rs16982400

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CECR2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0208 (6233/29934,GnomAD)
C=0239 (6976/29116,TOPMED)
C=0239 (1197/5008,1000G)
C=0117 (452/3854,ALSPAC)
C=0116 (431/3708,TWINSUK)

Position: chr22:17418497 (GRCh38.p7) (22q11.21)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 386 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 22	NC_000022.11:g.17418497T>C
GRCh37.p13 chr 22	NC_000022.10:g.17897544T>C
CECR2 RefSeqGene	NG_033989.1:g.63549T>C

Gene: CECR2, cat eye syndrome chromosome region, candidate 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CECR2 transcript variant 2	NM_001290046.1:c.	N/A	Intron Variant
CECR2 transcript variant 1	NM_001290047.1:c.	N/A	Intron Variant
CECR2 transcript variant X2	XM_011546128.2:c.	N/A	Intron Variant
CECR2 transcript variant X3	XM_011546129.2:c.	N/A	Intron Variant
CECR2 transcript variant X5	XM_011546132.2:c.	N/A	Intron Variant
CECR2 transcript variant X1	XM_017028785.1:c.	N/A	Intron Variant
CECR2 transcript variant X6	XM_006724079.3:c.	N/A	Genic Upstream Transcript Variant
CECR2 transcript variant X7	XR_951200.2:n.	N/A	Intron Variant
CECR2 transcript variant X8	XR_951201.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.562	C=0.438
1000Genomes	American	Sub	694	T=0.900	C=0.100
1000Genomes	East Asian	Sub	1008	T=0.816	C=0.184
1000Genomes	Europe	Sub	1006	T=0.865	C=0.135
1000Genomes	Global	Study-wide	5008	T=0.761	C=0.239
1000Genomes	South Asian	Sub	978	T=0.770	C=0.230
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.883	C=0.117
The Genome Aggregation Database	African	Sub	8698	T=0.603	C=0.397
The Genome Aggregation Database	American	Sub	836	T=0.880	C=0.120
The Genome Aggregation Database	East Asian	Sub	1616	T=0.789	C=0.211
The Genome Aggregation Database	Europe	Sub	18482	T=0.874	C=0.125
The Genome Aggregation Database	Global	Study-wide	29934	T=0.791	C=0.208
The Genome Aggregation Database	Other	Sub	302	T=0.940	C=0.060
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.760	C=0.239
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.884	C=0.116

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs16982400	4.06E-05	nicotine smoking	19268276

eQTL of rs16982400 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 rs16982400 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 )
chr22	17859164	17860200	E067	-37344
chr22	17860243	17860654	E067	-36890
chr22	17860690	17860956	E067	-36588
chr22	17861191	17861765	E067	-35779
chr22	17867174	17867534	E067	-30010
chr22	17886495	17886945	E067	-10599
chr22	17889809	17890085	E067	-7459
chr22	17890124	17890240	E067	-7304
chr22	17890273	17890712	E067	-6832
chr22	17890737	17890797	E067	-6747
chr22	17890868	17890922	E067	-6622
chr22	17890975	17891057	E067	-6487
chr22	17892019	17892069	E067	-5475
chr22	17892148	17892329	E067	-5215
chr22	17903480	17903530	E067	5936
chr22	17907900	17908161	E067	10356
chr22	17909176	17909907	E067	11632
chr22	17909946	17910564	E067	12402
chr22	17912255	17912305	E067	14711
chr22	17912591	17912764	E067	15047
chr22	17913662	17913735	E067	16118
chr22	17913841	17914220	E067	16297
chr22	17914258	17914360	E067	16714
chr22	17914384	17914464	E067	16840
chr22	17914519	17914688	E067	16975
chr22	17915384	17916551	E067	17840
chr22	17917159	17917576	E067	19615
chr22	17921876	17922024	E067	24332
chr22	17922095	17922248	E067	24551
chr22	17922340	17922390	E067	24796
chr22	17922479	17922901	E067	24935
chr22	17923099	17923235	E067	25555
chr22	17852011	17852099	E068	-45445
chr22	17852141	17852181	E068	-45363
chr22	17852376	17852530	E068	-45014
chr22	17859164	17860200	E068	-37344
chr22	17860243	17860654	E068	-36890
chr22	17860690	17860956	E068	-36588
chr22	17861191	17861765	E068	-35779
chr22	17867174	17867534	E068	-30010
chr22	17867574	17867640	E068	-29904
chr22	17868228	17868394	E068	-29150
chr22	17878161	17878216	E068	-19328
chr22	17878347	17878397	E068	-19147
chr22	17889809	17890085	E068	-7459
chr22	17890124	17890240	E068	-7304
chr22	17890273	17890712	E068	-6832
chr22	17890737	17890797	E068	-6747
chr22	17890868	17890922	E068	-6622
chr22	17890975	17891057	E068	-6487
chr22	17892019	17892069	E068	-5475
chr22	17892148	17892329	E068	-5215
chr22	17892409	17892549	E068	-4995
chr22	17907900	17908161	E068	10356
chr22	17908427	17908477	E068	10883
chr22	17908480	17908535	E068	10936
chr22	17908739	17908844	E068	11195
chr22	17908893	17908951	E068	11349
chr22	17909176	17909907	E068	11632
chr22	17909946	17910564	E068	12402
chr22	17912255	17912305	E068	14711
chr22	17912591	17912764	E068	15047
chr22	17913158	17913225	E068	15614
chr22	17913424	17913536	E068	15880
chr22	17913662	17913735	E068	16118
chr22	17913841	17914220	E068	16297
chr22	17914258	17914360	E068	16714
chr22	17914384	17914464	E068	16840
chr22	17914519	17914688	E068	16975
chr22	17914969	17915029	E068	17425
chr22	17917159	17917576	E068	19615
chr22	17918405	17918525	E068	20861
chr22	17918812	17918943	E068	21268
chr22	17919020	17919070	E068	21476
chr22	17919645	17919748	E068	22101
chr22	17922479	17922901	E068	24935
chr22	17847786	17848245	E069	-49299
chr22	17848310	17848360	E069	-49184
chr22	17848419	17848469	E069	-49075
chr22	17859164	17860200	E069	-37344
chr22	17860243	17860654	E069	-36890
chr22	17860690	17860956	E069	-36588
chr22	17867174	17867534	E069	-30010
chr22	17867574	17867640	E069	-29904
chr22	17868228	17868394	E069	-29150
chr22	17871307	17871473	E069	-26071
chr22	17890124	17890240	E069	-7304
chr22	17890273	17890712	E069	-6832
chr22	17890737	17890797	E069	-6747
chr22	17890868	17890922	E069	-6622
chr22	17890975	17891057	E069	-6487
chr22	17891277	17891622	E069	-5922
chr22	17891636	17891976	E069	-5568
chr22	17892019	17892069	E069	-5475
chr22	17892148	17892329	E069	-5215
chr22	17903480	17903530	E069	5936
chr22	17903808	17903876	E069	6264
chr22	17907900	17908161	E069	10356
chr22	17908427	17908477	E069	10883
chr22	17908480	17908535	E069	10936
chr22	17908739	17908844	E069	11195
chr22	17908893	17908951	E069	11349
chr22	17909176	17909907	E069	11632
chr22	17912255	17912305	E069	14711
chr22	17912591	17912764	E069	15047
chr22	17913158	17913225	E069	15614
chr22	17913424	17913536	E069	15880
chr22	17913662	17913735	E069	16118
chr22	17913841	17914220	E069	16297
chr22	17914258	17914360	E069	16714
chr22	17914384	17914464	E069	16840
chr22	17914519	17914688	E069	16975
chr22	17914969	17915029	E069	17425
chr22	17917159	17917576	E069	19615
chr22	17918812	17918943	E069	21268
chr22	17919020	17919070	E069	21476
chr22	17922479	17922901	E069	24935
chr22	17923099	17923235	E069	25555
chr22	17939100	17939183	E069	41556
chr22	17939959	17940046	E069	42415
chr22	17940071	17940219	E069	42527
chr22	17847545	17847753	E070	-49791
chr22	17853667	17853717	E070	-43827
chr22	17853830	17853880	E070	-43664
chr22	17853962	17854012	E070	-43532
chr22	17854248	17854324	E070	-43220
chr22	17859164	17860200	E070	-37344
chr22	17860243	17860654	E070	-36890
chr22	17860690	17860956	E070	-36588
chr22	17861191	17861765	E070	-35779
chr22	17866820	17866870	E070	-30674
chr22	17867174	17867534	E070	-30010
chr22	17867574	17867640	E070	-29904
chr22	17871022	17871073	E070	-26471
chr22	17871307	17871473	E070	-26071
chr22	17877723	17877898	E070	-19646
chr22	17877904	17877944	E070	-19600
chr22	17878161	17878216	E070	-19328
chr22	17887023	17887103	E070	-10441
chr22	17887601	17887867	E070	-9677
chr22	17887983	17888070	E070	-9474
chr22	17890124	17890240	E070	-7304
chr22	17890273	17890712	E070	-6832
chr22	17890737	17890797	E070	-6747
chr22	17890868	17890922	E070	-6622
chr22	17890975	17891057	E070	-6487
chr22	17892409	17892549	E070	-4995
chr22	17909176	17909907	E070	11632
chr22	17909946	17910564	E070	12402
chr22	17915384	17916551	E070	17840
chr22	17922479	17922901	E070	24935
chr22	17859164	17860200	E071	-37344
chr22	17860243	17860654	E071	-36890
chr22	17860690	17860956	E071	-36588
chr22	17861191	17861765	E071	-35779
chr22	17866091	17866141	E071	-31403
chr22	17867174	17867534	E071	-30010
chr22	17867574	17867640	E071	-29904
chr22	17870103	17870224	E071	-27320
chr22	17870314	17870467	E071	-27077
chr22	17870912	17870989	E071	-26555
chr22	17871022	17871073	E071	-26471
chr22	17871307	17871473	E071	-26071
chr22	17877904	17877944	E071	-19600
chr22	17878874	17878957	E071	-18587
chr22	17886495	17886945	E071	-10599
chr22	17887023	17887103	E071	-10441
chr22	17889719	17889798	E071	-7746
chr22	17889809	17890085	E071	-7459
chr22	17890124	17890240	E071	-7304
chr22	17890273	17890712	E071	-6832
chr22	17890737	17890797	E071	-6747
chr22	17890868	17890922	E071	-6622
chr22	17890975	17891057	E071	-6487
chr22	17892019	17892069	E071	-5475
chr22	17892148	17892329	E071	-5215
chr22	17903808	17903876	E071	6264
chr22	17907900	17908161	E071	10356
chr22	17908427	17908477	E071	10883
chr22	17908480	17908535	E071	10936
chr22	17908739	17908844	E071	11195
chr22	17908893	17908951	E071	11349
chr22	17909176	17909907	E071	11632
chr22	17909946	17910564	E071	12402
chr22	17910976	17911052	E071	13432
chr22	17911394	17911444	E071	13850
chr22	17911510	17911686	E071	13966
chr22	17912255	17912305	E071	14711
chr22	17912591	17912764	E071	15047
chr22	17913158	17913225	E071	15614
chr22	17913424	17913536	E071	15880
chr22	17913662	17913735	E071	16118
chr22	17913841	17914220	E071	16297
chr22	17914258	17914360	E071	16714
chr22	17914384	17914464	E071	16840
chr22	17914519	17914688	E071	16975
chr22	17914969	17915029	E071	17425
chr22	17915384	17916551	E071	17840
chr22	17917159	17917576	E071	19615
chr22	17917945	17918023	E071	20401
chr22	17918405	17918525	E071	20861
chr22	17918812	17918943	E071	21268
chr22	17919020	17919070	E071	21476
chr22	17920277	17920960	E071	22733
chr22	17921876	17922024	E071	24332
chr22	17922095	17922248	E071	24551
chr22	17922340	17922390	E071	24796
chr22	17922479	17922901	E071	24935
chr22	17939959	17940046	E071	42415
chr22	17940071	17940219	E071	42527
chr22	17940379	17940670	E071	42835
chr22	17940736	17940786	E071	43192
chr22	17859164	17860200	E072	-37344
chr22	17860243	17860654	E072	-36890
chr22	17860690	17860956	E072	-36588
chr22	17861191	17861765	E072	-35779
chr22	17871022	17871073	E072	-26471
chr22	17871307	17871473	E072	-26071
chr22	17877723	17877898	E072	-19646
chr22	17877904	17877944	E072	-19600
chr22	17878161	17878216	E072	-19328
chr22	17878347	17878397	E072	-19147
chr22	17878874	17878957	E072	-18587
chr22	17886495	17886945	E072	-10599
chr22	17889809	17890085	E072	-7459
chr22	17890124	17890240	E072	-7304
chr22	17890273	17890712	E072	-6832
chr22	17890737	17890797	E072	-6747
chr22	17890868	17890922	E072	-6622
chr22	17890975	17891057	E072	-6487
chr22	17891277	17891622	E072	-5922
chr22	17891636	17891976	E072	-5568
chr22	17892019	17892069	E072	-5475
chr22	17892148	17892329	E072	-5215
chr22	17892409	17892549	E072	-4995
chr22	17903480	17903530	E072	5936
chr22	17907900	17908161	E072	10356
chr22	17908427	17908477	E072	10883
chr22	17908480	17908535	E072	10936
chr22	17908739	17908844	E072	11195
chr22	17908893	17908951	E072	11349
chr22	17909176	17909907	E072	11632
chr22	17909946	17910564	E072	12402
chr22	17911394	17911444	E072	13850
chr22	17911510	17911686	E072	13966
chr22	17912255	17912305	E072	14711
chr22	17912591	17912764	E072	15047
chr22	17913158	17913225	E072	15614
chr22	17913424	17913536	E072	15880
chr22	17913662	17913735	E072	16118
chr22	17913841	17914220	E072	16297
chr22	17915384	17916551	E072	17840
chr22	17918812	17918943	E072	21268
chr22	17919020	17919070	E072	21476
chr22	17922479	17922901	E072	24935
chr22	17923099	17923235	E072	25555
chr22	17940071	17940219	E072	42527
chr22	17940379	17940670	E072	42835
chr22	17940736	17940786	E072	43192
chr22	17891636	17891976	E073	-5568
chr22	17892019	17892069	E073	-5475
chr22	17892148	17892329	E073	-5215
chr22	17892409	17892549	E073	-4995
chr22	17903808	17903876	E073	6264
chr22	17904586	17904665	E073	7042
chr22	17909176	17909907	E073	11632
chr22	17909946	17910564	E073	12402
chr22	17914969	17915029	E073	17425
chr22	17915384	17916551	E073	17840
chr22	17847786	17848245	E074	-49299
chr22	17848310	17848360	E074	-49184
chr22	17848419	17848469	E074	-49075
chr22	17858810	17858885	E074	-38659
chr22	17858911	17858961	E074	-38583
chr22	17859164	17860200	E074	-37344
chr22	17860243	17860654	E074	-36890
chr22	17860690	17860956	E074	-36588
chr22	17861191	17861765	E074	-35779
chr22	17870103	17870224	E074	-27320
chr22	17870314	17870467	E074	-27077
chr22	17870912	17870989	E074	-26555
chr22	17871022	17871073	E074	-26471
chr22	17871307	17871473	E074	-26071
chr22	17876505	17876758	E074	-20786
chr22	17876763	17877004	E074	-20540
chr22	17877204	17877244	E074	-20300
chr22	17877723	17877898	E074	-19646
chr22	17877904	17877944	E074	-19600
chr22	17878161	17878216	E074	-19328
chr22	17878347	17878397	E074	-19147
chr22	17879937	17880421	E074	-17123
chr22	17880434	17880618	E074	-16926
chr22	17880757	17880817	E074	-16727
chr22	17886495	17886945	E074	-10599
chr22	17887023	17887103	E074	-10441
chr22	17889719	17889798	E074	-7746
chr22	17889809	17890085	E074	-7459
chr22	17890124	17890240	E074	-7304
chr22	17890273	17890712	E074	-6832
chr22	17890737	17890797	E074	-6747
chr22	17890868	17890922	E074	-6622
chr22	17890975	17891057	E074	-6487
chr22	17892409	17892549	E074	-4995
chr22	17896407	17896457	E074	-1087
chr22	17896542	17896684	E074	-860
chr22	17903480	17903530	E074	5936
chr22	17903808	17903876	E074	6264
chr22	17904586	17904665	E074	7042
chr22	17907900	17908161	E074	10356
chr22	17908427	17908477	E074	10883
chr22	17908480	17908535	E074	10936
chr22	17908739	17908844	E074	11195
chr22	17908893	17908951	E074	11349
chr22	17909176	17909907	E074	11632
chr22	17909946	17910564	E074	12402
chr22	17910976	17911052	E074	13432
chr22	17911394	17911444	E074	13850
chr22	17911510	17911686	E074	13966
chr22	17912255	17912305	E074	14711
chr22	17912591	17912764	E074	15047
chr22	17913158	17913225	E074	15614
chr22	17913424	17913536	E074	15880
chr22	17913662	17913735	E074	16118
chr22	17913841	17914220	E074	16297
chr22	17914258	17914360	E074	16714
chr22	17914384	17914464	E074	16840
chr22	17914519	17914688	E074	16975
chr22	17914969	17915029	E074	17425
chr22	17917159	17917576	E074	19615
chr22	17918812	17918943	E074	21268
chr22	17919020	17919070	E074	21476
chr22	17919645	17919748	E074	22101
chr22	17939959	17940046	E074	42415
chr22	17940071	17940219	E074	42527
chr22	17847786	17848245	E081	-49299
chr22	17848310	17848360	E081	-49184
chr22	17848419	17848469	E081	-49075
chr22	17859164	17860200	E081	-37344
chr22	17860243	17860654	E081	-36890
chr22	17860690	17860956	E081	-36588
chr22	17861191	17861765	E081	-35779
chr22	17886371	17886491	E081	-11053
chr22	17886495	17886945	E081	-10599
chr22	17887023	17887103	E081	-10441
chr22	17887601	17887867	E081	-9677
chr22	17887983	17888070	E081	-9474
chr22	17888239	17888372	E081	-9172
chr22	17889809	17890085	E081	-7459
chr22	17890124	17890240	E081	-7304
chr22	17890273	17890712	E081	-6832
chr22	17890737	17890797	E081	-6747
chr22	17890868	17890922	E081	-6622
chr22	17890975	17891057	E081	-6487
chr22	17891277	17891622	E081	-5922
chr22	17891636	17891976	E081	-5568
chr22	17892019	17892069	E081	-5475
chr22	17892148	17892329	E081	-5215
chr22	17892409	17892549	E081	-4995
chr22	17915384	17916551	E081	17840
chr22	17847786	17848245	E082	-49299
chr22	17848310	17848360	E082	-49184
chr22	17848419	17848469	E082	-49075
chr22	17856172	17856555	E082	-40989
chr22	17859164	17860200	E082	-37344
chr22	17860243	17860654	E082	-36890
chr22	17860690	17860956	E082	-36588
chr22	17861191	17861765	E082	-35779
chr22	17887023	17887103	E082	-10441
chr22	17887601	17887867	E082	-9677
chr22	17887983	17888070	E082	-9474
chr22	17888239	17888372	E082	-9172
chr22	17889809	17890085	E082	-7459
chr22	17890124	17890240	E082	-7304
chr22	17890273	17890712	E082	-6832
chr22	17890737	17890797	E082	-6747
chr22	17890868	17890922	E082	-6622
chr22	17890975	17891057	E082	-6487
chr22	17891277	17891622	E082	-5922
chr22	17892409	17892549	E082	-4995
chr22	17921211	17921261	E082	23667
chr22	17921336	17921397	E082	23792
chr22	17921876	17922024	E082	24332
chr22	17922095	17922248	E082	24551
chr22	17922340	17922390	E082	24796
chr22	17922479	17922901	E082	24935
chr22	17923099	17923235	E082	25555

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr22	17848946	17851539	E067	-46005
chr22	17848946	17851539	E068	-46005
chr22	17851546	17851659	E068	-45885
chr22	17848849	17848938	E069	-48606
chr22	17848946	17851539	E069	-46005
chr22	17848608	17848808	E070	-48736
chr22	17848849	17848938	E070	-48606
chr22	17848946	17851539	E070	-46005
chr22	17851546	17851659	E070	-45885
chr22	17848946	17851539	E071	-46005
chr22	17848946	17851539	E072	-46005
chr22	17851546	17851659	E072	-45885
chr22	17848946	17851539	E073	-46005
chr22	17851546	17851659	E073	-45885
chr22	17848946	17851539	E074	-46005
chr22	17851546	17851659	E074	-45885
chr22	17848946	17851539	E081	-46005
chr22	17851546	17851659	E081	-45885
chr22	17848946	17851539	E082	-46005
chr22	17851546	17851659	E082	-45885