SNP Detail Info-rs2274626

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.179552797G>T
GRCh37.p13 chr 1	NC_000001.10:g.179521932G>T
AXDND1 RefSeqGene	NG_033075.1:g.192078G>T
NPHS2 RefSeqGene	LRG_887

Gene: NPHS2, NPHS2 podocin(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NPHS2 transcript variant 2	NM_001297575.1:c.	N/A	Intron Variant
NPHS2 transcript variant 1	NM_014625.3:c.	N/A	Intron Variant
NPHS2 transcript variant X1	XM_005245483.3:c.	N/A	Intron Variant
NPHS2 transcript variant X2	XM_017002298.1:c.	N/A	Intron Variant
NPHS2 transcript variant X3	XM_017002299.1:c.	N/A	Intron Variant

Gene: AXDND1, axonemal dynein light chain domain containing 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AXDND1 transcript variant 1	NM_144696.5:c.	N/A	Intron Variant
AXDND1 transcript variant 2	NR_073544.1:n.	N/A	Intron Variant
AXDND1 transcript variant X1	XM_011509165.1:c.	N/A	Intron Variant
AXDND1 transcript variant X3	XM_011509166.2:c.	N/A	Intron Variant
AXDND1 transcript variant X2	XM_011509167.2:c.	N/A	Intron Variant
AXDND1 transcript variant X2	XM_011509168.1:c.	N/A	Intron Variant
AXDND1 transcript variant X5	XM_011509169.1:c.	N/A	Intron Variant
AXDND1 transcript variant X6	XM_011509170.1:c.	N/A	Intron Variant
AXDND1 transcript variant X7	XM_011509171.1:c.	N/A	Intron Variant
AXDND1 transcript variant X10	XM_011509174.1:c.	N/A	Intron Variant
AXDND1 transcript variant X11	XM_011509175.1:c.	N/A	Intron Variant
AXDND1 transcript variant X12	XM_011509176.1:c.	N/A	Intron Variant
AXDND1 transcript variant X14	XM_011509179.2:c.	N/A	Intron Variant
AXDND1 transcript variant X21	XM_011509181.2:c.	N/A	Intron Variant
AXDND1 transcript variant X16	XM_017000257.1:c.	N/A	Intron Variant
AXDND1 transcript variant X17	XM_017000258.1:c.	N/A	Intron Variant
AXDND1 transcript variant X20	XM_017000259.1:c.	N/A	Intron Variant
AXDND1 transcript variant X13	XM_011509178.2:c.	N/A	Genic Downstream Transcript Variant
AXDND1 transcript variant X15	XM_011509180.1:c.	N/A	Genic Downstream Transcript Variant
AXDND1 transcript variant X16	XR_921741.1:n.	N/A	Genic Downstream Transcript Variant
AXDND1 transcript variant X17	XR_921742.2:n.	N/A	Genic Downstream Transcript Variant
AXDND1 transcript variant X18	XR_921743.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.427	T=0.573
1000Genomes	American	Sub	694	G=0.570	T=0.430
1000Genomes	East Asian	Sub	1008	G=0.548	T=0.452
1000Genomes	Europe	Sub	1006	G=0.625	T=0.375
1000Genomes	Global	Study-wide	5008	G=0.538	T=0.462
1000Genomes	South Asian	Sub	978	G=0.560	T=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.651	T=0.349
The Genome Aggregation Database	African	Sub	8704	G=0.446	T=0.554
The Genome Aggregation Database	American	Sub	838	G=0.580	T=0.420
The Genome Aggregation Database	East Asian	Sub	1606	G=0.580	T=0.420
The Genome Aggregation Database	Europe	Sub	18482	G=0.661	T=0.338
The Genome Aggregation Database	Global	Study-wide	29932	G=0.592	T=0.407
The Genome Aggregation Database	Other	Sub	302	G=0.680	T=0.320
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.537	T=0.462
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.663	T=0.337

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
17903305	A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study.	Murabito JM	BMC Med Genet

P-Value

SNP ID	p-value	Traits	Study
rs2274626	0.00078	alcohol dependence	20201924

eQTL of rs2274626 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:179521932	TDRD5	ENSG00000162782.11	G>T	4.5502e-23	-38816	Cerebellum
Chr1:179521932	TDRD5	ENSG00000162782.11	G>T	5.6214e-10	-38816	Frontal_Cortex_BA9
Chr1:179521932	TDRD5	ENSG00000162782.11	G>T	3.1814e-16	-38816	Hypothalamus
Chr1:179521932	TDRD5	ENSG00000162782.11	G>T	3.7157e-14	-38816	Cortex
Chr1:179521932	TDRD5	ENSG00000162782.11	G>T	1.0260e-15	-38816	Cerebellar_Hemisphere
Chr1:179521932	TDRD5	ENSG00000162782.11	G>T	2.0170e-8	-38816	Anterior_cingulate_cortex

meQTL of rs2274626 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	179555187	179555994	E067	33255
chr1	179555187	179555994	E068	33255
chr1	179560610	179561210	E068	38678
chr1	179561345	179561526	E068	39413
chr1	179555187	179555994	E069	33255
chr1	179544596	179544720	E070	22664
chr1	179544739	179545058	E070	22807
chr1	179545099	179545388	E070	23167
chr1	179555187	179555994	E070	33255
chr1	179555187	179555994	E071	33255
chr1	179555187	179555994	E072	33255
chr1	179560610	179561210	E072	38678
chr1	179561345	179561526	E072	39413
chr1	179555187	179555994	E073	33255
chr1	179555187	179555994	E074	33255
chr1	179544739	179545058	E082	22807
chr1	179545099	179545388	E082	23167
chr1	179555187	179555994	E082	33255
chr1	179560610	179561210	E082	38678
chr1	179561345	179561526	E082	39413

rs2274626

Genomic Coordinates

Gene: NPHS2, NPHS2 podocin(minus strand)

Gene: AXDND1, axonemal dynein light chain domain containing 1(plus strand)

Population Frequency

P-Value

eQTL of rs2274626 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2274626 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)