rs1410587

Organism: Homo sapiens

Alleles: C>G / C>T

Gene : Feature

AXDND1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0405 (12132/29912,GnomAD)
C==0408 (11902/29118,TOPMED)
C==0443 (2218/5008,1000G)
C==0468 (1802/3854,ALSPAC)
C==0455 (1688/3708,TWINSUK)

Position: chr1:179546937 (GRCh38.p7) (1q25.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 264 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.179546937C>G
GRCh38.p7 chr 1	NC_000001.11:g.179546937C>T
GRCh37.p13 chr 1	NC_000001.10:g.179516072C>G
GRCh37.p13 chr 1	NC_000001.10:g.179516072C>T
AXDND1 RefSeqGene	NG_033075.1:g.186218C>G
AXDND1 RefSeqGene	NG_033075.1:g.186218C>T

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	C=0.277	T=0.723
1000Genomes	American	Sub	694	C=0.470	T=0.530
1000Genomes	East Asian	Sub	1008	C=0.474	T=0.526
1000Genomes	Europe	Sub	1006	C=0.498	T=0.502
1000Genomes	Global	Study-wide	5008	C=0.443	T=0.557
1000Genomes	South Asian	Sub	978	C=0.560	T=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.468	T=0.532
The Genome Aggregation Database	African	Sub	8704	C=0.297	G=0.000
The Genome Aggregation Database	American	Sub	834	C=0.480	G=0.00,
The Genome Aggregation Database	East Asian	Sub	1608	C=0.438	G=0.000
The Genome Aggregation Database	Europe	Sub	18466	C=0.450	G=0.000
The Genome Aggregation Database	Global	Study-wide	29912	C=0.405	G=0.000
The Genome Aggregation Database	Other	Sub	300	C=0.420	G=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.408	T=0.591
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.455	T=0.545

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs1410587	0.0006	alcohol dependence	20201924

eQTL of rs1410587 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:179516072	TDRD5	ENSG00000162782.11	C>T	4.5502e-23	-44676	Cerebellum
Chr1:179516072	TDRD5	ENSG00000162782.11	C>T	5.6214e-10	-44676	Frontal_Cortex_BA9
Chr1:179516072	TDRD5	ENSG00000162782.11	C>T	3.7157e-14	-44676	Cortex

meQTL of rs1410587 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	35643934	35644954	E067	-33757
chr1	35645055	35645141	E067	-33570
chr1	35645307	35645362	E067	-33349
chr1	35645418	35645565	E067	-33146
chr1	35645624	35645777	E067	-32934
chr1	35645784	35645992	E067	-32719
chr1	35646072	35646178	E067	-32533
chr1	35646397	35646653	E067	-32058
chr1	35646720	35646837	E067	-31874
chr1	35646851	35646951	E067	-31760
chr1	35647466	35647540	E067	-31171
chr1	35647549	35647651	E067	-31060
chr1	35647692	35647778	E067	-30933
chr1	35648058	35648191	E067	-30520
chr1	35648556	35648606	E067	-30105
chr1	35648632	35648672	E067	-30039
chr1	35650148	35650202	E067	-28509
chr1	35650241	35650298	E067	-28413
chr1	35650521	35650585	E067	-28126
chr1	35650636	35650724	E067	-27987
chr1	35650829	35650869	E067	-27842
chr1	35651073	35651212	E067	-27499
chr1	35651394	35651480	E067	-27231
chr1	35651665	35651816	E067	-26895
chr1	35651888	35651938	E067	-26773
chr1	35652060	35652124	E067	-26587
chr1	35652185	35652425	E067	-26286
chr1	35652603	35652680	E067	-26031
chr1	35652776	35652840	E067	-25871
chr1	35653598	35653714	E067	-24997
chr1	35653848	35653931	E067	-24780
chr1	35653995	35654158	E067	-24553
chr1	35654204	35654264	E067	-24447
chr1	35654396	35654464	E067	-24247
chr1	35654596	35654855	E067	-23856
chr1	35655023	35655106	E067	-23605
chr1	35643934	35644954	E068	-33757
chr1	35645055	35645141	E068	-33570
chr1	35645307	35645362	E068	-33349
chr1	35645418	35645565	E068	-33146
chr1	35645624	35645777	E068	-32934
chr1	35645784	35645992	E068	-32719
chr1	35646072	35646178	E068	-32533
chr1	35646397	35646653	E068	-32058
chr1	35646720	35646837	E068	-31874
chr1	35646851	35646951	E068	-31760
chr1	35648556	35648606	E068	-30105
chr1	35648632	35648672	E068	-30039
chr1	35649120	35649160	E068	-29551
chr1	35649277	35649327	E068	-29384
chr1	35649379	35649639	E068	-29072
chr1	35652060	35652124	E068	-26587
chr1	35652185	35652425	E068	-26286
chr1	35652603	35652680	E068	-26031
chr1	35652776	35652840	E068	-25871
chr1	35653598	35653714	E068	-24997
chr1	35653848	35653931	E068	-24780
chr1	35653995	35654158	E068	-24553
chr1	35654204	35654264	E068	-24447
chr1	35654396	35654464	E068	-24247
chr1	35654596	35654855	E068	-23856
chr1	35667655	35668280	E068	-10431
chr1	35643934	35644954	E069	-33757
chr1	35645055	35645141	E069	-33570
chr1	35645307	35645362	E069	-33349
chr1	35645418	35645565	E069	-33146
chr1	35645624	35645777	E069	-32934
chr1	35645784	35645992	E069	-32719
chr1	35646072	35646178	E069	-32533
chr1	35646397	35646653	E069	-32058
chr1	35646720	35646837	E069	-31874
chr1	35646851	35646951	E069	-31760
chr1	35650148	35650202	E069	-28509
chr1	35650241	35650298	E069	-28413
chr1	35650521	35650585	E069	-28126
chr1	35650636	35650724	E069	-27987
chr1	35650829	35650869	E069	-27842
chr1	35651073	35651212	E069	-27499
chr1	35651394	35651480	E069	-27231
chr1	35651665	35651816	E069	-26895
chr1	35651888	35651938	E069	-26773
chr1	35652060	35652124	E069	-26587
chr1	35652185	35652425	E069	-26286
chr1	35652603	35652680	E069	-26031
chr1	35652776	35652840	E069	-25871
chr1	35653598	35653714	E069	-24997
chr1	35653848	35653931	E069	-24780
chr1	35653995	35654158	E069	-24553
chr1	35654204	35654264	E069	-24447
chr1	35654396	35654464	E069	-24247
chr1	35654596	35654855	E069	-23856
chr1	35655023	35655106	E069	-23605
chr1	35655268	35655336	E069	-23375
chr1	35667655	35668280	E069	-10431
chr1	35675830	35676630	E069	-2081
chr1	35646072	35646178	E070	-32533
chr1	35646397	35646653	E070	-32058
chr1	35646720	35646837	E070	-31874
chr1	35646851	35646951	E070	-31760
chr1	35647466	35647540	E070	-31171
chr1	35647549	35647651	E070	-31060
chr1	35647692	35647778	E070	-30933
chr1	35648058	35648191	E070	-30520
chr1	35648556	35648606	E070	-30105
chr1	35648632	35648672	E070	-30039
chr1	35649120	35649160	E070	-29551
chr1	35649277	35649327	E070	-29384
chr1	35649379	35649639	E070	-29072
chr1	35650057	35650107	E070	-28604
chr1	35650148	35650202	E070	-28509
chr1	35650241	35650298	E070	-28413
chr1	35650521	35650585	E070	-28126
chr1	35651665	35651816	E070	-26895
chr1	35651888	35651938	E070	-26773
chr1	35652060	35652124	E070	-26587
chr1	35652185	35652425	E070	-26286
chr1	35652603	35652680	E070	-26031
chr1	35652776	35652840	E070	-25871
chr1	35653598	35653714	E070	-24997
chr1	35653848	35653931	E070	-24780
chr1	35653995	35654158	E070	-24553
chr1	35654204	35654264	E070	-24447
chr1	35654396	35654464	E070	-24247
chr1	35666820	35667036	E070	-11675
chr1	35667042	35667102	E070	-11609
chr1	35667352	35667406	E070	-11305
chr1	35667655	35668280	E070	-10431
chr1	35675830	35676630	E070	-2081
chr1	35687031	35687159	E070	8320
chr1	35688003	35688873	E070	9292
chr1	35688989	35689134	E070	10278
chr1	35643934	35644954	E071	-33757
chr1	35645055	35645141	E071	-33570
chr1	35645307	35645362	E071	-33349
chr1	35645418	35645565	E071	-33146
chr1	35645624	35645777	E071	-32934
chr1	35645784	35645992	E071	-32719
chr1	35646072	35646178	E071	-32533
chr1	35646397	35646653	E071	-32058
chr1	35646720	35646837	E071	-31874
chr1	35646851	35646951	E071	-31760
chr1	35648058	35648191	E071	-30520
chr1	35648556	35648606	E071	-30105
chr1	35650829	35650869	E071	-27842
chr1	35651073	35651212	E071	-27499
chr1	35652185	35652425	E071	-26286
chr1	35652603	35652680	E071	-26031
chr1	35652776	35652840	E071	-25871
chr1	35653995	35654158	E071	-24553
chr1	35654204	35654264	E071	-24447
chr1	35654396	35654464	E071	-24247
chr1	35654596	35654855	E071	-23856
chr1	35655023	35655106	E071	-23605
chr1	35667655	35668280	E071	-10431
chr1	35675830	35676630	E071	-2081
chr1	35645624	35645777	E072	-32934
chr1	35645784	35645992	E072	-32719
chr1	35646072	35646178	E072	-32533
chr1	35646397	35646653	E072	-32058
chr1	35646720	35646837	E072	-31874
chr1	35648058	35648191	E072	-30520
chr1	35650057	35650107	E072	-28604
chr1	35650148	35650202	E072	-28509
chr1	35650241	35650298	E072	-28413
chr1	35650521	35650585	E072	-28126
chr1	35650636	35650724	E072	-27987
chr1	35650829	35650869	E072	-27842
chr1	35651073	35651212	E072	-27499
chr1	35651394	35651480	E072	-27231
chr1	35651665	35651816	E072	-26895
chr1	35651888	35651938	E072	-26773
chr1	35652060	35652124	E072	-26587
chr1	35652185	35652425	E072	-26286
chr1	35652603	35652680	E072	-26031
chr1	35652776	35652840	E072	-25871
chr1	35654204	35654264	E072	-24447
chr1	35654396	35654464	E072	-24247
chr1	35654596	35654855	E072	-23856
chr1	35655023	35655106	E072	-23605
chr1	35675830	35676630	E072	-2081
chr1	35645055	35645141	E073	-33570
chr1	35645307	35645362	E073	-33349
chr1	35645418	35645565	E073	-33146
chr1	35645624	35645777	E073	-32934
chr1	35645784	35645992	E073	-32719
chr1	35646072	35646178	E073	-32533
chr1	35646397	35646653	E073	-32058
chr1	35646720	35646837	E073	-31874
chr1	35646851	35646951	E073	-31760
chr1	35650148	35650202	E073	-28509
chr1	35650241	35650298	E073	-28413
chr1	35650521	35650585	E073	-28126
chr1	35650636	35650724	E073	-27987
chr1	35650829	35650869	E073	-27842
chr1	35651073	35651212	E073	-27499
chr1	35651394	35651480	E073	-27231
chr1	35651665	35651816	E073	-26895
chr1	35651888	35651938	E073	-26773
chr1	35652060	35652124	E073	-26587
chr1	35652185	35652425	E073	-26286
chr1	35653598	35653714	E073	-24997
chr1	35653848	35653931	E073	-24780
chr1	35653995	35654158	E073	-24553
chr1	35654204	35654264	E073	-24447
chr1	35654396	35654464	E073	-24247
chr1	35654596	35654855	E073	-23856
chr1	35655023	35655106	E073	-23605
chr1	35667655	35668280	E073	-10431
chr1	35645784	35645992	E074	-32719
chr1	35646072	35646178	E074	-32533
chr1	35646397	35646653	E074	-32058
chr1	35646720	35646837	E074	-31874
chr1	35646851	35646951	E074	-31760
chr1	35648058	35648191	E074	-30520
chr1	35648556	35648606	E074	-30105
chr1	35651665	35651816	E074	-26895
chr1	35651888	35651938	E074	-26773
chr1	35652060	35652124	E074	-26587
chr1	35653598	35653714	E074	-24997
chr1	35653848	35653931	E074	-24780
chr1	35653995	35654158	E074	-24553
chr1	35654204	35654264	E074	-24447
chr1	35654396	35654464	E074	-24247
chr1	35654596	35654855	E074	-23856
chr1	35655023	35655106	E074	-23605
chr1	35655268	35655336	E074	-23375
chr1	35655572	35655720	E074	-22991
chr1	35655841	35655892	E074	-22819
chr1	35667655	35668280	E074	-10431
chr1	35645418	35645565	E081	-33146
chr1	35651665	35651816	E081	-26895
chr1	35651888	35651938	E081	-26773
chr1	35652060	35652124	E081	-26587
chr1	35652185	35652425	E081	-26286
chr1	35652603	35652680	E081	-26031
chr1	35652776	35652840	E081	-25871
chr1	35654596	35654855	E081	-23856
chr1	35655023	35655106	E081	-23605
chr1	35655268	35655336	E081	-23375
chr1	35667655	35668280	E081	-10431
chr1	35688003	35688873	E081	9292
chr1	35688989	35689134	E081	10278
chr1	35643934	35644954	E082	-33757
chr1	35645055	35645141	E082	-33570
chr1	35645307	35645362	E082	-33349
chr1	35645418	35645565	E082	-33146
chr1	35645624	35645777	E082	-32934
chr1	35645784	35645992	E082	-32719
chr1	35646072	35646178	E082	-32533
chr1	35646397	35646653	E082	-32058
chr1	35646720	35646837	E082	-31874
chr1	35646851	35646951	E082	-31760
chr1	35647466	35647540	E082	-31171
chr1	35647549	35647651	E082	-31060
chr1	35650057	35650107	E082	-28604
chr1	35651665	35651816	E082	-26895
chr1	35651888	35651938	E082	-26773
chr1	35652060	35652124	E082	-26587
chr1	35652185	35652425	E082	-26286
chr1	35652603	35652680	E082	-26031
chr1	35652776	35652840	E082	-25871
chr1	35653995	35654158	E082	-24553
chr1	35654204	35654264	E082	-24447
chr1	35654396	35654464	E082	-24247

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	35657032	35659526	E067	-19185
chr1	35657032	35659526	E068	-19185
chr1	35657032	35659526	E069	-19185
chr1	35657032	35659526	E070	-19185
chr1	35657032	35659526	E071	-19185
chr1	35657032	35659526	E072	-19185
chr1	35657032	35659526	E073	-19185
chr1	35657032	35659526	E074	-19185
chr1	35657032	35659526	E082	-19185