rs7577450

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

KIF5C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0357 (10688/29898,GnomAD)
A==0332 (9672/29118,TOPMED)
A==0393 (1970/5008,1000G)
A==0395 (1521/3854,ALSPAC)
A==0390 (1446/3708,TWINSUK)

Position: chr2:149019447 (GRCh38.p7) (2q23.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 167 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.149019447A>G
GRCh37.p13 chr 2	NC_000002.11:g.149875961A>G
KIF5C RefSeqGene	NG_042216.1:g.149225A>G
GRCh38.p7 chr 2 alt locus HSCHR2_2_CTG7_2	NW_003571033.2:g.91459A>G

Gene: KIF5C, kinesin family member 5C(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KIF5C transcript variant 1	NM_004522.2:c.	N/A	Intron Variant
KIF5C transcript variant 2	NR_111932.1:n.	N/A	Intron Variant
KIF5C transcript variant X2	XM_011511157.2:c.	N/A	Intron Variant
KIF5C transcript variant X1	XM_017004062.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.222	G=0.778
1000Genomes	American	Sub	694	A=0.360	G=0.640
1000Genomes	East Asian	Sub	1008	A=0.688	G=0.312
1000Genomes	Europe	Sub	1006	A=0.370	G=0.630
1000Genomes	Global	Study-wide	5008	A=0.393	G=0.607
1000Genomes	South Asian	Sub	978	A=0.370	G=0.630
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.395	G=0.605
The Genome Aggregation Database	African	Sub	8690	A=0.264	G=0.736
The Genome Aggregation Database	American	Sub	836	A=0.390	G=0.610
The Genome Aggregation Database	East Asian	Sub	1614	A=0.715	G=0.285
The Genome Aggregation Database	Europe	Sub	18456	A=0.369	G=0.630
The Genome Aggregation Database	Global	Study-wide	29898	A=0.357	G=0.642
The Genome Aggregation Database	Other	Sub	302	A=0.350	G=0.650
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.332	G=0.667
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.390	G=0.610

PMID	Title	Author	Journal

P-Value

SNP ID	p-value	Traits	Study
rs7577450	8.32E-05	alcoholism	pha002893

eQTL of rs7577450 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 rs7577450 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 )
chr2	149830129	149830186	E067	-45775
chr2	149830395	149830510	E067	-45451
chr2	149834655	149834817	E067	-41144
chr2	149834895	149835009	E067	-40952
chr2	149835075	149835233	E067	-40728
chr2	149837906	149838131	E067	-37830
chr2	149838287	149839249	E067	-36712
chr2	149846322	149846408	E067	-29553
chr2	149846459	149846723	E067	-29238
chr2	149854829	149854927	E067	-21034
chr2	149855158	149855224	E067	-20737
chr2	149855279	149855333	E067	-20628
chr2	149855461	149855550	E067	-20411
chr2	149855746	149855800	E067	-20161
chr2	149855877	149856491	E067	-19470
chr2	149856612	149856662	E067	-19299
chr2	149856819	149856947	E067	-19014
chr2	149873784	149874238	E067	-1723
chr2	149834655	149834817	E068	-41144
chr2	149834895	149835009	E068	-40952
chr2	149835075	149835233	E068	-40728
chr2	149835289	149835514	E068	-40447
chr2	149835552	149835655	E068	-40306
chr2	149838287	149839249	E068	-36712
chr2	149854829	149854927	E068	-21034
chr2	149855158	149855224	E068	-20737
chr2	149855279	149855333	E068	-20628
chr2	149855461	149855550	E068	-20411
chr2	149855746	149855800	E068	-20161
chr2	149855877	149856491	E068	-19470
chr2	149856612	149856662	E068	-19299
chr2	149856819	149856947	E068	-19014
chr2	149857160	149857268	E068	-18693
chr2	149873784	149874238	E068	-1723
chr2	149826159	149826476	E069	-49485
chr2	149834655	149834817	E069	-41144
chr2	149834895	149835009	E069	-40952
chr2	149835289	149835514	E069	-40447
chr2	149838287	149839249	E069	-36712
chr2	149854829	149854927	E069	-21034
chr2	149855158	149855224	E069	-20737
chr2	149855877	149856491	E069	-19470
chr2	149856612	149856662	E069	-19299
chr2	149856819	149856947	E069	-19014
chr2	149857160	149857268	E069	-18693
chr2	149858124	149858274	E069	-17687
chr2	149859275	149859325	E069	-16636
chr2	149873784	149874238	E069	-1723
chr2	149874326	149874761	E069	-1200
chr2	149835728	149835895	E070	-40066
chr2	149835963	149836031	E070	-39930
chr2	149836130	149836461	E070	-39500
chr2	149836507	149836579	E070	-39382
chr2	149855158	149855224	E070	-20737
chr2	149855279	149855333	E070	-20628
chr2	149855461	149855550	E070	-20411
chr2	149855746	149855800	E070	-20161
chr2	149855877	149856491	E070	-19470
chr2	149884133	149884705	E070	8172
chr2	149884750	149884924	E070	8789
chr2	149838287	149839249	E071	-36712
chr2	149847685	149847747	E071	-28214
chr2	149854829	149854927	E071	-21034
chr2	149855158	149855224	E071	-20737
chr2	149855279	149855333	E071	-20628
chr2	149855461	149855550	E071	-20411
chr2	149855746	149855800	E071	-20161
chr2	149855877	149856491	E071	-19470
chr2	149856612	149856662	E071	-19299
chr2	149856819	149856947	E071	-19014
chr2	149857160	149857268	E071	-18693
chr2	149858124	149858274	E071	-17687
chr2	149873784	149874238	E071	-1723
chr2	149878345	149878523	E071	2384
chr2	149826159	149826476	E072	-49485
chr2	149830129	149830186	E072	-45775
chr2	149830395	149830510	E072	-45451
chr2	149834655	149834817	E072	-41144
chr2	149834895	149835009	E072	-40952
chr2	149835075	149835233	E072	-40728
chr2	149835289	149835514	E072	-40447
chr2	149835963	149836031	E072	-39930
chr2	149836130	149836461	E072	-39500
chr2	149836507	149836579	E072	-39382
chr2	149838287	149839249	E072	-36712
chr2	149846322	149846408	E072	-29553
chr2	149846459	149846723	E072	-29238
chr2	149854829	149854927	E072	-21034
chr2	149855158	149855224	E072	-20737
chr2	149855279	149855333	E072	-20628
chr2	149855461	149855550	E072	-20411
chr2	149855746	149855800	E072	-20161
chr2	149855877	149856491	E072	-19470
chr2	149856612	149856662	E072	-19299
chr2	149856819	149856947	E072	-19014
chr2	149857160	149857268	E072	-18693
chr2	149858124	149858274	E072	-17687
chr2	149859275	149859325	E072	-16636
chr2	149873784	149874238	E072	-1723
chr2	149830129	149830186	E073	-45775
chr2	149834655	149834817	E073	-41144
chr2	149834895	149835009	E073	-40952
chr2	149835075	149835233	E073	-40728
chr2	149835963	149836031	E073	-39930
chr2	149836130	149836461	E073	-39500
chr2	149836507	149836579	E073	-39382
chr2	149846322	149846408	E073	-29553
chr2	149846459	149846723	E073	-29238
chr2	149854829	149854927	E073	-21034
chr2	149855158	149855224	E073	-20737
chr2	149855279	149855333	E073	-20628
chr2	149855461	149855550	E073	-20411
chr2	149855746	149855800	E073	-20161
chr2	149855877	149856491	E073	-19470
chr2	149856612	149856662	E073	-19299
chr2	149856819	149856947	E073	-19014
chr2	149858124	149858274	E073	-17687
chr2	149859275	149859325	E073	-16636
chr2	149862077	149862614	E073	-13347
chr2	149873784	149874238	E073	-1723
chr2	149837906	149838131	E074	-37830
chr2	149838287	149839249	E074	-36712
chr2	149846322	149846408	E074	-29553
chr2	149846459	149846723	E074	-29238
chr2	149847685	149847747	E074	-28214
chr2	149855158	149855224	E074	-20737
chr2	149855279	149855333	E074	-20628
chr2	149855461	149855550	E074	-20411
chr2	149855746	149855800	E074	-20161
chr2	149855877	149856491	E074	-19470
chr2	149856612	149856662	E074	-19299
chr2	149856819	149856947	E074	-19014
chr2	149857160	149857268	E074	-18693
chr2	149858124	149858274	E074	-17687
chr2	149878345	149878523	E074	2384
chr2	149826159	149826476	E081	-49485
chr2	149834655	149834817	E081	-41144
chr2	149834895	149835009	E081	-40952
chr2	149835075	149835233	E081	-40728
chr2	149835289	149835514	E081	-40447
chr2	149837906	149838131	E081	-37830
chr2	149838287	149839249	E081	-36712
chr2	149854829	149854927	E081	-21034
chr2	149855158	149855224	E081	-20737
chr2	149855279	149855333	E081	-20628
chr2	149855461	149855550	E081	-20411
chr2	149855746	149855800	E081	-20161
chr2	149855877	149856491	E081	-19470
chr2	149856612	149856662	E081	-19299
chr2	149856819	149856947	E081	-19014
chr2	149858124	149858274	E081	-17687
chr2	149859275	149859325	E081	-16636
chr2	149826159	149826476	E082	-49485
chr2	149835552	149835655	E082	-40306
chr2	149835728	149835895	E082	-40066
chr2	149835963	149836031	E082	-39930
chr2	149836130	149836461	E082	-39500
chr2	149836507	149836579	E082	-39382
chr2	149837906	149838131	E082	-37830
chr2	149854829	149854927	E082	-21034
chr2	149855158	149855224	E082	-20737
chr2	149855279	149855333	E082	-20628
chr2	149855461	149855550	E082	-20411
chr2	149855746	149855800	E082	-20161
chr2	149855877	149856491	E082	-19470
chr2	149856612	149856662	E082	-19299
chr2	149856819	149856947	E082	-19014

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	149895682	149895807	E067	19721
chr2	149894497	149895676	E069	18536
chr2	149895682	149895807	E069	19721
chr2	149894497	149895676	E070	18536
chr2	149895682	149895807	E070	19721
chr2	149894497	149895676	E071	18536
chr2	149894497	149895676	E072	18536
chr2	149894497	149895676	E073	18536
chr2	149894497	149895676	E082	18536
chr2	149895682	149895807	E082	19721