rs17427473

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

DYNC1I2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0249 (7459/29924,GnomAD)
G=0220 (6419/29118,TOPMED)
G=0201 (1005/5008,1000G)
G=0332 (1278/3854,ALSPAC)
G=0344 (1276/3708,TWINSUK)

Position: chr2:171719501 (GRCh38.p7) (2q31.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 97 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.171719501A>G
GRCh37.p13 chr 2	NC_000002.11:g.172576011A>G

Gene: DYNC1I2, dynein cytoplasmic 1 intermediate chain 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DYNC1I2 transcript variant 2	NM_001271785.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 3	NM_001271786.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 4	NM_001271787.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 5	NM_001271788.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 6	NM_001271789.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 7	NM_001271790.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 9	NM_001320882.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 10	NM_001320883.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 8	NM_001320884.1:c.	N/A	Intron Variant
DYNC1I2 transcript variant 1	NM_001378.2:c.	N/A	Intron Variant
DYNC1I2 transcript variant X1	XM_006712347.3:c.	N/A	Intron Variant
DYNC1I2 transcript variant X2	XM_017003525.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.957	G=0.043
1000Genomes	American	Sub	694	A=0.770	G=0.230
1000Genomes	East Asian	Sub	1008	A=0.903	G=0.097
1000Genomes	Europe	Sub	1006	A=0.658	G=0.342
1000Genomes	Global	Study-wide	5008	A=0.799	G=0.201
1000Genomes	South Asian	Sub	978	A=0.650	G=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.668	G=0.332
The Genome Aggregation Database	African	Sub	8716	A=0.914	G=0.086
The Genome Aggregation Database	American	Sub	836	A=0.740	G=0.260
The Genome Aggregation Database	East Asian	Sub	1614	A=0.890	G=0.110
The Genome Aggregation Database	Europe	Sub	18458	A=0.662	G=0.337
The Genome Aggregation Database	Global	Study-wide	29924	A=0.750	G=0.249
The Genome Aggregation Database	Other	Sub	300	A=0.690	G=0.310
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.779	G=0.220
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.656	G=0.344

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

P-Value

SNP ID	p-value	Traits	Study
rs17427473	0.000532	nicotine dependence	17158188

eQTL of rs17427473 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:172576011	SLC25A12	ENSG00000115840.9	A>G	7.7077e-9	-280341	Cerebellum
Chr2:172576011	METAP1D	ENSG00000172878.9	A>G	2.5178e-3	-288479	Cerebellum
Chr2:172576011	METAP1D	ENSG00000172878.9	A>G	9.7963e-3	-288479	Frontal_Cortex_BA9
Chr2:172576011	METAP1D	ENSG00000172878.9	A>G	1.0867e-3	-288479	Cortex
Chr2:172576011	AC068039.4	ENSG00000228389.1	A>G	1.6830e-25	-53981	Cerebellar_Hemisphere
Chr2:172576011	AC068039.4	ENSG00000228389.1	A>G	3.3883e-13	-53981	Hippocampus
Chr2:172576011	AC068039.4	ENSG00000228389.1	A>G	2.6066e-20	-53981	Anterior_cingulate_cortex
Chr2:172576011	METAP1D	ENSG00000172878.9	A>G	1.6879e-3	-288479	Anterior_cingulate_cortex

meQTL of rs17427473 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	172546016	172546078	E067	-29933
chr2	172560214	172560438	E067	-15573
chr2	172560469	172560586	E067	-15425
chr2	172560665	172560765	E067	-15246
chr2	172592706	172592901	E067	16695
chr2	172619868	172620090	E067	43857
chr2	172546016	172546078	E068	-29933
chr2	172580202	172580512	E068	4191
chr2	172580782	172581251	E068	4771
chr2	172592706	172592901	E068	16695
chr2	172597825	172598067	E068	21814
chr2	172619577	172619659	E068	43566
chr2	172619868	172620090	E068	43857
chr2	172620216	172620417	E068	44205
chr2	172558461	172558533	E069	-17478
chr2	172558583	172558666	E069	-17345
chr2	172558745	172558976	E069	-17035
chr2	172559431	172559568	E069	-16443
chr2	172559622	172559685	E069	-16326
chr2	172560214	172560438	E069	-15573
chr2	172560469	172560586	E069	-15425
chr2	172560665	172560765	E069	-15246
chr2	172580202	172580512	E069	4191
chr2	172580782	172581251	E069	4771
chr2	172592706	172592901	E069	16695
chr2	172558461	172558533	E070	-17478
chr2	172558583	172558666	E070	-17345
chr2	172558745	172558976	E070	-17035
chr2	172560214	172560438	E070	-15573
chr2	172560469	172560586	E070	-15425
chr2	172560665	172560765	E070	-15246
chr2	172562798	172562917	E070	-13094
chr2	172562967	172563091	E070	-12920
chr2	172578833	172579067	E070	2822
chr2	172579281	172579331	E070	3270
chr2	172580202	172580512	E070	4191
chr2	172580782	172581251	E070	4771
chr2	172529311	172529375	E071	-46636
chr2	172546016	172546078	E071	-29933
chr2	172559431	172559568	E071	-16443
chr2	172559622	172559685	E071	-16326
chr2	172560214	172560438	E071	-15573
chr2	172560469	172560586	E071	-15425
chr2	172560665	172560765	E071	-15246
chr2	172568016	172568148	E071	-7863
chr2	172568647	172568879	E071	-7132
chr2	172568919	172569018	E071	-6993
chr2	172569063	172569122	E071	-6889
chr2	172570072	172570227	E071	-5784
chr2	172580202	172580512	E071	4191
chr2	172580782	172581251	E071	4771
chr2	172592706	172592901	E071	16695
chr2	172619577	172619659	E071	43566
chr2	172619868	172620090	E071	43857
chr2	172620216	172620417	E071	44205
chr2	172546016	172546078	E072	-29933
chr2	172558583	172558666	E072	-17345
chr2	172558745	172558976	E072	-17035
chr2	172559431	172559568	E072	-16443
chr2	172559622	172559685	E072	-16326
chr2	172560214	172560438	E072	-15573
chr2	172560469	172560586	E072	-15425
chr2	172560665	172560765	E072	-15246
chr2	172562798	172562917	E072	-13094
chr2	172562967	172563091	E072	-12920
chr2	172580202	172580512	E072	4191
chr2	172580782	172581251	E072	4771
chr2	172560469	172560586	E073	-15425
chr2	172580202	172580512	E073	4191
chr2	172580782	172581251	E073	4771
chr2	172546016	172546078	E074	-29933
chr2	172558583	172558666	E074	-17345
chr2	172558745	172558976	E074	-17035
chr2	172559431	172559568	E074	-16443
chr2	172559622	172559685	E074	-16326
chr2	172560214	172560438	E074	-15573
chr2	172560469	172560586	E074	-15425
chr2	172560665	172560765	E074	-15246
chr2	172580202	172580512	E074	4191
chr2	172580782	172581251	E074	4771
chr2	172619577	172619659	E074	43566
chr2	172619868	172620090	E074	43857
chr2	172620216	172620417	E074	44205
chr2	172546016	172546078	E081	-29933
chr2	172578833	172579067	E081	2822
chr2	172579281	172579331	E081	3270
chr2	172580202	172580512	E081	4191
chr2	172580782	172581251	E081	4771
chr2	172581634	172581694	E081	5623
chr2	172578833	172579067	E082	2822
chr2	172579281	172579331	E082	3270
chr2	172580202	172580512	E082	4191
chr2	172580782	172581251	E082	4771
chr2	172581634	172581694	E082	5623
chr2	172583503	172583648	E082	7492
chr2	172583732	172583894	E082	7721
chr2	172583969	172584019	E082	7958

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	172543627	172545117	E067	-30894
chr2	172545166	172545263	E067	-30748
chr2	172543627	172545117	E068	-30894
chr2	172545166	172545263	E068	-30748
chr2	172543627	172545117	E069	-30894
chr2	172545166	172545263	E069	-30748
chr2	172543627	172545117	E070	-30894
chr2	172545166	172545263	E070	-30748
chr2	172543627	172545117	E071	-30894
chr2	172545166	172545263	E071	-30748
chr2	172543627	172545117	E072	-30894
chr2	172545166	172545263	E072	-30748
chr2	172543627	172545117	E073	-30894
chr2	172545166	172545263	E073	-30748
chr2	172543627	172545117	E074	-30894
chr2	172545166	172545263	E074	-30748
chr2	172543627	172545117	E081	-30894
chr2	172545166	172545263	E081	-30748
chr2	172543627	172545117	E082	-30894
chr2	172545166	172545263	E082	-30748