rs2701

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CEACAM6 : 3 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0449 (13443/29914,GnomAD)
A==0400 (11653/29118,TOPMED)
A==0413 (2068/5008,1000G)
G=0429 (1652/3854,ALSPAC)
G=0442 (1639/3708,TWINSUK)

Position: chr19:41771194 (GRCh38.p7) (19q13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 177 Enhancers around

Promoter: 13 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.41771194G>A
GRCh37.p13 chr 19 fix patch HG1350_HG959_PATCH	NW_004775434.1:g.340233G>A
GRCh37.p13 chr 19	NC_000019.9:g.42275099A>G

Gene: CEACAM6, carcinoembryonic antigen related cell adhesion molecule 6(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CEACAM6 transcript	NM_002483.6:c.	N/A	3 Prime UTR Variant
CEACAM6 transcript variant X1	XM_011526990.1:c.	N/A	3 Prime UTR Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.123	G==0.877
1000Genomes	American	Sub	694	A=0.440	G==0.560
1000Genomes	East Asian	Sub	1008	A=0.436	G==0.564
1000Genomes	Europe	Sub	1006	A=0.593	G==0.407
1000Genomes	Global	Study-wide	5008	A=0.413	G==0.587
1000Genomes	South Asian	Sub	978	A=0.580	G==0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.571	G==0.429
The Genome Aggregation Database	African	Sub	8710	A=0.188	G==0.812
The Genome Aggregation Database	American	Sub	836	A=0.470	G==0.530
The Genome Aggregation Database	East Asian	Sub	1616	A=0.394	G==0.606
The Genome Aggregation Database	Europe	Sub	18450	A=0.574	G==0.425
The Genome Aggregation Database	Global	Study-wide	29914	A=0.449	G==0.550
The Genome Aggregation Database	Other	Sub	302	A=0.600	G==0.400
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.400	G==0.599
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.558	G==0.442

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
21559399	CEACAM6 gene variants in inflammatory bowel disease.	Glas J	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs2701	1.05E-05	alcohol dependence	21314694

eQTL of rs2701 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 rs2701 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	404
chr19	341036	341102	E067	803
chr19	341268	341364	E067	1035
chr19	341410	341555	E067	1177
chr19	341640	341716	E067	1407
chr19	341809	341927	E067	1576
chr19	342038	342121	E067	1805
chr19	342131	342440	E067	1898
chr19	342494	342560	E067	2261
chr19	371478	371602	E067	31245
chr19	371622	371770	E067	31389
chr19	371843	372122	E067	31610
chr19	372202	372294	E067	31969
chr19	372358	372637	E067	32125
chr19	372762	372814	E067	32529
chr19	372987	373037	E067	32754
chr19	341036	341102	E068	803
chr19	341268	341364	E068	1035
chr19	341410	341555	E068	1177
chr19	341640	341716	E068	1407
chr19	341809	341927	E068	1576
chr19	342038	342121	E068	1805
chr19	342131	342440	E068	1898
chr19	342494	342560	E068	2261
chr19	371478	371602	E068	31245
chr19	371622	371770	E068	31389
chr19	371843	372122	E068	31610
chr19	372202	372294	E068	31969
chr19	372358	372637	E068	32125
chr19	383005	383071	E068	42772
chr19	295688	295986	E069	-44247
chr19	296032	296208	E069	-44025
chr19	296280	296345	E069	-43888
chr19	340637	340866	E069	404
chr19	341036	341102	E069	803
chr19	341268	341364	E069	1035
chr19	341410	341555	E069	1177
chr19	341640	341716	E069	1407
chr19	341809	341927	E069	1576
chr19	342038	342121	E069	1805
chr19	342131	342440	E069	1898
chr19	342494	342560	E069	2261
chr19	371478	371602	E069	31245
chr19	371622	371770	E069	31389
chr19	371843	372122	E069	31610
chr19	372202	372294	E069	31969
chr19	372358	372637	E069	32125
chr19	372762	372814	E069	32529
chr19	372987	373037	E069	32754
chr19	383870	384771	E069	43637
chr19	340637	340866	E070	404
chr19	341036	341102	E070	803
chr19	341268	341364	E070	1035
chr19	341410	341555	E070	1177
chr19	342131	342440	E070	1898
chr19	342494	342560	E070	2261
chr19	368193	368306	E070	27960
chr19	368311	368933	E070	28078
chr19	371005	371189	E070	30772
chr19	371260	371300	E070	31027
chr19	371478	371602	E070	31245
chr19	371622	371770	E070	31389
chr19	372202	372294	E070	31969
chr19	372358	372637	E070	32125
chr19	372762	372814	E070	32529
chr19	372987	373037	E070	32754
chr19	373043	373089	E070	32810
chr19	373111	373151	E070	32878
chr19	373415	373479	E070	33182
chr19	373566	373616	E070	33333
chr19	373689	373745	E070	33456
chr19	296032	296208	E071	-44025
chr19	296280	296345	E071	-43888
chr19	336130	336564	E071	-3669
chr19	340637	340866	E071	404
chr19	341036	341102	E071	803
chr19	341268	341364	E071	1035
chr19	341410	341555	E071	1177
chr19	341640	341716	E071	1407
chr19	341809	341927	E071	1576
chr19	342038	342121	E071	1805
chr19	342131	342440	E071	1898
chr19	342494	342560	E071	2261
chr19	371478	371602	E071	31245
chr19	371622	371770	E071	31389
chr19	371843	372122	E071	31610
chr19	372202	372294	E071	31969
chr19	372358	372637	E071	32125
chr19	372762	372814	E071	32529
chr19	336712	336819	E072	-3414
chr19	340637	340866	E072	404
chr19	341036	341102	E072	803
chr19	341268	341364	E072	1035
chr19	341410	341555	E072	1177
chr19	341640	341716	E072	1407
chr19	341809	341927	E072	1576
chr19	342038	342121	E072	1805
chr19	342131	342440	E072	1898
chr19	342494	342560	E072	2261
chr19	371478	371602	E072	31245
chr19	371622	371770	E072	31389
chr19	372202	372294	E072	31969
chr19	372358	372637	E072	32125
chr19	372762	372814	E072	32529
chr19	372987	373037	E072	32754
chr19	373043	373089	E072	32810
chr19	373111	373151	E072	32878
chr19	383870	384771	E072	43637
chr19	292480	292751	E073	-47482
chr19	340637	340866	E073	404
chr19	341036	341102	E073	803
chr19	341268	341364	E073	1035
chr19	341410	341555	E073	1177
chr19	341640	341716	E073	1407
chr19	341809	341927	E073	1576
chr19	342038	342121	E073	1805
chr19	342131	342440	E073	1898
chr19	364614	364664	E073	24381
chr19	364955	365046	E073	24722
chr19	365111	365169	E073	24878
chr19	371478	371602	E073	31245
chr19	371622	371770	E073	31389
chr19	371843	372122	E073	31610
chr19	372202	372294	E073	31969
chr19	372358	372637	E073	32125
chr19	372762	372814	E073	32529
chr19	372987	373037	E073	32754
chr19	373043	373089	E073	32810
chr19	373111	373151	E073	32878
chr19	341036	341102	E074	803
chr19	341268	341364	E074	1035
chr19	341410	341555	E074	1177
chr19	341640	341716	E074	1407
chr19	341809	341927	E074	1576
chr19	342038	342121	E074	1805
chr19	342131	342440	E074	1898
chr19	342494	342560	E074	2261
chr19	371843	372122	E074	31610
chr19	372202	372294	E074	31969
chr19	340637	340866	E081	404
chr19	341036	341102	E081	803
chr19	341268	341364	E081	1035
chr19	341410	341555	E081	1177
chr19	341640	341716	E081	1407
chr19	341809	341927	E081	1576
chr19	342038	342121	E081	1805
chr19	342131	342440	E081	1898
chr19	342494	342560	E081	2261
chr19	370613	370668	E081	30380
chr19	370737	370777	E081	30504
chr19	370949	370999	E081	30716
chr19	371005	371189	E081	30772
chr19	371260	371300	E081	31027
chr19	371478	371602	E081	31245
chr19	371622	371770	E081	31389
chr19	371843	372122	E081	31610
chr19	372202	372294	E081	31969
chr19	372358	372637	E081	32125
chr19	372762	372814	E081	32529
chr19	372987	373037	E081	32754
chr19	373043	373089	E081	32810
chr19	373111	373151	E081	32878
chr19	373415	373479	E081	33182
chr19	373566	373616	E081	33333
chr19	373689	373745	E081	33456
chr19	383870	384771	E081	43637
chr19	341268	341364	E082	1035
chr19	341410	341555	E082	1177
chr19	342131	342440	E082	1898
chr19	342494	342560	E082	2261
chr19	371478	371602	E082	31245
chr19	371622	371770	E082	31389
chr19	371843	372122	E082	31610
chr19	372202	372294	E082	31969
chr19	372358	372637	E082	32125
chr19	372762	372814	E082	32529
chr19	372987	373037	E082	32754

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	342620	345624	E067	2387
chr19	310128	310182	E068	-30051
chr19	342620	345624	E068	2387
chr19	342620	345624	E069	2387
chr19	310128	310182	E070	-30051
chr19	342620	345624	E070	2387
chr19	345861	346000	E070	5628
chr19	342620	345624	E071	2387
chr19	342620	345624	E072	2387
chr19	342620	345624	E073	2387
chr19	342620	345624	E074	2387
chr19	310128	310182	E082	-30051
chr19	342620	345624	E082	2387