rs2275863

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

TNNT2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0220 (6589/29912,GnomAD)
A=0281 (8186/29118,TOPMED)
G==0224 (2921/13002,GO-ESP)
A=0277 (1388/5008,1000G)
A=0096 (370/3854,ALSPAC)
A=0099 (366/3708,TWINSUK)

Position: chr1:201359696 (GRCh38.p7) (1q32.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 128 Enhancers around

Promoter: 30 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.201359696G>A
GRCh38.p7 chr 1	NC_000001.11:g.201359696G>T
GRCh37.p13 chr 1	NC_000001.10:g.201328824G>A
GRCh37.p13 chr 1	NC_000001.10:g.201328824G>T
TNNT2 RefSeqGene	NG_007556.1:g.22982C>T
TNNT2 RefSeqGene	NG_007556.1:g.22982C>A

Gene: TNNT2, troponin T2, cardiac type(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TNNT2 transcript variant 1	NM_000364.3:c.	N/A	Intron Variant
TNNT2 transcript variant 2	NM_001001430.2:c.	N/A	Intron Variant
TNNT2 transcript variant 3	NM_001001431.2:c.	N/A	Intron Variant
TNNT2 transcript variant 4	NM_001001432.2:c.	N/A	Intron Variant
TNNT2 transcript variant 5	NM_001276345.1:c.	N/A	Intron Variant
TNNT2 transcript variant 6	NM_001276346.1:c.	N/A	Intron Variant
TNNT2 transcript variant 7	NM_001276347.1:c.	N/A	Intron Variant
TNNT2 transcript variant X6	XM_006711508.3:c.	N/A	Intron Variant
TNNT2 transcript variant X7	XM_006711509.3:c.	N/A	Intron Variant
TNNT2 transcript variant X2	XM_011509938.2:c.	N/A	Intron Variant
TNNT2 transcript variant X3	XM_011509939.1:c.	N/A	Intron Variant
TNNT2 transcript variant X4	XM_011509940.2:c.	N/A	Intron Variant
TNNT2 transcript variant X5	XM_011509941.2:c.	N/A	Intron Variant
TNNT2 transcript variant X12	XM_011509942.2:c.	N/A	Intron Variant
TNNT2 transcript variant X13	XM_011509943.2:c.	N/A	Intron Variant
TNNT2 transcript variant X14	XM_011509944.2:c.	N/A	Intron Variant
TNNT2 transcript variant X15	XM_011509946.1:c.	N/A	Intron Variant
TNNT2 transcript variant X7	XM_017002216.1:c.	N/A	Intron Variant
TNNT2 transcript variant X11	XM_017002217.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.456	A=0.544
1000Genomes	American	Sub	694	G=0.900	A=0.100
1000Genomes	East Asian	Sub	1008	G=0.715	A=0.285
1000Genomes	Europe	Sub	1006	G=0.906	A=0.094
1000Genomes	Global	Study-wide	5008	G=0.723	A=0.277
1000Genomes	South Asian	Sub	978	G=0.780	A=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.904	A=0.096
The Genome Aggregation Database	African	Sub	8692	G=0.531	A=0.469
The Genome Aggregation Database	American	Sub	836	G=0.880	A=0.120
The Genome Aggregation Database	East Asian	Sub	1618	G=0.726	A=0.274
The Genome Aggregation Database	Europe	Sub	18464	G=0.895	A=0.104
The Genome Aggregation Database	Global	Study-wide	29912	G=0.779	A=0.220
The Genome Aggregation Database	Other	Sub	302	G=0.870	A=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.718	A=0.281
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.901	A=0.099

PMID	Title	Author	Journal
21529783	A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.	Heath AC	Biol Psychiatry
23233322	Early results of sarcomeric gene screening from the Egyptian National BA-HCM Program.	Kassem HSh	J Cardiovasc Transl Res
24992688	A novel arginine to tryptophan (R144W) mutation in troponin T (cTnT) gene in an indian multigenerational family with dilated cardiomyopathy (FDCM).	Rani DS	PLoS One
25741868	Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.	Richards S	Genet Med

P-Value

SNP ID	p-value	Traits	Study
rs2275863	7.4E-05	alcoholism (heaviness of drinking)	21529783

eQTL of rs2275863 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 rs2275863 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	32481965	32482005	E067	4692
chr1	32485904	32486290	E067	8631
chr1	32486363	32486442	E067	9090
chr1	32497132	32497220	E067	19859
chr1	32500749	32501006	E067	23476
chr1	32501071	32501151	E067	23798
chr1	32501335	32501375	E067	24062
chr1	32506434	32506725	E067	29161
chr1	32507618	32507658	E067	30345
chr1	32521111	32521296	E067	43838
chr1	32521709	32521774	E067	44436
chr1	32521978	32522028	E067	44705
chr1	32429629	32430220	E068	-47053
chr1	32456905	32457042	E068	-20231
chr1	32481965	32482005	E068	4692
chr1	32485904	32486290	E068	8631
chr1	32486363	32486442	E068	9090
chr1	32506057	32506418	E068	28784
chr1	32506434	32506725	E068	29161
chr1	32507618	32507658	E068	30345
chr1	32429629	32430220	E069	-47053
chr1	32430278	32430328	E069	-46945
chr1	32430332	32430376	E069	-46897
chr1	32452745	32453438	E069	-23835
chr1	32469161	32469465	E069	-7808
chr1	32481965	32482005	E069	4692
chr1	32485904	32486290	E069	8631
chr1	32486363	32486442	E069	9090
chr1	32506057	32506418	E069	28784
chr1	32506434	32506725	E069	29161
chr1	32507618	32507658	E069	30345
chr1	32521709	32521774	E069	44436
chr1	32446430	32446504	E070	-30769
chr1	32446576	32446706	E070	-30567
chr1	32447056	32447515	E070	-29758
chr1	32447616	32447944	E070	-29329
chr1	32450255	32451439	E070	-25834
chr1	32451466	32451555	E070	-25718
chr1	32451625	32451692	E070	-25581
chr1	32452267	32452337	E070	-24936
chr1	32452466	32452539	E070	-24734
chr1	32452543	32452657	E070	-24616
chr1	32460732	32460782	E070	-16491
chr1	32460821	32460871	E070	-16402
chr1	32461059	32461225	E070	-16048
chr1	32461943	32462040	E070	-15233
chr1	32462068	32462243	E070	-15030
chr1	32485904	32486290	E070	8631
chr1	32486363	32486442	E070	9090
chr1	32506434	32506725	E070	29161
chr1	32521111	32521296	E070	43838
chr1	32521709	32521774	E070	44436
chr1	32521978	32522028	E070	44705
chr1	32429629	32430220	E071	-47053
chr1	32430278	32430328	E071	-46945
chr1	32430332	32430376	E071	-46897
chr1	32446237	32446309	E071	-30964
chr1	32446369	32446409	E071	-30864
chr1	32446430	32446504	E071	-30769
chr1	32446576	32446706	E071	-30567
chr1	32450255	32451439	E071	-25834
chr1	32452543	32452657	E071	-24616
chr1	32452686	32452736	E071	-24537
chr1	32452745	32453438	E071	-23835
chr1	32481965	32482005	E071	4692
chr1	32485904	32486290	E071	8631
chr1	32486363	32486442	E071	9090
chr1	32506057	32506418	E071	28784
chr1	32506434	32506725	E071	29161
chr1	32507618	32507658	E071	30345
chr1	32508662	32508712	E071	31389
chr1	32521111	32521296	E071	43838
chr1	32521709	32521774	E071	44436
chr1	32429629	32430220	E072	-47053
chr1	32469161	32469465	E072	-7808
chr1	32481965	32482005	E072	4692
chr1	32485904	32486290	E072	8631
chr1	32486363	32486442	E072	9090
chr1	32497132	32497220	E072	19859
chr1	32497373	32497478	E072	20100
chr1	32506057	32506418	E072	28784
chr1	32506434	32506725	E072	29161
chr1	32507618	32507658	E072	30345
chr1	32429629	32430220	E073	-47053
chr1	32452745	32453438	E073	-23835
chr1	32481965	32482005	E073	4692
chr1	32485904	32486290	E073	8631
chr1	32506057	32506418	E073	28784
chr1	32506434	32506725	E073	29161
chr1	32429629	32430220	E074	-47053
chr1	32452543	32452657	E074	-24616
chr1	32452686	32452736	E074	-24537
chr1	32452745	32453438	E074	-23835
chr1	32481965	32482005	E074	4692
chr1	32485904	32486290	E074	8631
chr1	32486363	32486442	E074	9090
chr1	32506057	32506418	E074	28784
chr1	32506434	32506725	E074	29161
chr1	32507618	32507658	E074	30345
chr1	32508662	32508712	E074	31389
chr1	32446760	32446888	E081	-30385
chr1	32447056	32447515	E081	-29758
chr1	32447616	32447944	E081	-29329
chr1	32450255	32451439	E081	-25834
chr1	32455310	32455505	E081	-21768
chr1	32456499	32456559	E081	-20714
chr1	32456905	32457042	E081	-20231
chr1	32481965	32482005	E081	4692
chr1	32485904	32486290	E081	8631
chr1	32486363	32486442	E081	9090
chr1	32521709	32521774	E081	44436
chr1	32521978	32522028	E081	44705
chr1	32430278	32430328	E082	-46945
chr1	32430332	32430376	E082	-46897
chr1	32446237	32446309	E082	-30964
chr1	32446369	32446409	E082	-30864
chr1	32446430	32446504	E082	-30769
chr1	32446576	32446706	E082	-30567
chr1	32446760	32446888	E082	-30385
chr1	32447056	32447515	E082	-29758
chr1	32450255	32451439	E082	-25834
chr1	32452745	32453438	E082	-23835
chr1	32485904	32486290	E082	8631
chr1	32486363	32486442	E082	9090
chr1	32493757	32493810	E082	16484
chr1	32493908	32493952	E082	16635
chr1	32494440	32494618	E082	17167
chr1	32506434	32506725	E082	29161

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	32478349	32480903	E067	1076
chr1	32481088	32481138	E067	3815
chr1	32481224	32481335	E067	3951
chr1	32478349	32480903	E068	1076
chr1	32481088	32481138	E068	3815
chr1	32481224	32481335	E068	3951
chr1	32478349	32480903	E069	1076
chr1	32481088	32481138	E069	3815
chr1	32481224	32481335	E069	3951
chr1	32478349	32480903	E070	1076
chr1	32481088	32481138	E070	3815
chr1	32481224	32481335	E070	3951
chr1	32478349	32480903	E071	1076
chr1	32481088	32481138	E071	3815
chr1	32481224	32481335	E071	3951
chr1	32478349	32480903	E072	1076
chr1	32481088	32481138	E072	3815
chr1	32481224	32481335	E072	3951
chr1	32478349	32480903	E073	1076
chr1	32481088	32481138	E073	3815
chr1	32481224	32481335	E073	3951
chr1	32478349	32480903	E074	1076
chr1	32481088	32481138	E074	3815
chr1	32481224	32481335	E074	3951
chr1	32478349	32480903	E081	1076
chr1	32481088	32481138	E081	3815
chr1	32481224	32481335	E081	3951
chr1	32478349	32480903	E082	1076
chr1	32481088	32481138	E082	3815
chr1	32481224	32481335	E082	3951