rs2229569

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

SELL : Missense Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0183 (5506/29938,GnomAD)
A=0204 (5941/29118,TOPMED)
G==0159 (1885/11838,GO-ESP)
A=0244 (1222/5008,1000G)
A=0143 (550/3854,ALSPAC)
A=0135 (499/3708,TWINSUK)

Position: chr1:169704697 (GRCh38.p7) (1q24.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 73 Enhancers around

Promoter: 59 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.169704697G>A
GRCh38.p7 chr 1	NC_000001.11:g.169704697G>T
GRCh37.p13 chr 1	NC_000001.10:g.169673838G>A
GRCh37.p13 chr 1	NC_000001.10:g.169673838G>T
SELL RefSeqGene	NG_016132.1:g.12006C>T
SELL RefSeqGene	NG_016132.1:g.12006C>A

Gene: SELL, selectin L(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SELL transcript variant 1	NM_000655.4:c.676C>T	P [CCT]> S [TCT]	Coding Sequence Variant
L-selectin precursor	NP_000646.2:p.Pro...NP_000646.2:p.Pro226Ser	P [Pro]> S [Ser]	Missense Variant
SELL transcript variant 1	NM_000655.4:c.676C>A	P [CCT]> T [ACT]	Coding Sequence Variant
L-selectin precursor	NP_000646.2:p.Pro...NP_000646.2:p.Pro226Thr	P [Pro]> T [Thr]	Missense Variant
SELL transcript variant 2	NR_029467.1:n.605C>T	C>T	Non Coding Transcript Variant
SELL transcript variant 2	NR_029467.1:n.605C>A	C>A	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.730	A=0.270
1000Genomes	American	Sub	694	G=0.720	A=0.280
1000Genomes	East Asian	Sub	1008	G=0.746	A=0.254
1000Genomes	Europe	Sub	1006	G=0.825	A=0.175
1000Genomes	Global	Study-wide	5008	G=0.756	A=0.244
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=0.857	A=0.143
The Genome Aggregation Database	African	Sub	8708	G=0.757	A=0.243
The Genome Aggregation Database	American	Sub	838	G=0.670	A=0.330
The Genome Aggregation Database	East Asian	Sub	1608	G=0.753	A=0.247
The Genome Aggregation Database	Europe	Sub	18482	G=0.855	A=0.144
The Genome Aggregation Database	Global	Study-wide	29938	G=0.816	A=0.183
The Genome Aggregation Database	Other	Sub	302	G=0.860	A=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.796	A=0.204
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.865	A=0.135

PMID	Title	Author	Journal
22646485	Association between genetic variants in adhesion molecules and outcomes after hematopoietic cell transplants.	Thyagarajan B	Int J Immunogenet
19064790	Predictive genomics of cardioembolic stroke.	Ramoni RB	Stroke
19240957	Candidate gene analysis of selectin cluster in patients with multiple sclerosis.	Fenoglio C	J Neurol

P-Value

SNP ID	p-value	Traits	Study
rs2229569	9.88E-06	alcoholism	pha002891

eQTL of rs2229569 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 rs2229569 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 )
chr1	973985	974025	E067	-48654
chr1	974027	974101	E067	-48578
chr1	974205	974384	E067	-48295
chr1	974999	975166	E068	-47513
chr1	972752	972843	E069	-49836
chr1	1034310	1034946	E069	11631
chr1	1058049	1058200	E069	35370
chr1	973985	974025	E070	-48654
chr1	974027	974101	E070	-48578
chr1	974205	974384	E070	-48295
chr1	974767	974823	E070	-47856
chr1	974999	975166	E070	-47513
chr1	1002881	1003029	E070	-19650
chr1	1070290	1070359	E070	47611
chr1	973985	974025	E071	-48654
chr1	974027	974101	E071	-48578
chr1	974205	974384	E071	-48295
chr1	974767	974823	E071	-47856
chr1	974999	975166	E071	-47513
chr1	1034310	1034946	E071	11631
chr1	1058049	1058200	E071	35370
chr1	1058208	1058822	E071	35529
chr1	972752	972843	E072	-49836
chr1	973168	973320	E072	-49359
chr1	973379	973430	E072	-49249
chr1	973489	973641	E072	-49038
chr1	973695	973795	E072	-48884
chr1	973985	974025	E072	-48654
chr1	974027	974101	E072	-48578
chr1	974205	974384	E072	-48295
chr1	974767	974823	E072	-47856
chr1	974999	975166	E072	-47513
chr1	1034310	1034946	E072	11631
chr1	1058049	1058200	E072	35370
chr1	1058208	1058822	E072	35529
chr1	972752	972843	E073	-49836
chr1	973168	973320	E073	-49359
chr1	973379	973430	E073	-49249
chr1	973489	973641	E073	-49038
chr1	973695	973795	E073	-48884
chr1	973985	974025	E073	-48654
chr1	974027	974101	E073	-48578
chr1	974205	974384	E073	-48295
chr1	974767	974823	E073	-47856
chr1	974999	975166	E073	-47513
chr1	986142	986404	E073	-36275
chr1	1016370	1016468	E073	-6211
chr1	1052659	1052846	E073	29980
chr1	1034310	1034946	E074	11631
chr1	1043430	1043581	E074	20751
chr1	1052659	1052846	E074	29980
chr1	1058049	1058200	E074	35370
chr1	1058208	1058822	E074	35529
chr1	973168	973320	E081	-49359
chr1	973379	973430	E081	-49249
chr1	973489	973641	E081	-49038
chr1	973695	973795	E081	-48884
chr1	973985	974025	E081	-48654
chr1	974027	974101	E081	-48578
chr1	974205	974384	E081	-48295
chr1	974767	974823	E081	-47856
chr1	974999	975166	E081	-47513
chr1	1002881	1003029	E081	-19650
chr1	1052659	1052846	E081	29980
chr1	1052909	1053225	E081	30230
chr1	1070290	1070359	E081	47611
chr1	1070674	1071648	E081	47995
chr1	973489	973641	E082	-49038
chr1	973695	973795	E082	-48884
chr1	973985	974025	E082	-48654
chr1	974027	974101	E082	-48578
chr1	974205	974384	E082	-48295
chr1	974767	974823	E082	-47856

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	975518	975606	E067	-47073
chr1	994015	995554	E067	-27125
chr1	1003841	1005074	E067	-17605
chr1	1050405	1050863	E067	27726
chr1	1051044	1051109	E067	28365
chr1	1051131	1052445	E067	28452
chr1	975518	975606	E068	-47073
chr1	975975	976470	E068	-46209
chr1	994015	995554	E068	-27125
chr1	1050405	1050863	E068	27726
chr1	1051044	1051109	E068	28365
chr1	1051131	1052445	E068	28452
chr1	975518	975606	E069	-47073
chr1	975975	976470	E069	-46209
chr1	976502	976882	E069	-45797
chr1	994015	995554	E069	-27125
chr1	1003841	1005074	E069	-17605
chr1	1005082	1005282	E069	-17397
chr1	1050405	1050863	E069	27726
chr1	1051044	1051109	E069	28365
chr1	1051131	1052445	E069	28452
chr1	975518	975606	E070	-47073
chr1	975975	976470	E070	-46209
chr1	976502	976882	E070	-45797
chr1	1003841	1005074	E070	-17605
chr1	1005082	1005282	E070	-17397
chr1	1050405	1050863	E070	27726
chr1	1051044	1051109	E070	28365
chr1	1051131	1052445	E070	28452
chr1	975518	975606	E071	-47073
chr1	994015	995554	E071	-27125
chr1	1050405	1050863	E071	27726
chr1	1051044	1051109	E071	28365
chr1	1051131	1052445	E071	28452
chr1	975518	975606	E072	-47073
chr1	994015	995554	E072	-27125
chr1	1003841	1005074	E072	-17605
chr1	1050405	1050863	E072	27726
chr1	1051044	1051109	E072	28365
chr1	1051131	1052445	E072	28452
chr1	975518	975606	E073	-47073
chr1	975975	976470	E073	-46209
chr1	994015	995554	E073	-27125
chr1	1003841	1005074	E073	-17605
chr1	1005082	1005282	E073	-17397
chr1	1050405	1050863	E073	27726
chr1	1051044	1051109	E073	28365
chr1	1051131	1052445	E073	28452
chr1	994015	995554	E074	-27125
chr1	1051131	1052445	E074	28452
chr1	975518	975606	E082	-47073
chr1	975975	976470	E082	-46209
chr1	976502	976882	E082	-45797
chr1	994015	995554	E082	-27125
chr1	1003841	1005074	E082	-17605
chr1	1005082	1005282	E082	-17397
chr1	1050405	1050863	E082	27726
chr1	1051044	1051109	E082	28365
chr1	1051131	1052445	E082	28452