	410093	E082	37370